A State Event Detection Algorithm for Numerically Simulating Hybrid Systems with Model Singularities

DTIC Science & Technology

2007-01-01

the case of non- constant step sizes. Therefore the event dynamics after the predictor and corrector phases are, respectively, gpk +1 = g( xk + hk+1{ m...the Extrapolation Polynomial Using a Taylor series expansion of the predicted event function eq.(6) gpk +1 = gk + hk+1 dgp dt ∣∣∣∣ (x,t)=(xk,tk) + h2k...1 2! d2gp dt2 ∣∣∣∣ (x,t)=(xk,tk) + . . . , (8) we can determine the value of gpk +1 as a function of the, yet undetermined, step size hk+1. Recalling

Simulation of dynamic processes when machining transition surfaces of stepped shafts

NASA Astrophysics Data System (ADS)

Maksarov, V. V.; Krasnyy, V. A.; Viushin, R. V.

2018-03-01

The paper addresses the characteristics of stepped surfaces of parts categorized as "solids of revolution". It is noted that in the conditions of transition modes during the switch to end surface machining, there is cutting with varied load intensity in the section of the cut layer, which leads to change in cutting force, onset of vibrations, an increase in surface layer roughness, a decrease of size precision, and increased wear of a tool's cutting edge. This work proposes a method that consists in developing a CNC program output code that allows one to process complex forms of stepped shafts with only one machine setup. The authors developed and justified a mathematical model of a technological system for mechanical processing with consideration for the resolution of tool movement at the stages of transition processes to assess the dynamical stability of a system in the process of manufacturing stepped surfaces of parts of “solid of revolution” type.

Universality of (2+1)-dimensional restricted solid-on-solid models

NASA Astrophysics Data System (ADS)

Kelling, Jeffrey; Ódor, Géza; Gemming, Sibylle

2016-08-01

Extensive dynamical simulations of restricted solid-on-solid models in D =2 +1 dimensions have been done using parallel multisurface algorithms implemented on graphics cards. Numerical evidence is presented that these models exhibit Kardar-Parisi-Zhang surface growth scaling, irrespective of the step heights N . We show that by increasing N the corrections to scaling increase, thus smaller step-sized models describe better the asymptotic, long-wave-scaling behavior.

Short-term Time Step Convergence in a Climate Model

DOE PAGES

Wan, Hui; Rasch, Philip J.; Taylor, Mark; ...

2015-02-11

A testing procedure is designed to assess the convergence property of a global climate model with respect to time step size, based on evaluation of the root-mean-square temperature difference at the end of very short (1 h) simulations with time step sizes ranging from 1 s to 1800 s. A set of validation tests conducted without sub-grid scale parameterizations confirmed that the method was able to correctly assess the convergence rate of the dynamical core under various configurations. The testing procedure was then applied to the full model, and revealed a slow convergence of order 0.4 in contrast to themore » expected first-order convergence. Sensitivity experiments showed without ambiguity that the time stepping errors in the model were dominated by those from the stratiform cloud parameterizations, in particular the cloud microphysics. This provides a clear guidance for future work on the design of more accurate numerical methods for time stepping and process coupling in the model.« less

Efficiency and flexibility using implicit methods within atmosphere dycores

NASA Astrophysics Data System (ADS)

Evans, K. J.; Archibald, R.; Norman, M. R.; Gardner, D. J.; Woodward, C. S.; Worley, P.; Taylor, M.

2016-12-01

A suite of explicit and implicit methods are evaluated for a range of configurations of the shallow water dynamical core within the spectral-element Community Atmosphere Model (CAM-SE) to explore their relative computational performance. The configurations are designed to explore the attributes of each method under different but relevant model usage scenarios including varied spectral order within an element, static regional refinement, and scaling to large problem sizes. The limitations and benefits of using explicit versus implicit, with different discretizations and parameters, are discussed in light of trade-offs such as MPI communication, memory, and inherent efficiency bottlenecks. For the regionally refined shallow water configurations, the implicit BDF2 method is about the same efficiency as an explicit Runge-Kutta method, without including a preconditioner. Performance of the implicit methods with the residual function executed on a GPU is also presented; there is speed up for the residual relative to a CPU, but overwhelming transfer costs motivate moving more of the solver to the device. Given the performance behavior of implicit methods within the shallow water dynamical core, the recommendation for future work using implicit solvers is conditional based on scale separation and the stiffness of the problem. The strong growth of linear iterations with increasing resolution or time step size is the main bottleneck to computational efficiency. Within the hydrostatic dynamical core, of CAM-SE, we present results utilizing approximate block factorization preconditioners implemented using the Trilinos library of solvers. They reduce the cost of linear system solves and improve parallel scalability. We provide a summary of the remaining efficiency considerations within the preconditioner and utilization of the GPU, as well as a discussion about the benefits of a time stepping method that provides converged and stable solutions for a much wider range of time step sizes. As more complex model components, for example new physics and aerosols, are connected in the model, having flexibility in the time stepping will enable more options for combining and resolving multiple scales of behavior.

Single cardiac ventricular myosins are autonomous motors

PubMed Central

Wang, Yihua; Yuan, Chen-Ching; Kazmierczak, Katarzyna; Szczesna-Cordary, Danuta

2018-01-01

Myosin transduces ATP free energy into mechanical work in muscle. Cardiac muscle has dynamically wide-ranging power demands on the motor as the muscle changes modes in a heartbeat from relaxation, via auxotonic shortening, to isometric contraction. The cardiac power output modulation mechanism is explored in vitro by assessing single cardiac myosin step-size selection versus load. Transgenic mice express human ventricular essential light chain (ELC) in wild- type (WT), or hypertrophic cardiomyopathy-linked mutant forms, A57G or E143K, in a background of mouse α-cardiac myosin heavy chain. Ensemble motility and single myosin mechanical characteristics are consistent with an A57G that impairs ELC N-terminus actin binding and an E143K that impairs lever-arm stability, while both species down-shift average step-size with increasing load. Cardiac myosin in vivo down-shifts velocity/force ratio with increasing load by changed unitary step-size selections. Here, the loaded in vitro single myosin assay indicates quantitative complementarity with the in vivo mechanism. Both have two embedded regulatory transitions, one inhibiting ADP release and a second novel mechanism inhibiting actin detachment via strain on the actin-bound ELC N-terminus. Competing regulators filter unitary step-size selection to control force-velocity modulation without myosin integration into muscle. Cardiac myosin is muscle in a molecule. PMID:29669825

Getting to One from Title 10 + Title 32: Unity of Effort in the Homeland

DTIC Science & Technology

2011-09-01

the relationship between the States and the Federal 6 Government, as well as a critical step forward in living up to our mutual obligation...Influence Authorities The sheer size, population and mass differences between Israel and the United States have influenced the political dynamics ...command negatively impact operations and create perceptions that have impacted the cultural dynamic between them. In reference to Title 10 Active

Rare events in stochastic populations under bursty reproduction

NASA Astrophysics Data System (ADS)

Be'er, Shay; Assaf, Michael

2016-11-01

Recently, a first step was made by the authors towards a systematic investigation of the effect of reaction-step-size noise—uncertainty in the step size of the reaction—on the dynamics of stochastic populations. This was done by investigating the effect of bursty influx on the switching dynamics of stochastic populations. Here we extend this formalism to account for bursty reproduction processes, and improve the accuracy of the formalism to include subleading-order corrections. Bursty reproduction appears in various contexts, where notable examples include bursty viral production from infected cells, and reproduction of mammals involving varying number of offspring. The main question we quantitatively address is how bursty reproduction affects the overall fate of the population. We consider two complementary scenarios: population extinction and population survival; in the former a population gets extinct after maintaining a long-lived metastable state, whereas in the latter a population proliferates despite undergoing a deterministic drift towards extinction. In both models reproduction occurs in bursts, sampled from an arbitrary distribution. Using the WKB approach, we show in the extinction problem that bursty reproduction broadens the quasi-stationary distribution of population sizes in the metastable state, which results in a drastic reduction of the mean time to extinction compared to the non-bursty case. In the survival problem, it is shown that bursty reproduction drastically increases the survival probability of the population. Close to the bifurcation limit our analytical results simplify considerably and are shown to depend solely on the mean and variance of the burst-size distribution. Our formalism is demonstrated on several realistic distributions which all compare well with numerical Monte-Carlo simulations.

Simulation methods with extended stability for stiff biochemical Kinetics.

PubMed

Rué, Pau; Villà-Freixa, Jordi; Burrage, Kevin

2010-08-11

With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, tau, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where tau can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called tau-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as tau grows. In this paper we extend Poisson tau-leap methods to a general class of Runge-Kutta (RK) tau-leap methods. We show that with the proper selection of the coefficients, the variance of the extended tau-leap can be well-behaved, leading to significantly larger step sizes. The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original tau-leap method. The approach paves the way to explore new multiscale methods to simulate (bio)chemical systems.

Ballistic heat transport in laser generated nano-bubbles

NASA Astrophysics Data System (ADS)

Lombard, Julien; Biben, Thierry; Merabia, Samy

2016-08-01

Nanobubbles generated by laser heated plasmonic nanoparticles are of interest for biomedical and energy harvesting applications. Of utmost importance is the maximal size of these transient bubbles. Here, we report hydrodynamic phase field simulations of the dynamics of laser induced nanobubbles, with the aim to understand which physical processes govern their maximal size. We show that the nanobubble maximal size and lifetime are to a large extent controlled by the ballistic thermal flux which is present inside the bubble. Taking into account this thermal flux, we can reproduce the fluence dependence of the maximal nanobubble radius as reported experimentally. We also discuss the influence of the laser pulse duration on the number of nanobubbles generated and their maximal size. These studies represent a significant step toward the optimization of the nanobubble size, which is of crucial importance for photothermal cancer therapy applications.Nanobubbles generated by laser heated plasmonic nanoparticles are of interest for biomedical and energy harvesting applications. Of utmost importance is the maximal size of these transient bubbles. Here, we report hydrodynamic phase field simulations of the dynamics of laser induced nanobubbles, with the aim to understand which physical processes govern their maximal size. We show that the nanobubble maximal size and lifetime are to a large extent controlled by the ballistic thermal flux which is present inside the bubble. Taking into account this thermal flux, we can reproduce the fluence dependence of the maximal nanobubble radius as reported experimentally. We also discuss the influence of the laser pulse duration on the number of nanobubbles generated and their maximal size. These studies represent a significant step toward the optimization of the nanobubble size, which is of crucial importance for photothermal cancer therapy applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/C6NR02144A

A two-step initial mass function:. Consequences of clustered star formation for binary properties

NASA Astrophysics Data System (ADS)

Durisen, R. H.; Sterzik, M. F.; Pickett, B. K.

2001-06-01

If stars originate in transient bound clusters of moderate size, these clusters will decay due to dynamic interactions in which a hard binary forms and ejects most or all the other stars. When the cluster members are chosen at random from a reasonable initial mass function (IMF), the resulting binary characteristics do not match current observations. We find a significant improvement in the trends of binary properties from this scenario when an additional constraint is taken into account, namely that there is a distribution of total cluster masses set by the masses of the cloud cores from which the clusters form. Two distinct steps then determine final stellar masses - the choice of a cluster mass and the formation of the individual stars. We refer to this as a ``two-step'' IMF. Simple statistical arguments are used in this paper to show that a two-step IMF, combined with typical results from dynamic few-body system decay, tends to give better agreement between computed binary characteristics and observations than a one-step mass selection process.

The wiper model: avalanche dynamics in an exclusion process

NASA Astrophysics Data System (ADS)

Politi, Antonio; Romano, M. Carmen

2013-10-01

The exclusion-process model (Ciandrini et al 2010 Phys. Rev. E 81 051904) describing traffic of particles with internal stepping dynamics reveals the presence of strong correlations in realistic regimes. Here we study such a model in the limit of an infinitely fast translocation time, where the evolution can be interpreted as a ‘wiper’ that moves to dry neighbouring sites. We trace back the existence of long-range correlations to the existence of avalanches, where many sites are dried at once. At variance with self-organized criticality, in the wiper model avalanches have a typical size equal to the logarithm of the lattice size. In the thermodynamic limit, we find that the hydrodynamic behaviour is a mixture of stochastic (diffusive) fluctuations and increasingly coherent periodic oscillations that are reminiscent of a collective dynamics.

The effect of monocular and binocular viewing on the accommodation response to real targets in emmetropia and myopia.

PubMed

Seidel, Dirk; Gray, Lyle S; Heron, Gordon

2005-04-01

Decreased blur-sensitivity found in myopia has been linked with reduced accommodation responses and myopigenesis. Although the mechanism for myopia progression remains unclear, it is commonly known that myopic patients rarely report near visual symptoms and are generally very sensitive to small changes in their distance prescription. This experiment investigated the effect of monocular and binocular viewing on static and dynamic accommodation in emmetropes and myopes for real targets to monitor whether inaccuracies in the myopic accommodation response are maintained when a full set of visual cues, including size and disparity, is available. Monocular and binocular steady-state accommodation responses were measured with a Canon R1 autorefractor for target vergences ranging from 0-5 D in emmetropes (EMM), late-onset myopes (LOM), and early-onset myopes (EOM). Dynamic closed-loop accommodation responses for a stationary target at 0.25 m and step stimuli of two different magnitudes were recorded for both monocular and binocular viewing. All refractive groups showed similar accommodation stimulus response curves consistent with previously published data. Viewing a stationary near target monocularly, LOMs demonstrated slightly larger accommodation microfluctuations compared with EMMs and EOMs; however, this difference was absent under binocular viewing conditions. Dynamic accommodation step responses revealed significantly (p < 0.05) longer response times for the myopic subject groups for a number of step stimuli. No significant difference in either reaction time or the number of correct responses for a given number of step-vergence changes was found between the myopic groups and EMMs. When viewing real targets with size and disparity cues available, no significant differences in the accuracy of static and dynamic accommodation responses were found among EMM, EOM, and LOM. The results suggest that corrected myopes do not experience dioptric blur levels that are substantially different from emmetropes when they view free space targets.

Least-squares finite element methods for compressible Euler equations

NASA Technical Reports Server (NTRS)

Jiang, Bo-Nan; Carey, G. F.

1990-01-01

A method based on backward finite differencing in time and a least-squares finite element scheme for first-order systems of partial differential equations in space is applied to the Euler equations for gas dynamics. The scheme minimizes the L-sq-norm of the residual within each time step. The method naturally generates numerical dissipation proportional to the time step size. An implicit method employing linear elements has been implemented and proves robust. For high-order elements, computed solutions based on the L-sq method may have oscillations for calculations at similar time step sizes. To overcome this difficulty, a scheme which minimizes the weighted H1-norm of the residual is proposed and leads to a successful scheme with high-degree elements. Finally, a conservative least-squares finite element method is also developed. Numerical results for two-dimensional problems are given to demonstrate the shock resolution of the methods and compare different approaches.

Adaptive Implicit Non-Equilibrium Radiation Diffusion

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

Philip, Bobby; Wang, Zhen; Berrill, Mark A

2013-01-01

We describe methods for accurate and efficient long term time integra- tion of non-equilibrium radiation diffusion systems: implicit time integration for effi- cient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while control- ling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

Implicit integration methods for dislocation dynamics

DOE PAGES

Gardner, D. J.; Woodward, C. S.; Reynolds, D. R.; ...

2015-01-20

In dislocation dynamics simulations, strain hardening simulations require integrating stiff systems of ordinary differential equations in time with expensive force calculations, discontinuous topological events, and rapidly changing problem size. Current solvers in use often result in small time steps and long simulation times. Faster solvers may help dislocation dynamics simulations accumulate plastic strains at strain rates comparable to experimental observations. Here, this paper investigates the viability of high order implicit time integrators and robust nonlinear solvers to reduce simulation run times while maintaining the accuracy of the computed solution. In particular, implicit Runge-Kutta time integrators are explored as a waymore » of providing greater accuracy over a larger time step than is typically done with the standard second-order trapezoidal method. In addition, both accelerated fixed point and Newton's method are investigated to provide fast and effective solves for the nonlinear systems that must be resolved within each time step. Results show that integrators of third order are the most effective, while accelerated fixed point and Newton's method both improve solver performance over the standard fixed point method used for the solution of the nonlinear systems.« less

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

PubMed Central

Miller, Craig R.; Joyce, Paul; Wichman, Holly A.

2011-01-01

Adaptation in haploid organisms has been extensively modeled but little tested. Using a microvirid bacteriophage (ID11), we conducted serial passage adaptations at two bottleneck sizes (104 and 106), followed by fitness assays and whole-genome sequencing of 631 individual isolates. Extensive genetic variation was observed including 22 beneficial, several nearly neutral, and several deleterious mutations. In the three large bottleneck lines, up to eight different haplotypes were observed in samples of 23 genomes from the final time point. The small bottleneck lines were less diverse. The small bottleneck lines appeared to operate near the transition between isolated selective sweeps and conditions of complex dynamics (e.g., clonal interference). The large bottleneck lines exhibited extensive interference and less stochasticity, with multiple beneficial mutations establishing on a variety of backgrounds. Several leapfrog events occurred. The distribution of first-step adaptive mutations differed significantly from the distribution of second-steps, and a surprisingly large number of second-step beneficial mutations were observed on a highly fit first-step background. Furthermore, few first-step mutations appeared as second-steps and second-steps had substantially smaller selection coefficients. Collectively, the results indicate that the fitness landscape falls between the extremes of smooth and fully uncorrelated, violating the assumptions of many current mutational landscape models. PMID:21041559

Quantization improves stabilization of dynamical systems with delayed feedback

NASA Astrophysics Data System (ADS)

Stepan, Gabor; Milton, John G.; Insperger, Tamas

2017-11-01

We show that an unstable scalar dynamical system with time-delayed feedback can be stabilized by quantizing the feedback. The discrete time model corresponds to a previously unrecognized case of the microchaotic map in which the fixed point is both locally and globally repelling. In the continuous-time model, stabilization by quantization is possible when the fixed point in the absence of feedback is an unstable node, and in the presence of feedback, it is an unstable focus (spiral). The results are illustrated with numerical simulation of the unstable Hayes equation. The solutions of the quantized Hayes equation take the form of oscillations in which the amplitude is a function of the size of the quantization step. If the quantization step is sufficiently small, the amplitude of the oscillations can be small enough to practically approximate the dynamics around a stable fixed point.

Dynamics of laser-induced damage of spherical nanoparticles by high-intensity ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Komolov, Vladimir L.; Gruzdev, Vitaly E.; Przhibelskii, Sergey G.; Smirnov, Dmitry S.

2012-12-01

Damage of a metal spherical nanoparticle by femtosecond laser pulses is analyzed by splitting the overall process into two steps. The fast step includes electron photoemission from a nanoparticle. It takes place during direct action of a laser pulse and its rate is evaluated as a function of laser and particle parameters by two approaches. Obtained results suggest the formation of significant positive charge of the nanoparticles due to the photoemission. The next step includes ion emission that removes the excessive positive charge and modifies particle structure. It is delayed with respect to the photo-emission and is analyzed by a simple analytical model and modified molecular dynamics. Obtained energy distribution suggests generation of fast ions capable of penetrating into surrounding material and generating defects next to the nanoparticle. The modeling is extended to the case of a nanoparticle on a solid surface to understand the basic mechanism of surface laser damage initiated by nano-contamination. Simulations predict embedding the emitted ions into substrate within a spot with size significantly exceeding the original particle size. We discuss the relation of those effects to the problem of bulk and surface laser-induced damage of optical materials by single and multiple ultrashort laser pulses.

Finite Memory Walk and Its Application to Small-World Network

NASA Astrophysics Data System (ADS)

Oshima, Hiraku; Odagaki, Takashi

2012-07-01

In order to investigate the effects of cycles on the dynamical process on both regular lattices and complex networks, we introduce a finite memory walk (FMW) as an extension of the simple random walk (SRW), in which a walker is prohibited from moving to sites visited during m steps just before the current position. This walk interpolates the simple random walk (SRW), which has no memory (m = 0), and the self-avoiding walk (SAW), which has an infinite memory (m = ∞). We investigate the FMW on regular lattices and clarify the fundamental characteristics of the walk. We find that (1) the mean-square displacement (MSD) of the FMW shows a crossover from the SAW at a short time step to the SRW at a long time step, and the crossover time is approximately equivalent to the number of steps remembered, and that the MSD can be rescaled in terms of the time step and the size of memory; (2) the mean first-return time (MFRT) of the FMW changes significantly at the number of remembered steps that corresponds to the size of the smallest cycle in the regular lattice, where ``smallest'' indicates that the size of the cycle is the smallest in the network; (3) the relaxation time of the first-return time distribution (FRTD) decreases as the number of cycles increases. We also investigate the FMW on the Watts--Strogatz networks that can generate small-world networks, and show that the clustering coefficient of the Watts--Strogatz network is strongly related to the MFRT of the FMW that can remember two steps.

Don't break a leg: running birds from quail to ostrich prioritise leg safety and economy on uneven terrain.

PubMed

Birn-Jeffery, Aleksandra V; Hubicki, Christian M; Blum, Yvonne; Renjewski, Daniel; Hurst, Jonathan W; Daley, Monica A

2014-11-01

Cursorial ground birds are paragons of bipedal running that span a 500-fold mass range from quail to ostrich. Here we investigate the task-level control priorities of cursorial birds by analysing how they negotiate single-step obstacles that create a conflict between body stability (attenuating deviations in body motion) and consistent leg force-length dynamics (for economy and leg safety). We also test the hypothesis that control priorities shift between body stability and leg safety with increasing body size, reflecting use of active control to overcome size-related challenges. Weight-support demands lead to a shift towards straighter legs and stiffer steady gait with increasing body size, but it remains unknown whether non-steady locomotor priorities diverge with size. We found that all measured species used a consistent obstacle negotiation strategy, involving unsteady body dynamics to minimise fluctuations in leg posture and loading across multiple steps, not directly prioritising body stability. Peak leg forces remained remarkably consistent across obstacle terrain, within 0.35 body weights of level running for obstacle heights from 0.1 to 0.5 times leg length. All species used similar stance leg actuation patterns, involving asymmetric force-length trajectories and posture-dependent actuation to add or remove energy depending on landing conditions. We present a simple stance leg model that explains key features of avian bipedal locomotion, and suggests economy as a key priority on both level and uneven terrain. We suggest that running ground birds target the closely coupled priorities of economy and leg safety as the direct imperatives of control, with adequate stability achieved through appropriately tuned intrinsic dynamics. © 2014. Published by The Company of Biologists Ltd.

Don't break a leg: running birds from quail to ostrich prioritise leg safety and economy on uneven terrain

PubMed Central

Birn-Jeffery, Aleksandra V.; Hubicki, Christian M.; Blum, Yvonne; Renjewski, Daniel; Hurst, Jonathan W.; Daley, Monica A.

2014-01-01

Cursorial ground birds are paragons of bipedal running that span a 500-fold mass range from quail to ostrich. Here we investigate the task-level control priorities of cursorial birds by analysing how they negotiate single-step obstacles that create a conflict between body stability (attenuating deviations in body motion) and consistent leg force–length dynamics (for economy and leg safety). We also test the hypothesis that control priorities shift between body stability and leg safety with increasing body size, reflecting use of active control to overcome size-related challenges. Weight-support demands lead to a shift towards straighter legs and stiffer steady gait with increasing body size, but it remains unknown whether non-steady locomotor priorities diverge with size. We found that all measured species used a consistent obstacle negotiation strategy, involving unsteady body dynamics to minimise fluctuations in leg posture and loading across multiple steps, not directly prioritising body stability. Peak leg forces remained remarkably consistent across obstacle terrain, within 0.35 body weights of level running for obstacle heights from 0.1 to 0.5 times leg length. All species used similar stance leg actuation patterns, involving asymmetric force–length trajectories and posture-dependent actuation to add or remove energy depending on landing conditions. We present a simple stance leg model that explains key features of avian bipedal locomotion, and suggests economy as a key priority on both level and uneven terrain. We suggest that running ground birds target the closely coupled priorities of economy and leg safety as the direct imperatives of control, with adequate stability achieved through appropriately tuned intrinsic dynamics. PMID:25355848

Simulating galactic dust grain evolution on a moving mesh

NASA Astrophysics Data System (ADS)

McKinnon, Ryan; Vogelsberger, Mark; Torrey, Paul; Marinacci, Federico; Kannan, Rahul

2018-05-01

Interstellar dust is an important component of the galactic ecosystem, playing a key role in multiple galaxy formation processes. We present a novel numerical framework for the dynamics and size evolution of dust grains implemented in the moving-mesh hydrodynamics code AREPO suited for cosmological galaxy formation simulations. We employ a particle-based method for dust subject to dynamical forces including drag and gravity. The drag force is implemented using a second-order semi-implicit integrator and validated using several dust-hydrodynamical test problems. Each dust particle has a grain size distribution, describing the local abundance of grains of different sizes. The grain size distribution is discretised with a second-order piecewise linear method and evolves in time according to various dust physical processes, including accretion, sputtering, shattering, and coagulation. We present a novel scheme for stochastically forming dust during stellar evolution and new methods for sub-cycling of dust physics time-steps. Using this model, we simulate an isolated disc galaxy to study the impact of dust physical processes that shape the interstellar grain size distribution. We demonstrate, for example, how dust shattering shifts the grain size distribution to smaller sizes resulting in a significant rise of radiation extinction from optical to near-ultraviolet wavelengths. Our framework for simulating dust and gas mixtures can readily be extended to account for other dynamical processes relevant in galaxy formation, like magnetohydrodynamics, radiation pressure, and thermo-chemical processes.

Hybrid spiral-dynamic bacteria-chemotaxis algorithm with application to control two-wheeled machines.

PubMed

Goher, K M; Almeshal, A M; Agouri, S A; Nasir, A N K; Tokhi, M O; Alenezi, M R; Al Zanki, T; Fadlallah, S O

2017-01-01

This paper presents the implementation of the hybrid spiral-dynamic bacteria-chemotaxis (HSDBC) approach to control two different configurations of a two-wheeled vehicle. The HSDBC is a combination of bacterial chemotaxis used in bacterial forging algorithm (BFA) and the spiral-dynamic algorithm (SDA). BFA provides a good exploration strategy due to the chemotaxis approach. However, it endures an oscillation problem near the end of the search process when using a large step size. Conversely; for a small step size, it affords better exploitation and accuracy with slower convergence. SDA provides better stability when approaching an optimum point and has faster convergence speed. This may cause the search agents to get trapped into local optima which results in low accurate solution. HSDBC exploits the chemotactic strategy of BFA and fitness accuracy and convergence speed of SDA so as to overcome the problems associated with both the SDA and BFA algorithms alone. The HSDBC thus developed is evaluated in optimizing the performance and energy consumption of two highly nonlinear platforms, namely single and double inverted pendulum-like vehicles with an extended rod. Comparative results with BFA and SDA show that the proposed algorithm is able to result in better performance of the highly nonlinear systems.

Numerical Analysis of the Acoustic Field of Tip-Clearance Flow

NASA Astrophysics Data System (ADS)

Alavi Moghadam, S. M.; M. Meinke Team; W. Schröder Team

2015-11-01

Numerical simulations of the acoustic field generated by a shrouded axial fan are studied by a hybrid fluid-dynamics-acoustics method. In a first step, large-eddy simulations are performed to investigate the dynamics of tip clearance flow for various tip gap sizes and to determine the acoustic sources. The simulations are performed for a single blade out of five blades with periodic boundary conditions in the circumferential direction on a multi-block structured mesh with 1.4 ×108 grid points. The turbulent flow is simulated at a Reynolds number of 9.36 ×105 at undisturbed inflow condition and the results are compared with experimental data. The diameter and strength of the tip vortex increase with the tip gap size, while simultaneously the efficiency of the fan decreases. In a second step, the acoustic field on the near field is determined by solving the acoustic perturbation equations (APE) on a mesh for a single blade consisting of approx. 9.8 ×108 grid points. The overall agreement of the pressure spectrum and its directivity with measurements confirm the correct identification of the sound sources and accurate prediction of the acoustic duct propagation. The results show that the longer the tip gap size the higher the broadband noise level. Senior Scientist, Institute of Aerodynamics, RWTH Aachen University.

Individual-based modelling of population growth and diffusion in discrete time.

PubMed

Tkachenko, Natalie; Weissmann, John D; Petersen, Wesley P; Lake, George; Zollikofer, Christoph P E; Callegari, Simone

2017-01-01

Individual-based models (IBMs) of human populations capture spatio-temporal dynamics using rules that govern the birth, behavior, and death of individuals. We explore a stochastic IBM of logistic growth-diffusion with constant time steps and independent, simultaneous actions of birth, death, and movement that approaches the Fisher-Kolmogorov model in the continuum limit. This model is well-suited to parallelization on high-performance computers. We explore its emergent properties with analytical approximations and numerical simulations in parameter ranges relevant to human population dynamics and ecology, and reproduce continuous-time results in the limit of small transition probabilities. Our model prediction indicates that the population density and dispersal speed are affected by fluctuations in the number of individuals. The discrete-time model displays novel properties owing to the binomial character of the fluctuations: in certain regimes of the growth model, a decrease in time step size drives the system away from the continuum limit. These effects are especially important at local population sizes of <50 individuals, which largely correspond to group sizes of hunter-gatherers. As an application scenario, we model the late Pleistocene dispersal of Homo sapiens into the Americas, and discuss the agreement of model-based estimates of first-arrival dates with archaeological dates in dependence of IBM model parameter settings.

Long range personalized cancer treatment strategies incorporating evolutionary dynamics.

PubMed

Yeang, Chen-Hsiang; Beckman, Robert A

2016-10-22

Current cancer precision medicine strategies match therapies to static consensus molecular properties of an individual's cancer, thus determining the next therapeutic maneuver. These strategies typically maintain a constant treatment while the cancer is not worsening. However, cancers feature complicated sub-clonal structure and dynamic evolution. We have recently shown, in a comprehensive simulation of two non-cross resistant therapies across a broad parameter space representing realistic tumors, that substantial improvement in cure rates and median survival can be obtained utilizing dynamic precision medicine strategies. These dynamic strategies explicitly consider intratumoral heterogeneity and evolutionary dynamics, including predicted future drug resistance states, and reevaluate optimal therapy every 45 days. However, the optimization is performed in single 45 day steps ("single-step optimization"). Herein we evaluate analogous strategies that think multiple therapeutic maneuvers ahead, considering potential outcomes at 5 steps ahead ("multi-step optimization") or 40 steps ahead ("adaptive long term optimization (ALTO)") when recommending the optimal therapy in each 45 day block, in simulations involving both 2 and 3 non-cross resistant therapies. We also evaluate an ALTO approach for situations where simultaneous combination therapy is not feasible ("Adaptive long term optimization: serial monotherapy only (ALTO-SMO)"). Simulations utilize populations of 764,000 and 1,700,000 virtual patients for 2 and 3 drug cases, respectively. Each virtual patient represents a unique clinical presentation including sizes of major and minor tumor subclones, growth rates, evolution rates, and drug sensitivities. While multi-step optimization and ALTO provide no significant average survival benefit, cure rates are significantly increased by ALTO. Furthermore, in the subset of individual virtual patients demonstrating clinically significant difference in outcome between approaches, by far the majority show an advantage of multi-step or ALTO over single-step optimization. ALTO-SMO delivers cure rates superior or equal to those of single- or multi-step optimization, in 2 and 3 drug cases respectively. In selected virtual patients incurable by dynamic precision medicine using single-step optimization, analogous strategies that "think ahead" can deliver long-term survival and cure without any disadvantage for non-responders. When therapies require dose reduction in combination (due to toxicity), optimal strategies feature complex patterns involving rapidly interleaved pulses of combinations and high dose monotherapy. This article was reviewed by Wendy Cornell, Marek Kimmel, and Andrzej Swierniak. Wendy Cornell and Andrzej Swierniak are external reviewers (not members of the Biology Direct editorial board). Andrzej Swierniak was nominated by Marek Kimmel.

Dynamic sensitivity analysis of biological systems

PubMed Central

Wu, Wu Hsiung; Wang, Feng Sheng; Chang, Maw Shang

2008-01-01

Background A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differential equation (ODE) system. How to simulate the dynamic behavior and dynamic parameter sensitivities of systems described by ODEs efficiently and accurately is a critical job. In many practical applications, e.g., the fed-batch fermentation systems, the system admissible input (corresponding to independent variables of the system) can be time-dependent. The main difficulty for investigating the dynamic log gains of these systems is the infinite dimension due to the time-dependent input. The classical dynamic sensitivity analysis does not take into account this case for the dynamic log gains. Results We present an algorithm with an adaptive step size control that can be used for computing the solution and dynamic sensitivities of an autonomous ODE system simultaneously. Although our algorithm is one of the decouple direct methods in computing dynamic sensitivities of an ODE system, the step size determined by model equations can be used on the computations of the time profile and dynamic sensitivities with moderate accuracy even when sensitivity equations are more stiff than model equations. To show this algorithm can perform the dynamic sensitivity analysis on very stiff ODE systems with moderate accuracy, it is implemented and applied to two sets of chemical reactions: pyrolysis of ethane and oxidation of formaldehyde. The accuracy of this algorithm is demonstrated by comparing the dynamic parameter sensitivities obtained from this new algorithm and from the direct method with Rosenbrock stiff integrator based on the indirect method. The same dynamic sensitivity analysis was performed on an ethanol fed-batch fermentation system with a time-varying feed rate to evaluate the applicability of the algorithm to realistic models with time-dependent admissible input. Conclusion By combining the accuracy we show with the efficiency of being a decouple direct method, our algorithm is an excellent method for computing dynamic parameter sensitivities in stiff problems. We extend the scope of classical dynamic sensitivity analysis to the investigation of dynamic log gains of models with time-dependent admissible input. PMID:19091016

Devil's staircase and the absence of chaos in the dc- and ac-driven overdamped Frenkel-Kontorova model

NASA Astrophysics Data System (ADS)

Sokolović, I.; Mali, P.; Odavić, J.; Radošević, S.; Medvedeva, S. Yu.; Botha, A. E.; Shukrinov, Yu. M.; Tekić, J.

2017-08-01

The devil's staircase structure arising from the complete mode locking of an entirely nonchaotic system, the overdamped dc+ac driven Frenkel-Kontorova model with deformable substrate potential, was observed. Even though no chaos was found, a hierarchical ordering of the Shapiro steps was made possible through the use of a previously introduced continued fraction formula. The absence of chaos, deduced here from Lyapunov exponent analyses, can be attributed to the overdamped character and the Middleton no-passing rule. A comparative analysis of a one-dimensional stack of Josephson junctions confirmed the disappearance of chaos with increasing dissipation. Other common dynamic features were also identified through this comparison. A detailed analysis of the amplitude dependence of the Shapiro steps revealed that only for the case of a purely sinusoidal substrate potential did the relative sizes of the steps follow a Farey sequence. For nonsinusoidal (deformed) potentials, the symmetry of the Stern-Brocot tree, depicting all members of particular Farey sequence, was seen to be increasingly broken, with certain steps being more prominent and their relative sizes not following the Farey rule.

Representation of Nucleation Mode Microphysics in a Global Aerosol Model with Sectional Microphysics

NASA Technical Reports Server (NTRS)

Lee, Y. H.; Pierce, J. R.; Adams, P. J.

2013-01-01

In models, nucleation mode (1 nm

Frequency-velocity mismatch: a fundamental abnormality in parkinsonian gait.

PubMed

Cho, Catherine; Kunin, Mikhail; Kudo, Koji; Osaki, Yasuhiro; Olanow, C Warren; Cohen, Bernard; Raphan, Theodore

2010-03-01

Gait dysfunction and falling are major sources of disability for patients with advanced Parkinson's disease (PD). It is presently thought that the fundamental defect is an inability to generate normal stride length. Our data suggest, however, that the basic problem in PD gait is an impaired ability to match step frequency to walking velocity. In this study, foot movements of PD and normal subjects were monitored with an OPTOTRAK motion-detection system while they walked on a treadmill at different velocities. PD subjects were also paced with auditory stimuli at different frequencies. PD gait was characterized by step frequencies that were faster and stride lengths that were shorter than those of normal controls. At low walking velocities, PD stepping had a reduced or absent terminal toe lift, which truncated swing phases, producing shortened steps. Auditory pacing was not able to normalize step frequency at these lower velocities. Peak forward toe velocities increased with walking velocity and PD subjects could initiate appropriate foot dynamics during initial phases of the swing. They could not control the foot appropriately in terminal phases, however. Increased treadmill velocity, which matched the natural PD step frequency, generated a second toe lift, normalizing step size. Levodopa increased the bandwidth of step frequencies, but was not as effective as increases in walking velocity in normalizing gait. We postulate that the inability to control step frequency and adjust swing phase dynamics to slower walking velocities are major causes for the gait impairment in PD.

Frequency-Velocity Mismatch: A Fundamental Abnormality in Parkinsonian Gait

PubMed Central

Kunin, Mikhail; Kudo, Koji; Osaki, Yasuhiro; Olanow, C. Warren; Cohen, Bernard; Raphan, Theodore

2010-01-01

Gait dysfunction and falling are major sources of disability for patients with advanced Parkinson's disease (PD). It is presently thought that the fundamental defect is an inability to generate normal stride length. Our data suggest, however, that the basic problem in PD gait is an impaired ability to match step frequency to walking velocity. In this study, foot movements of PD and normal subjects were monitored with an OPTOTRAK motion-detection system while they walked on a treadmill at different velocities. PD subjects were also paced with auditory stimuli at different frequencies. PD gait was characterized by step frequencies that were faster and stride lengths that were shorter than those of normal controls. At low walking velocities, PD stepping had a reduced or absent terminal toe lift, which truncated swing phases, producing shortened steps. Auditory pacing was not able to normalize step frequency at these lower velocities. Peak forward toe velocities increased with walking velocity and PD subjects could initiate appropriate foot dynamics during initial phases of the swing. They could not control the foot appropriately in terminal phases, however. Increased treadmill velocity, which matched the natural PD step frequency, generated a second toe lift, normalizing step size. Levodopa increased the bandwidth of step frequencies, but was not as effective as increases in walking velocity in normalizing gait. We postulate that the inability to control step frequency and adjust swing phase dynamics to slower walking velocities are major causes for the gait impairment in PD. PMID:20042701

Non-orthogonal internally contracted multi-configurational perturbation theory (NICPT): Dynamic electron correlation for large, compact active spaces

NASA Astrophysics Data System (ADS)

Kähler, Sven; Olsen, Jeppe

2017-11-01

A computational method is presented for systems that require high-level treatments of static and dynamic electron correlation but cannot be treated using conventional complete active space self-consistent field-based methods due to the required size of the active space. Our method introduces an efficient algorithm for perturbative dynamic correlation corrections for compact non-orthogonal MCSCF calculations. In the algorithm, biorthonormal expansions of orbitals and CI-wave functions are used to reduce the scaling of the performance determining step from quadratic to linear in the number of configurations. We describe a hierarchy of configuration spaces that can be chosen for the active space. Potential curves for the nitrogen molecule and the chromium dimer are compared for different configuration spaces. Already the most compact spaces yield qualitatively correct potentials that with increasing size of configuration spaces systematically approach complete active space results.

Tank Investigation of a Powered Dynamic Model of a Large Long-Range Flying Boat

NASA Technical Reports Server (NTRS)

Parkinson, John B; Olson, Roland E; Harr, Marvin I

1947-01-01

Principles for designing the optimum hull for a large long-range flying boat to meet the requirements of seaworthiness, minimum drag, and ability to take off and land at all operational gross loads were incorporated in a 1/12-size powered dynamic model of a four-engine transport flying boat having a design gross load of 165,000 pounds. These design principles included the selection of a moderate beam loading, ample forebody length, sufficient depth of step, and close adherence to the form of a streamline body. The aerodynamic and hydrodynamic characteristics of the model were investigated in Langley tank no. 1. Tests were made to determine the minimum allowable depth of step for adequate landing stability, the suitability of the fore-and-aft location of the step, the take-off performance, the spray characteristics, and the effects of simple spray-control devices. The application of the design criterions used and test results should be useful in the preliminary design of similar large flying boats.

Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

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

Schiffmann, Florian; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch

2015-06-28

We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filteringmore » small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.« less

A parallelization method for time periodic steady state in simulation of radio frequency sheath dynamics

NASA Astrophysics Data System (ADS)

Kwon, Deuk-Chul; Shin, Sung-Sik; Yu, Dong-Hun

2017-10-01

In order to reduce the computing time in simulation of radio frequency (rf) plasma sources, various numerical schemes were developed. It is well known that the upwind, exponential, and power-law schemes can efficiently overcome the limitation on the grid size for fluid transport simulations of high density plasma discharges. Also, the semi-implicit method is a well-known numerical scheme to overcome on the simulation time step. However, despite remarkable advances in numerical techniques and computing power over the last few decades, efficient multi-dimensional modeling of low temperature plasma discharges has remained a considerable challenge. In particular, there was a difficulty on parallelization in time for the time periodic steady state problems such as capacitively coupled plasma discharges and rf sheath dynamics because values of plasma parameters in previous time step are used to calculate new values each time step. Therefore, we present a parallelization method for the time periodic steady state problems by using period-slices. In order to evaluate the efficiency of the developed method, one-dimensional fluid simulations are conducted for describing rf sheath dynamics. The result shows that speedup can be achieved by using a multithreading method.

Dynamical System Approach for Edge Detection Using Coupled FitzHugh-Nagumo Neurons.

PubMed

Li, Shaobai; Dasmahapatra, Srinandan; Maharatna, Koushik

2015-12-01

The prospect of emulating the impressive computational capabilities of biological systems has led to considerable interest in the design of analog circuits that are potentially implementable in very large scale integration CMOS technology and are guided by biologically motivated models. For example, simple image processing tasks, such as the detection of edges in binary and grayscale images, have been performed by networks of FitzHugh-Nagumo-type neurons using the reaction-diffusion models. However, in these studies, the one-to-one mapping of image pixels to component neurons makes the size of the network a critical factor in any such implementation. In this paper, we develop a simplified version of the employed reaction-diffusion model in three steps. In the first step, we perform a detailed study to locate this threshold using continuous Lyapunov exponents from dynamical system theory. Furthermore, we render the diffusion in the system to be anisotropic, with the degree of anisotropy being set by the gradients of grayscale values in each image. The final step involves a simplification of the model that is achieved by eliminating the terms that couple the membrane potentials of adjacent neurons. We apply our technique to detect edges in data sets of artificially generated and real images, and we demonstrate that the performance is as good if not better than that of the previous methods without increasing the size of the network.

Improving the Dynamic Characteristics of Body-in-White Structure Using Structural Optimization

PubMed Central

Yahaya Rashid, Aizzat S.; Mohamed Haris, Sallehuddin; Alias, Anuar

2014-01-01

The dynamic behavior of a body-in-white (BIW) structure has significant influence on the noise, vibration, and harshness (NVH) and crashworthiness of a car. Therefore, by improving the dynamic characteristics of BIW, problems and failures associated with resonance and fatigue can be prevented. The design objectives attempt to improve the existing torsion and bending modes by using structural optimization subjected to dynamic load without compromising other factors such as mass and stiffness of the structure. The natural frequency of the design was modified by identifying and reinforcing the structure at critical locations. These crucial points are first identified by topology optimization using mass and natural frequencies as the design variables. The individual components obtained from the analysis go through a size optimization step to find their target thickness of the structure. The thickness of affected regions of the components will be modified according to the analysis. The results of both optimization steps suggest several design modifications to achieve the target vibration specifications without compromising the stiffness of the structure. A method of combining both optimization approaches is proposed to improve the design modification process. PMID:25101312

Aging effect on step adjustments and stability control in visually perturbed gait initiation.

PubMed

Sun, Ruopeng; Cui, Chuyi; Shea, John B

2017-10-01

Gait adaptability is essential for fall avoidance during locomotion. It requires the ability to rapidly inhibit original motor planning, select and execute alternative motor commands, while also maintaining the stability of locomotion. This study investigated the aging effect on gait adaptability and dynamic stability control during a visually perturbed gait initiation task. A novel approach was used such that the anticipatory postural adjustment (APA) during gait initiation were used to trigger the unpredictable relocation of a foot-size stepping target. Participants (10 young adults and 10 older adults) completed visually perturbed gait initiation in three adjustment timing conditions (early, intermediate, late; all extracted from the stereotypical APA pattern) and two adjustment direction conditions (medial, lateral). Stepping accuracy, foot rotation at landing, and Margin of Dynamic Stability (MDS) were analyzed and compared across test conditions and groups using a linear mixed model. Stepping accuracy decreased as a function of adjustment timing as well as stepping direction, with older subjects exhibited a significantly greater undershoot in foot placement to late lateral stepping. Late adjustment also elicited a reaching-like movement (i.e. foot rotation prior to landing in order to step on the target), regardless of stepping direction. MDS measures in the medial-lateral and anterior-posterior direction revealed both young and older adults exhibited reduced stability in the adjustment step and subsequent steps. However, young adults returned to stable gait faster than older adults. These findings could be useful for future study of screening deficits in gait adaptability and preventing falls. Copyright © 2017 Elsevier B.V. All rights reserved.

Finite-element approach to Brownian dynamics of polymers.

PubMed

Cyron, Christian J; Wall, Wolfgang A

2009-12-01

In the last decades simulation tools for Brownian dynamics of polymers have attracted more and more interest. Such simulation tools have been applied to a large variety of problems and accelerated the scientific progress significantly. However, the currently most frequently used explicit bead models exhibit severe limitations, especially with respect to time step size, the necessity of artificial constraints and the lack of a sound mathematical foundation. Here we present a framework for simulations of Brownian polymer dynamics based on the finite-element method. This approach allows simulating a wide range of physical phenomena at a highly attractive computational cost on the basis of a far-developed mathematical background.

Statistical analyses support power law distributions found in neuronal avalanches.

PubMed

Klaus, Andreas; Yu, Shan; Plenz, Dietmar

2011-01-01

The size distribution of neuronal avalanches in cortical networks has been reported to follow a power law distribution with exponent close to -1.5, which is a reflection of long-range spatial correlations in spontaneous neuronal activity. However, identifying power law scaling in empirical data can be difficult and sometimes controversial. In the present study, we tested the power law hypothesis for neuronal avalanches by using more stringent statistical analyses. In particular, we performed the following steps: (i) analysis of finite-size scaling to identify scale-free dynamics in neuronal avalanches, (ii) model parameter estimation to determine the specific exponent of the power law, and (iii) comparison of the power law to alternative model distributions. Consistent with critical state dynamics, avalanche size distributions exhibited robust scaling behavior in which the maximum avalanche size was limited only by the spatial extent of sampling ("finite size" effect). This scale-free dynamics suggests the power law as a model for the distribution of avalanche sizes. Using both the Kolmogorov-Smirnov statistic and a maximum likelihood approach, we found the slope to be close to -1.5, which is in line with previous reports. Finally, the power law model for neuronal avalanches was compared to the exponential and to various heavy-tail distributions based on the Kolmogorov-Smirnov distance and by using a log-likelihood ratio test. Both the power law distribution without and with exponential cut-off provided significantly better fits to the cluster size distributions in neuronal avalanches than the exponential, the lognormal and the gamma distribution. In summary, our findings strongly support the power law scaling in neuronal avalanches, providing further evidence for critical state dynamics in superficial layers of cortex.

A new algorithm for modeling friction in dynamic mechanical systems

NASA Technical Reports Server (NTRS)

Hill, R. E.

1988-01-01

A method of modeling friction forces that impede the motion of parts of dynamic mechanical systems is described. Conventional methods in which the friction effect is assumed a constant force, or torque, in a direction opposite to the relative motion, are applicable only to those cases where applied forces are large in comparison to the friction, and where there is little interest in system behavior close to the times of transitions through zero velocity. An algorithm is described that provides accurate determination of friction forces over a wide range of applied force and velocity conditions. The method avoids the simulation errors resulting from a finite integration interval used in connection with a conventional friction model, as is the case in many digital computer-based simulations. The algorithm incorporates a predictive calculation based on initial conditions of motion, externally applied forces, inertia, and integration step size. The predictive calculation in connection with an external integration process provides an accurate determination of both static and Coulomb friction forces and resulting motions in dynamic simulations. Accuracy of the results is improved over that obtained with conventional methods and a relatively large integration step size is permitted. A function block for incorporation in a specific simulation program is described. The general form of the algorithm facilitates implementation with various programming languages such as FORTRAN or C, as well as with other simulation programs.

Demodulation algorithm for optical fiber F-P sensor.

PubMed

Yang, Huadong; Tong, Xinglin; Cui, Zhang; Deng, Chengwei; Guo, Qian; Hu, Pan

2017-09-10

The demodulation algorithm is very important to improving the measurement accuracy of a sensing system. In this paper, the variable step size hill climbing search method will be initially used for the optical fiber Fabry-Perot (F-P) sensing demodulation algorithm. Compared with the traditional discrete gap transformation demodulation algorithm, the computation is greatly reduced by changing step size of each climb, which could achieve nano-scale resolution, high measurement accuracy, high demodulation rates, and large dynamic demodulation range. An optical fiber F-P pressure sensor based on micro-electro-mechanical system (MEMS) has been fabricated to carry out the experiment, and the results show that the resolution of the algorithm can reach nano-scale level, the sensor's sensitivity is about 2.5  nm/KPa, which is similar to the theoretical value, and this sensor has great reproducibility.

Large scale crystallization of protein pharmaceuticals in microgravity via temperature change

NASA Technical Reports Server (NTRS)

Long, Marianna M.

1992-01-01

The major objective of this research effort is the temperature driven growth of protein crystals in large batches in the microgravity environment of space. Pharmaceutical houses are developing protein products for patient care, for example, human insulin, human growth hormone, interferons, and tissue plasminogen activator or TPA, the clot buster for heart attack victims. Except for insulin, these are very high value products; they are extremely potent in small quantities and have a great value per gram of material. It is feasible that microgravity crystallization can be a cost recoverable, economically sound final processing step in their manufacture. Large scale protein crystal growth in microgravity has significant advantages from the basic science and the applied science standpoints. Crystal growth can proceed unhindered due to lack of surface effects. Dynamic control is possible and relatively easy. The method has the potential to yield large quantities of pure crystalline product. Crystallization is a time honored procedure for purifying organic materials and microgravity crystallization could be the final step to remove trace impurities from high value protein pharmaceuticals. In addition, microgravity grown crystals could be the final formulation for those medicines that need to be administered in a timed release fashion. Long lasting insulin, insulin lente, is such a product. Also crystalline protein pharmaceuticals are more stable for long-term storage. Temperature, as the initiation step, has certain advantages. Again, dynamic control of the crystallization process is possible and easy. A temperature step is non-invasive and is the most subtle way to control protein solubility and therefore crystallization. Seeding is not necessary. Changes in protein and precipitant concentrations and pH are not necessary. Finally, this method represents a new way to crystallize proteins in space that takes advantage of the unique microgravity environment. The results from two flights showed that the hardware performed perfectly, many crystals were produced, and they were much larger than their ground grown controls. Morphometric analysis was done on over 4,000 crystals to establish crystal size, size distribution, and relative size. Space grown crystals were remarkably larger than their earth grown counterparts and crystal size was a function of PCF volume. That size distribution for the space grown crystals was a function of PCF volume may indicate that ultimate size was a function of temperature gradient. Since the insulin protein concentration was very low, 0.4 mg/ml, the size distribution could also be following the total amount of protein in each of the PCF's. X-ray analysis showed that the bigger space grown insulin crystals diffracted to higher resolution than their ground grown controls. When the data were normalized for size, they still indicated that the space crystals were better than the ground crystals.

Earthquake models using rate and state friction and fast multipoles

NASA Astrophysics Data System (ADS)

Tullis, T.

2003-04-01

The most realistic current earthquake models employ laboratory-derived non-linear constitutive laws. These are the rate and state friction laws having both a non-linear viscous or direct effect and an evolution effect in which frictional resistance depends on time of stationary contact and has a memory of past slip velocity that fades with slip. The frictional resistance depends on the log of the slip velocity as well as the log of stationary hold time, and the fading memory involves an approximately exponential decay with slip. Due to the nonlinearly of these laws, analytical earthquake models are not attainable and numerical models are needed. The situation is even more difficult if true dynamic models are sought that deal with inertial forces and slip velocities on the order of 1 m/s as are observed during dynamic earthquake slip. Additional difficulties that exist if the dynamic slip phase of earthquakes is modeled arise from two sources. First, many physical processes might operate during dynamic slip, but they are only poorly understood, the relative importance of the processes is unknown, and the processes are even more nonlinear than those described by the current rate and state laws. Constitutive laws describing such behaviors are still being developed. Second, treatment of inertial forces and the influence that dynamic stresses from elastic waves may have on slip on the fault requires keeping track of the history of slip on remote parts of the fault as far into the past as it takes waves to travel from there. This places even more stringent requirements on computer time. Challenges for numerical modeling of complete earthquake cycles are that both time steps and mesh sizes must be small. Time steps must be milliseconds during dynamic slip, and yet models must represent earthquake cycles 100 years or more in length; methods using adaptive step sizes are essential. Element dimensions need to be on the order of meters, both to approximate continuum behavior adequately and to model microseismicity as well as large earthquakes. In order to model significant sized earthquakes this requires millions of elements. Modeling methods like the boundary element method that involve Green's functions normally require computation times that increase with the number N of elements squared, so using large N becomes impossible. We have adapted the Fast Multipole method to this problem in which the influence of sufficiently remote elements are grouped together and the elements are indexed such that the computations more efficient when run on parallel computers. Compute time varies with N log N rather than N squared. Computer programs are available that use this approach (http://www.servogrid.org/slide/GEM/PARK). Whether the multipole approach can be adapted to dynamic modeling is unclear.

Analysis of real-time numerical integration methods applied to dynamic clamp experiments.

PubMed

Butera, Robert J; McCarthy, Maeve L

2004-12-01

Real-time systems are frequently used as an experimental tool, whereby simulated models interact in real time with neurophysiological experiments. The most demanding of these techniques is known as the dynamic clamp, where simulated ion channel conductances are artificially injected into a neuron via intracellular electrodes for measurement and stimulation. Methodologies for implementing the numerical integration of the gating variables in real time typically employ first-order numerical methods, either Euler or exponential Euler (EE). EE is often used for rapidly integrating ion channel gating variables. We find via simulation studies that for small time steps, both methods are comparable, but at larger time steps, EE performs worse than Euler. We derive error bounds for both methods, and find that the error can be characterized in terms of two ratios: time step over time constant, and voltage measurement error over the slope factor of the steady-state activation curve of the voltage-dependent gating variable. These ratios reliably bound the simulation error and yield results consistent with the simulation analysis. Our bounds quantitatively illustrate how measurement error restricts the accuracy that can be obtained by using smaller step sizes. Finally, we demonstrate that Euler can be computed with identical computational efficiency as EE.

Dynamic Scaling and Island Growth Kinetics in Pulsed Laser Deposition of SrTiO 3

DOE PAGES

Eres, Gyula; Tischler, J. Z.; Rouleau, C. M.; ...

2016-11-11

We use real-time diffuse surface x-ray diffraction to probe the evolution of island size distributions and its effects on surface smoothing in pulsed laser deposition (PLD) of SrTiO 3. In this study, we show that the island size evolution obeys dynamic scaling and two distinct regimes of island growth kinetics. Our data show that PLD film growth can persist without roughening despite thermally driven Ostwald ripening, the main mechanism for surface smoothing, being shut down. The absence of roughening is concomitant with decreasing island density, contradicting the prevailing view that increasing island density is the key to surface smoothing inmore » PLD. We also report a previously unobserved crossover from diffusion-limited to attachment-limited island growth that reveals the influence of nonequilibrium atomic level surface transport processes on the growth modes in PLD. We show by direct measurements that attachment-limited island growth is the dominant process in PLD that creates step flowlike behavior or quasistep flow as PLD “self-organizes” local step flow on a length scale consistent with the substrate temperature and PLD parameters.« less

Dynamic Scaling and Island Growth Kinetics in Pulsed Laser Deposition of SrTiO 3

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

Eres, Gyula; Tischler, J. Z.; Rouleau, C. M.

We use real-time diffuse surface x-ray diffraction to probe the evolution of island size distributions and its effects on surface smoothing in pulsed laser deposition (PLD) of SrTiO 3. In this study, we show that the island size evolution obeys dynamic scaling and two distinct regimes of island growth kinetics. Our data show that PLD film growth can persist without roughening despite thermally driven Ostwald ripening, the main mechanism for surface smoothing, being shut down. The absence of roughening is concomitant with decreasing island density, contradicting the prevailing view that increasing island density is the key to surface smoothing inmore » PLD. We also report a previously unobserved crossover from diffusion-limited to attachment-limited island growth that reveals the influence of nonequilibrium atomic level surface transport processes on the growth modes in PLD. We show by direct measurements that attachment-limited island growth is the dominant process in PLD that creates step flowlike behavior or quasistep flow as PLD “self-organizes” local step flow on a length scale consistent with the substrate temperature and PLD parameters.« less

Implicit-Explicit Time Integration Methods for Non-hydrostatic Atmospheric Models

NASA Astrophysics Data System (ADS)

Gardner, D. J.; Guerra, J. E.; Hamon, F. P.; Reynolds, D. R.; Ullrich, P. A.; Woodward, C. S.

2016-12-01

The Accelerated Climate Modeling for Energy (ACME) project is developing a non-hydrostatic atmospheric dynamical core for high-resolution coupled climate simulations on Department of Energy leadership class supercomputers. An important factor in computational efficiency is avoiding the overly restrictive time step size limitations of fully explicit time integration methods due to the stiffest modes present in the model (acoustic waves). In this work we compare the accuracy and performance of different Implicit-Explicit (IMEX) splittings of the non-hydrostatic equations and various Additive Runge-Kutta (ARK) time integration methods. Results utilizing the Tempest non-hydrostatic atmospheric model and the ARKode package show that the choice of IMEX splitting and ARK scheme has a significant impact on the maximum stable time step size as well as solution quality. Horizontally Explicit Vertically Implicit (HEVI) approaches paired with certain ARK methods lead to greatly improved runtimes. With effective preconditioning IMEX splittings that incorporate some implicit horizontal dynamics can be competitive with HEVI results. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-699187

Improved scaling of temperature-accelerated dynamics using localization

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques G.

2016-07-01

While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N3 where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary "bottlenecks" to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N1/2. Some additional possible methods to improve the scaling of TAD are also discussed.

Molecular dynamics modeling and simulation of void growth in two dimensions

NASA Astrophysics Data System (ADS)

Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.

2013-10-01

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

Langevin dynamics in inhomogeneous media: Re-examining the Itô-Stratonovich dilemma

NASA Astrophysics Data System (ADS)

Farago, Oded; Grønbech-Jensen, Niels

2014-01-01

The diffusive dynamics of a particle in a medium with space-dependent friction coefficient is studied within the framework of the inertial Langevin equation. In this description, the ambiguous interpretation of the stochastic integral, known as the Itô-Stratonovich dilemma, is avoided since all interpretations converge to the same solution in the limit of small time steps. We use a newly developed method for Langevin simulations to measure the probability distribution of a particle diffusing in a flat potential. Our results reveal that both the Itô and Stratonovich interpretations converge very slowly to the uniform equilibrium distribution for vanishing time step sizes. Three other conventions exhibit significantly improved accuracy: (i) the "isothermal" (Hänggi) convention, (ii) the Stratonovich convention corrected by a drift term, and (iii) a newly proposed convention employing two different effective friction coefficients representing two different averages of the friction function during the time step. We argue that the most physically accurate dynamical description is provided by the third convention, in which the particle experiences a drift originating from the dissipation instead of the fluctuation term. This feature is directly related to the fact that the drift is a result of an inertial effect that cannot be well understood in the Brownian, overdamped limit of the Langevin equation.

Molecular dynamics with rigid bodies: Alternative formulation and assessment of its limitations when employed to simulate liquid water

NASA Astrophysics Data System (ADS)

Silveira, Ana J.; Abreu, Charlles R. A.

2017-09-01

Sets of atoms collectively behaving as rigid bodies are often used in molecular dynamics to model entire molecules or parts thereof. This is a coarse-graining strategy that eliminates degrees of freedom and supposedly admits larger time steps without abandoning the atomistic character of a model. In this paper, we rely on a particular factorization of the rotation matrix to simplify the mechanical formulation of systems containing rigid bodies. We then propose a new derivation for the exact solution of torque-free rotations, which are employed as part of a symplectic numerical integration scheme for rigid-body dynamics. We also review methods for calculating pressure in systems of rigid bodies with pairwise-additive potentials and periodic boundary conditions. Finally, simulations of liquid phases, with special focus on water, are employed to analyze the numerical aspects of the proposed methodology. Our results show that energy drift is avoided for time step sizes up to 5 fs, but only if a proper smoothing is applied to the interatomic potentials. Despite this, the effects of discretization errors are relevant, even for smaller time steps. These errors induce, for instance, a systematic failure of the expected equipartition of kinetic energy between translational and rotational degrees of freedom.

Multi-passes warm rolling of AZ31 magnesium alloy, effect on evaluation of texture, microstructure, grain size and hardness

NASA Astrophysics Data System (ADS)

Kamran, J.; Hasan, B. A.; Tariq, N. H.; Izhar, S.; Sarwar, M.

2014-06-01

In this study the effect of multi-passes warm rolling of AZ31 magnesium alloy on texture, microstructure, grain size variation and hardness of as cast sample (A) and two rolled samples (B & C) taken from different locations of the as-cast ingot was investigated. The purpose was to enhance the formability of AZ31 alloy in order to help manufacturability. It was observed that multi-passes warm rolling (250°C to 350°C) of samples B & C with initial thickness 7.76mm and 7.73 mm was successfully achieved up to 85% reduction without any edge or surface cracks in ten steps with a total of 26 passes. The step numbers 1 to 4 consist of 5, 2, 11 and 3 passes respectively, the remaining steps 5 to 10 were single pass rolls. In each discrete step a fixed roll gap is used in a way that true strain per step increases very slowly from 0.0067 in the first step to 0.7118 in the 26th step. Both samples B & C showed very similar behavior after 26th pass and were successfully rolled up to 85% thickness reduction. However, during 10th step (27th pass) with a true strain value of 0.772 the sample B experienced very severe surface as well as edge cracks. Sample C was therefore not rolled for the 10th step and retained after 26 passes. Both samples were studied in terms of their basal texture, microstructure, grain size and hardness. Sample C showed an equiaxed grain structure after 85% total reduction. The equiaxed grain structure of sample C may be due to the effective involvement of dynamic recrystallization (DRX) which led to formation of these grains with relatively low misorientations with respect to the parent as cast grains. The sample B on the other hand showed a microstructure in which all the grains were elongated along the rolling direction (RD) after 90 % total reduction and DRX could not effectively play its role due to heavy strain and lack of plastic deformation systems. The microstructure of as cast sample showed a near-random texture (mrd 4.3), with average grain size of 44 & micro-hardness of 52 Hv. The grain size of sample B and C was 14μm and 27μm respectively and mrd intensity of basal texture was 5.34 and 5.46 respectively. The hardness of sample B and C came out to be 91 and 66 Hv respectively due to reduction in grain size and followed the well known Hall-Petch relationship.

Voxel based parallel post processor for void nucleation and growth analysis of atomistic simulations of material fracture.

PubMed

Hemani, H; Warrier, M; Sakthivel, N; Chaturvedi, S

2014-05-01

Molecular dynamics (MD) simulations are used in the study of void nucleation and growth in crystals that are subjected to tensile deformation. These simulations are run for typically several hundred thousand time steps depending on the problem. We output the atom positions at a required frequency for post processing to determine the void nucleation, growth and coalescence due to tensile deformation. The simulation volume is broken up into voxels of size equal to the unit cell size of crystal. In this paper, we present the algorithm to identify the empty unit cells (voids), their connections (void size) and dynamic changes (growth and coalescence of voids) for MD simulations of large atomic systems (multi-million atoms). We discuss the parallel algorithms that were implemented and discuss their relative applicability in terms of their speedup and scalability. We also present the results on scalability of our algorithm when it is incorporated into MD software LAMMPS. Copyright © 2014 Elsevier Inc. All rights reserved.

Advanced time integration algorithms for dislocation dynamics simulations of work hardening

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

Sills, Ryan B.; Aghaei, Amin; Cai, Wei

Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relativemore » to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.« less

Advanced time integration algorithms for dislocation dynamics simulations of work hardening

DOE PAGES

Sills, Ryan B.; Aghaei, Amin; Cai, Wei

2016-04-25

Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relativemore » to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.« less

The influence of number and values of ratios in stepped gearbox on mileage fuel consumption in NEDC test and real traffic

NASA Astrophysics Data System (ADS)

Bera, P.; Wędrychowicz, D.

2016-09-01

The article presents the influence of number and values of ratios in stepped gearbox on mileage fuel consumption in a city passenger car. The simulations were conducted for a particular vehicle characterized by its mass, body shape, size of tires and equipped with a combustion engine for which the characteristic of fuel consumption in dynamic states was already designated on the basis of engine test bed measurements. Several designs of transmission with different number of gears and their ratios were used in virtual simulations of road traffic, particularly in the NEDC test, to calculate mileage fuel consumption. This allows for a quantitative assessment of transmission parameters in terms of both vehicle economy and dynamic properties. Also, based on obtained results, recommendations for the selection of a particular vehicle for a specific type of exploitation have been formulated.

The dispersion of particles in a separated backward-facing step flow

NASA Astrophysics Data System (ADS)

Ruck, B.; Makiola, B.

1991-05-01

Flows in technical and natural circuits often involve a particulate phase. To measure the dynamics of suspended, naturally resident or artificially seeded particles in the flow, optical measuring techniques, e.g., laser Doppler anemometry (LDA) can be used advantageously. In this paper the dispersion of particles in a single-sided backward-facing step flow is investigated by LDA. The investigation is of relevance for both, two-phase flow problems in separated flows with the associated particle diameter range of 1-70 μm and the accuracy of LDA with tracer particles of different sizes. The latter is of interest for all LDA applications to measure continuous phase properties, where interest for experimental restraints require tracer diameters in the upper micrometer range, e.g., flame resistant particles for measurements inside reactors, cylinders, etc. For the experiments, a closed-loop wind tunnel with a step expansion was used. Part of this tunnel, the test section, was made of glass. The step had a height H=25 mm (channel height before the step 25 mm, after 50 mm, i.e., an expansion ratio of 2). The width of the channel was 500 mm. The length of the glass test section was chosen as 116 step heights. The wind tunnel, driven by a radial fan, allowed flow velocities up to 50 m/sec which is equivalent to ReH=105. Seeding was performed with particles of well-known size: 1, 15, 30, and 70 μm in diameter. As 1 μm tracers oil droplets were used, whereas for the upper micron range starch particles (density 1.500 kg/m3) were chosen. Starch particles have a spherical shape and are not soluble in cold water. Particle velocities were measured locally using a conventional 1-D LDA system. The measurements deliver the resultant ``flow'' field information stemming from different particle size classes. Thus, the particle behavior in the separated flow field can be resolved. The results show that with increasing particle size, the particle velocity field differs increasingly from the flow field of the continuous phase (inferred from the smallest tracers used). The velocity fluctuations successively decrease with increasing particle diameter. In separation zones, bigger particles have a lower mean velocity than smaller ones. The opposite holds for the streamwise portions of the particle velocity field, where bigger particles show a higher velocity. The measurements give detailed insight into the particle dynamics in separated flow regions. LDA-measured dividing streamlines and lines of zero velocity of different particle classes in the recirculation region have been plotted and compared. In LDA the use of tracer particles in the upper micrometer size range leads to erroneous determinations of continuous phase flow characteristics. It turned out that the dimensions of the measured recirculation zones are reduced with increasing particle diameter. The physical reasons for these findings (relaxation time of particles, Stokes numbers, etc.) are explained in detail.

Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

PubMed Central

Chng, Choon-Peng; Yang, Lee-Wei

2008-01-01

Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed. PMID:19812774

A Time Integration Algorithm Based on the State Transition Matrix for Structures with Time Varying and Nonlinear Properties

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2003-01-01

A variable order method of integrating the structural dynamics equations that is based on the state transition matrix has been developed. The method has been evaluated for linear time variant and nonlinear systems of equations. When the time variation of the system can be modeled exactly by a polynomial it produces nearly exact solutions for a wide range of time step sizes. Solutions of a model nonlinear dynamic response exhibiting chaotic behavior have been computed. Accuracy of the method has been demonstrated by comparison with solutions obtained by established methods.

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

PubMed

Komeiji, Y; Yokoyama, H; Uebayasi, M; Taiji, M; Fukushige, T; Sugimoto, D; Takata, R; Shimizu, A; Itsukashi, K

1996-01-01

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.

Single Molecule Stepping and Structural Dynamics of Myosin X

PubMed Central

Sun, Yujie; Sato, Osamu; Ruhnow, Felix; Arsenault, Mark E.; Ikebe, Mitsuo; Goldman, Yale E.

2010-01-01

Myosin X is an unconventional myosin with puzzling motility properties. We studied the motility of dimerized myosin X using single molecule fluorescence techniques – polTIRF, FIONA, and Parallax to measure rotation angles and 3-dimensional position of the molecule during its walk. It was found that Myosin X steps processively in a hand-over-hand manner following a left-handed helical path along both single actin filaments and bundles. Its step size and velocity are smaller on actin bundles than individual filaments, suggesting myosin X often steps onto neighboring filaments in a bundle. The data suggest that a previously postulated single α-helical domain mechanically extends the 3-IQ motif lever arm and either the neck-tail hinge or the tail is flexible. These structural features, in conjunction with the membrane and microtubule binding domains, enable myosin X to perform multiple functions on varied actin structures in cells. PMID:20364131

Step back! Niche dynamics in cave-dwelling predators

NASA Astrophysics Data System (ADS)

Mammola, Stefano; Piano, Elena; Isaia, Marco

2016-08-01

The geometry of the Hutchinson's hypervolume derives from multiple selective pressures defined, on one hand, by the physiological tolerance of the species, and on the other, by intra- and interspecific competition. The quantification of these evolutionary forces is essential for the understanding of the coexistence of predators in light of competitive exclusion dynamics. We address this topic by investigating the ecological niche of two medium-sized troglophile spiders (Meta menardi and Pimoa graphitica). Over one year, we surveyed several populations in four subterranean sites in the Western Italian Alps, monitoring monthly their spatial and temporal dynamics and the associated physical and ecological variables. We assessed competition between the two species by means of multi regression techniques and by evaluating the intersection between their multidimensional hypervolumes. We detected a remarkable overlap between the microclimatic and trophic niche of M. menardi and P. graphitica, however, the former -being larger in size- resulted the best competitor in proximity of the cave entrance, causing the latter to readjust its spatial niche towards the inner part, where prey availability is scarcer ("step back effect"). In parallel to the slight variations in the subterranean microclimatic condition, the niche of the two species was also found to be seasonal dependent, varying over the year. With this work, we aim at providing new insights about the relationships among predators, demonstrating that energy-poor environments such as caves maintain the potential for diversification of predators via niche differentiation and serve as useful models for theoretical ecological studies.

Heterogeneous nucleation of pits via step pinning during Si(100) homoepitaxy

NASA Astrophysics Data System (ADS)

Yitamben, E. N.; Butera, R. E.; Swartzentruber, B. S.; Simonson, R. J.; Misra, S.; Carroll, M. S.; Bussmann, E.

2017-11-01

Using scanning tunneling microscopy (STM), we investigate oxide-induced growth pits in Si thin films deposited by molecular beam epitaxy. In the transition temperature range from 2D adatom islanding to step-flow growth, systematic controlled air leaks into the growth chamber induce pits in the growth surface. We show that pits are also correlated with oxygen-contaminated flux from Si sublimation sources. From a thermodynamic standpoint, multilayer growth pits are unexpected in relaxed homoepitaxial growth, whereas oxidation is a known cause for step pinning, roughening, and faceting on elemental surfaces, both with and without growth flux. Not surprisingly, pits are thermodynamically metastable and heal by annealing to recover a smooth periodic step arrangement. STM reveals new details about the pits’ atomistic origins and growth dynamics. We give a model for heterogeneous nucleation of pits by preferential adsorption of Å-sized oxide nuclei at intrinsic growth antiphase boundaries, and subsequent step pinning and bunching around the nuclei.

Heterogeneous nucleation of pits via step pinning during Si(100) homoepitaxy

DOE PAGES

Yitamben, Esmeralda; Butera, Robert E.; Swartzentruber, Brian S.; ...

2017-10-16

Using scanning tunneling microscopy (STM), we investigate oxide-induced growth pits in Si thin films deposited by molecular beam epitaxy. In the transition temperature range from 2D adatom islanding to step-flow growth, systematic controlled air leaks into the growth chamber induce pits in the growth surface. We show that pits are also correlated with oxygen-contaminated flux from Si sublimation sources. From a thermodynamic standpoint, multilayer growth pits are unexpected in relaxed homoepitaxial growth, whereas oxidation is a known cause for step-pinning, roughening, and faceting on elemental surfaces, both with and without growth flux. Not surprisingly, pits are thermodynamically metastable and healmore » by annealing to recover a smooth periodic step arrangement. STM reveals new details about the pits' atomistic origins and growth dynamics. Here, we give a model for heterogeneous nucleation of pits by preferential adsorption of Å-sized oxide nuclei at intrinsic growth antiphase boundaries, and subsequent step pinning and bunching around the nuclei.« less

Equivalence of Brownian dynamics and dynamic Monte Carlo simulations in multicomponent colloidal suspensions.

PubMed

Cuetos, Alejandro; Patti, Alessandro

2015-08-01

We propose a simple but powerful theoretical framework to quantitatively compare Brownian dynamics (BD) and dynamic Monte Carlo (DMC) simulations of multicomponent colloidal suspensions. By extending our previous study focusing on monodisperse systems of rodlike colloids, here we generalize the formalism described there to multicomponent colloidal mixtures and validate it by investigating the dynamics in isotropic and liquid crystalline phases containing spherical and rodlike particles. In order to investigate the dynamics of multicomponent colloidal systems by DMC simulations, it is key to determine the elementary time step of each species and establish a unique timescale. This is crucial to consistently study the dynamics of colloidal particles with different geometry. By analyzing the mean-square displacement, the orientation autocorrelation functions, and the self part of the van Hove correlation functions, we show that DMC simulation is a very convenient and reliable technique to describe the stochastic dynamics of any multicomponent colloidal system. Our theoretical formalism can be easily extended to any colloidal system containing size and/or shape polydisperse particles.

A sandpile model of grain blocking and consequences for sediment dynamics in step-pool streams

NASA Astrophysics Data System (ADS)

Molnar, P.

2012-04-01

Coarse grains (cobbles to boulders) are set in motion in steep mountain streams by floods with sufficient energy to erode the particles locally and transport them downstream. During transport, grains are often blocked and form width-spannings structures called steps, separated by pools. The step-pool system is a transient, self-organizing and self-sustaining structure. The temporary storage of sediment in steps and the release of that sediment in avalanche-like pulses when steps collapse, leads to a complex nonlinear threshold-driven dynamics in sediment transport which has been observed in laboratory experiments (e.g., Zimmermann et al., 2010) and in the field (e.g., Turowski et al., 2011). The basic question in this paper is if the emergent statistical properties of sediment transport in step-pool systems may be linked to the transient state of the bed, i.e. sediment storage and morphology, and to the dynamics in sediment input. The hypothesis is that this state, in which sediment transporting events due to the collapse and rebuilding of steps of all sizes occur, is analogous to a critical state in self-organized open dissipative dynamical systems (Bak et al., 1988). To exlore the process of self-organization, a cellular automaton sandpile model is used to simulate the processes of grain blocking and hydraulically-driven step collapse in a 1-d channel. Particles are injected at the top of the channel and are allowed to travel downstream based on various local threshold rules, with the travel distance drawn from a chosen probability distribution. In sandpile modelling this is a simple 1-d limited non-local model, however it has been shown to have nontrivial dynamical behaviour (Kadanoff et al., 1989), and it captures the essence of stochastic sediment transport in step-pool systems. The numerical simulations are used to illustrate the differences between input and output sediment transport rates, mainly focussing on the magnification of intermittency and variability in the system response by the processes of grain blocking and step collapse. The temporal correlation in input and output rates and the number of grains stored in the system at any given time are quantified by spectral analysis and statistics of long-range dependence. Although the model is only conceptually conceived to represent the real processes of step formation and collapse, connections will be made between the modelling results and some field and laboratory data on step-pool systems. The main focus in the discussion will be to demonstrate how even in such a simple model the processes of grain blocking and step collapse may impact the sediment transport rates to the point that certain changes in input are not visible anymore, along the lines of "shredding the signals" proposed by Jerolmack and Paola (2010). The consequences are that the notions of stability and equilibrium, the attribution of cause and effect, and the timescales of process and form in step-pool systems, and perhaps in many other fluvial systems, may have very limited applicability.

Next generation extended Lagrangian first principles molecular dynamics

NASA Astrophysics Data System (ADS)

Niklasson, Anders M. N.

2017-08-01

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Next generation extended Lagrangian first principles molecular dynamics.

PubMed

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

How to Compute Electron Ionization Mass Spectra from First Principles.

PubMed

Bauer, Christoph Alexander; Grimme, Stefan

2016-06-02

The prediction of electron ionization (EI) mass spectra (MS) from first principles has been a major challenge for quantum chemistry (QC). The unimolecular reaction space grows rapidly with increasing molecular size. On the one hand, statistical models like Eyring's quasi-equilibrium theory and Rice-Ramsperger-Kassel-Marcus theory have provided valuable insight, and some predictions and quantitative results can be obtained from such calculations. On the other hand, molecular dynamics-based methods are able to explore automatically the energetically available regions of phase space and thus yield reaction paths in an unbiased way. We describe in this feature article the status of both methodologies in relation to mass spectrometry for small to medium sized molecules. We further present results obtained with the QCEIMS program developed in our laboratory. Our method, which incorporates stochastic and dynamic elements, has been a significant step toward the reliable routine calculation of EI mass spectra.

Voter dynamics on an adaptive network with finite average connectivity

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Abhishek; Schmittmann, Beate

2009-03-01

We study a simple model for voter dynamics in a two-party system. The opinion formation process is implemented in a random network of agents in which interactions are not restricted by geographical distance. In addition, we incorporate the rapidly changing nature of the interpersonal relations in the model. At each time step, agents can update their relationships, so that there is no history dependence in the model. This update is determined by their own opinion, and by their preference to make connections with individuals sharing the same opinion and with opponents. Using simulations and analytic arguments, we determine the final steady states and the relaxation into these states for different system sizes. In contrast to earlier studies, the average connectivity (``degree'') of each agent is constant here, independent of the system size. This has significant consequences for the long-time behavior of the model.

Design and dynamic analysis of a piezoelectric linear stage for pipetting liquid samples

NASA Astrophysics Data System (ADS)

Yu-Jen, Wang; Chien, Lee; Yi-Bin, Jiang; Kuo-Chieh, Fu

2017-06-01

Piezoelectric actuators have been widely used in positioning stages because of their compact size, stepping controllability, and holding force. This study proposes a piezoelectric-driven stage composed of a bi-electrode piezoelectric slab, capacitive position sensor, and capillary filling detector for filling liquid samples into nanopipettes using capillary flow. This automatic sample-filling device is suitable for transmission electron microscopy image-based quantitative analysis of aqueous products with added nanoparticles. The step length of the actuator is adjusted by a pulse width modulation signal that depends on the stage position; the actuator stops moving once the capillary filling has been detected. A novel dynamic model of the piezoelectric-driven stage based on collision interactions between the piezoelectric actuator and the sliding clipper is presented. Unknown model parameters are derived from the steady state solution of the equivalent steady phase angle. The output force of the piezoelectric actuator is formulated using the impulse and momentum principle. Considering the applied forces and related velocity between the sliding clipper and the piezoelectric slab, the stage dynamic response is confirmed with the experimental results. Moreover, the model can be used to explain the in-phase slanted trajectories of piezoelectric slab to drive sliders, but not elliptical trajectories. The maximum velocity and minimum step length of the piezoelectric-driven stage are 130 mm s-1 and 1 μm respectively.

Specific Features in Measuring Particle Size Distributions in Highly Disperse Aerosol Systems

NASA Astrophysics Data System (ADS)

Zagaynov, V. A.; Vasyanovich, M. E.; Maksimenko, V. V.; Lushnikov, A. A.; Biryukov, Yu. G.; Agranovskii, I. E.

2018-06-01

The distribution of highly dispersed aerosols is studied. Particular attention is given to the diffusion dynamic approach, as it is the best way to determine particle size distribution. It shown that the problem can be divided into two steps: directly measuring particle penetration through diffusion batteries and solving the inverse problem (obtaining a size distribution from the measured penetrations). No reliable way of solving the so-called inverse problem is found, but it can be done by introducing a parametrized size distribution (i.e., a gamma distribution). The integral equation is therefore reduced to a system of nonlinear equations that can be solved by elementary mathematical means. Further development of the method requires an increase in sensitivity (i.e., measuring the dimensions of molecular clusters with radioactive sources, along with the activity of diffusion battery screens).

Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

NASA Astrophysics Data System (ADS)

Ma, Zhanshan (Sam)

In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three categories of population dynamics models: deterministic modeling with Logistic chaos map as an example, stochastic modeling with spatial distribution patterns as an example, as well as survival analysis and extended evolutionary game theory (EEGT) modeling. Sample experiment results with Genetic algorithms (GA) are presented to demonstrate the applications of these models. The proposed EC population dynamics approach also makes survival selection largely unnecessary or much simplified since the individuals are naturally selected (controlled) by the mathematical models for EC population dynamics.

Nano-electron beam induced current and hole charge dynamics through uncapped Ge nanocrystals

NASA Astrophysics Data System (ADS)

Marchand, A.; El Hdiy, A.; Troyon, M.; Amiard, G.; Ronda, A.; Berbezier, I.

2012-04-01

Dynamics of hole storage in spherical Ge nanocrystals (NCs) formed by a two step dewetting/nucleation process on an oxide layer grown on an n-doped <001> silicon substrate is studied using a nano-electron beam induced current technique. Carrier generation is produced by an electron beam irradiation. The generated current is collected by an atomic force microscope—tip in contact mode at a fixed position away from the beam spot of about 0.5 µm. This distance represents the effective diffusion length of holes. The time constants of holes charging are determined and the effect of the NC size is underlined.

The role of particle jamming on the formation and stability of step-pool morphology: insight from a reduced-complexity model

NASA Astrophysics Data System (ADS)

Saletti, M.; Molnar, P.; Hassan, M. A.

2017-12-01

Granular processes have been recognized as key drivers in earth surface dynamics, especially in steep landscapes because of the large size of sediment found in channels. In this work we focus on step-pool morphologies, studying the effect of particle jamming on step formation. Starting from the jammed-state hypothesis, we assume that grains generate steps because of particle jamming and those steps are inherently more stable because of additional force chains in the transversal direction. We test this hypothesis with a particle-based reduced-complexity model, CAST2, where sediment is organized in patches and entrainment, transport and deposition of grains depend on flow stage and local topography through simplified phenomenological rules. The model operates with 2 grain sizes: fine grains, that can be mobilized both my large and moderate flows, and coarse grains, mobile only during large floods. First, we identify the minimum set of processes necessary to generate and maintain steps in a numerical channel: (a) occurrence of floods, (b) particle jamming, (c) low sediment supply, and (d) presence of sediment with different entrainment probabilities. Numerical results are compared with field observations collected in different step-pool channels in terms of step density, a variable that captures the proportion of the channel occupied by steps. Not only the longitudinal profiles of numerical channels display step sequences similar to those observed in real step-pool streams, but also the values of step density are very similar when all the processes mentioned before are considered. Moreover, with CAST2 it is possible to run long simulations with repeated flood events, to test the effect of flood frequency on step formation. Numerical results indicate that larger step densities belong to system more frequently perturbed by floods, compared to system having a lower flood frequency. Our results highlight the important interactions between external hydrological forcing and internal geomorphic adjustment (e.g. jamming) on the response of step-pool streams, showing the potential of reduced-complexity models in fluvial geomorphology.

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

PubMed

Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

2016-07-12

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.

Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations

DOE PAGES

Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; ...

2016-06-06

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive iterative re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance ismore » obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.« less

Nonlinear Response of Layer Growth Dynamics in the Mixed Kinetics-Bulk-Transport Regime

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.; Alexander, J. Iwan D.; Rosenberger, Franz

1996-01-01

In situ high-resolution interferometry on horizontal facets of the protein lysozyme reveal that the local growth rate R, vicinal slope p, and tangential (step) velocity v fluctuate by up to 80% of their average values. The time scale of these fluctuations, which occur under steady bulk transport conditions through the formation and decay of step bunches (macrosteps), is of the order of 10 min. The fluctuation amplitude of R increases with growth rate (supersaturation) and crystal size, while the amplitude of the v and p fluctuations changes relatively little. Based on a stability analysis for equidistant step trains in the mixed transport-interface-kinetics regime, we argue that the fluctuations originate from the coupling of bulk transport with nonlinear interface kinetics. Furthermore, step bunches moving across the interface in the direction of or opposite to the buoyancy-driven convective flow increase or decrease in height, respectively. This is in agreement with analytical treatments of the interaction of moving steps with solution flow. Major excursions in growth rate are associated with the formation of lattice defects (striations). We show that, in general, the system-dependent kinetic Peclet number, Pe(sub k) , i.e., the relative weight of bulk transport and interface kinetics in the control of the growth process, governs the step bunching dynamics. Since Pe(sub k) can be modified by either forced solution flow or suppression of buoyancy-driven convection under reduced gravity, this model provides a rationale for the choice of specific transport conditions to minimize the formation of compositional inhomogeneities under steady bulk nutrient crystallization conditions.

Direct modeling for computational fluid dynamics

NASA Astrophysics Data System (ADS)

Xu, Kun

2015-06-01

All fluid dynamic equations are valid under their modeling scales, such as the particle mean free path and mean collision time scale of the Boltzmann equation and the hydrodynamic scale of the Navier-Stokes (NS) equations. The current computational fluid dynamics (CFD) focuses on the numerical solution of partial differential equations (PDEs), and its aim is to get the accurate solution of these governing equations. Under such a CFD practice, it is hard to develop a unified scheme that covers flow physics from kinetic to hydrodynamic scales continuously because there is no such governing equation which could make a smooth transition from the Boltzmann to the NS modeling. The study of fluid dynamics needs to go beyond the traditional numerical partial differential equations. The emerging engineering applications, such as air-vehicle design for near-space flight and flow and heat transfer in micro-devices, do require further expansion of the concept of gas dynamics to a larger domain of physical reality, rather than the traditional distinguishable governing equations. At the current stage, the non-equilibrium flow physics has not yet been well explored or clearly understood due to the lack of appropriate tools. Unfortunately, under the current numerical PDE approach, it is hard to develop such a meaningful tool due to the absence of valid PDEs. In order to construct multiscale and multiphysics simulation methods similar to the modeling process of constructing the Boltzmann or the NS governing equations, the development of a numerical algorithm should be based on the first principle of physical modeling. In this paper, instead of following the traditional numerical PDE path, we introduce direct modeling as a principle for CFD algorithm development. Since all computations are conducted in a discretized space with limited cell resolution, the flow physics to be modeled has to be done in the mesh size and time step scales. Here, the CFD is more or less a direct construction of discrete numerical evolution equations, where the mesh size and time step will play dynamic roles in the modeling process. With the variation of the ratio between mesh size and local particle mean free path, the scheme will capture flow physics from the kinetic particle transport and collision to the hydrodynamic wave propagation. Based on the direct modeling, a continuous dynamics of flow motion will be captured in the unified gas-kinetic scheme. This scheme can be faithfully used to study the unexplored non-equilibrium flow physics in the transition regime.

Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

NASA Astrophysics Data System (ADS)

Philip, B.; Wang, Z.; Berrill, M. A.; Birke, M.; Pernice, M.

2014-04-01

The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

WAKES: Wavelet Adaptive Kinetic Evolution Solvers

NASA Astrophysics Data System (ADS)

Mardirian, Marine; Afeyan, Bedros; Larson, David

2016-10-01

We are developing a general capability to adaptively solve phase space evolution equations mixing particle and continuum techniques in an adaptive manner. The multi-scale approach is achieved using wavelet decompositions which allow phase space density estimation to occur with scale dependent increased accuracy and variable time stepping. Possible improvements on the SFK method of Larson are discussed, including the use of multiresolution analysis based Richardson-Lucy Iteration, adaptive step size control in explicit vs implicit approaches. Examples will be shown with KEEN waves and KEEPN (Kinetic Electrostatic Electron Positron Nonlinear) waves, which are the pair plasma generalization of the former, and have a much richer span of dynamical behavior. WAKES techniques are well suited for the study of driven and released nonlinear, non-stationary, self-organized structures in phase space which have no fluid, limit nor a linear limit, and yet remain undamped and coherent well past the drive period. The work reported here is based on the Vlasov-Poisson model of plasma dynamics. Work supported by a Grant from the AFOSR.

An atomistic simulation scheme for modeling crystal formation from solution.

PubMed

Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk

2006-01-14

We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.

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

Fath, L., E-mail: lukas.fath@kit.edu; Hochbruck, M., E-mail: marlis.hochbruck@kit.edu; Singh, C.V., E-mail: chandraveer.singh@utoronto.ca

Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementationmore » in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.« less

Evolution of size distribution, optical properties, and structure of Si nanoparticles obtained by laser-assisted fragmentation

NASA Astrophysics Data System (ADS)

Plautz, G. L.; Graff, I. L.; Schreiner, W. H.; Bezerra, A. G.

2017-05-01

We investigate the physical properties of Si-based nanoparticles produced by an environment-friendly three-step method relying on: (1) laser ablation of a solid target immersed in water, (2) centrifugation and separation, and (3) laser-assisted fragmentation. The evolution of size distribution is followed after each step by means of dynamic light scattering (DLS) measurements and crosschecked by transmission electron microscopy (TEM). The as-ablated colloidal suspension of Si nanoparticles presents a large size distribution, ranging from a few to hundreds of nanometers. Centrifugation drives the very large particles to the bottom eliminating them from the remaining suspension. Subsequent irradiation of height-separated suspensions with a second high-fluence (40 mJ/pulse) Nd:YAG laser operating at the fourth harmonic (λ =266 nm) leads to size reduction and ultra-small nanoparticles are obtainable depending on the starting size. Si nanoparticles as small as 1.5 nm with low dispersion (± 0.7 nm) are observed for the uppermost part after irradiation. These nanoparticles present a strong blue photoluminescence that remains stable for at least 8 weeks. Optical absorption (UV-Vis) measurements demonstrate an optical gap widening as a consequence of size decrease. Raman spectra present features related to pure silicon and silicon oxides for the irradiated sample. Interestingly, a defect band associated with silicon oxide is also identified, indicating the possible formation of defect states, which, in turn, supports the idea that the blue photoluminescence has its origin in defects.

Growth from Solutions: Kink dynamics, Stoichiometry, Face Kinetics and stability in turbulent flow

NASA Technical Reports Server (NTRS)

Chernov, A. A.; DeYoreo, J. J.; Rashkovich, L. N.; Vekilov, P. G.

2005-01-01

1. Kink dynamics. The first segment of a polygomized dislocation spiral step measured by AFM demonstrates up to 60% scattering in the critical length l*- the length when the segment starts to propagate. On orthorhombic lysozyme, this length is shorter than that the observed interkink distance. Step energy from the critical segment length based on the Gibbs-Thomson law (GTL), l* = 20(omega)alpha/(Delta)mu is several times larger than the energy from 2D nucleation rate. Here o is tine building block specific voiume, a is the step riser specific free energy, Delta(mu) is the crystallization driving force. These new data support our earlier assumption that the classical Frenkel, Burton -Cabrera-Frank concept of the abundant kink supply by fluctuations is not applicable for strongly polygonized steps. Step rate measurements on brushite confirms that statement. This is the1D nucleation of kinks that control step propagation. The GTL is valid only if l*

A unified gas-kinetic scheme for continuum and rarefied flows IV: Full Boltzmann and model equations

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

Liu, Chang, E-mail: cliuaa@ust.hk; Xu, Kun, E-mail: makxu@ust.hk; Sun, Quanhua, E-mail: qsun@imech.ac.cn

Fluid dynamic equations are valid in their respective modeling scales, such as the particle mean free path scale of the Boltzmann equation and the hydrodynamic scale of the Navier–Stokes (NS) equations. With a variation of the modeling scales, theoretically there should have a continuous spectrum of fluid dynamic equations. Even though the Boltzmann equation is claimed to be valid in all scales, many Boltzmann solvers, including direct simulation Monte Carlo method, require the cell resolution to the order of particle mean free path scale. Therefore, they are still single scale methods. In order to study multiscale flow evolution efficiently, themore » dynamics in the computational fluid has to be changed with the scales. A direct modeling of flow physics with a changeable scale may become an appropriate approach. The unified gas-kinetic scheme (UGKS) is a direct modeling method in the mesh size scale, and its underlying flow physics depends on the resolution of the cell size relative to the particle mean free path. The cell size of UGKS is not limited by the particle mean free path. With the variation of the ratio between the numerical cell size and local particle mean free path, the UGKS recovers the flow dynamics from the particle transport and collision in the kinetic scale to the wave propagation in the hydrodynamic scale. The previous UGKS is mostly constructed from the evolution solution of kinetic model equations. Even though the UGKS is very accurate and effective in the low transition and continuum flow regimes with the time step being much larger than the particle mean free time, it still has space to develop more accurate flow solver in the region, where the time step is comparable with the local particle mean free time. In such a scale, there is dynamic difference from the full Boltzmann collision term and the model equations. This work is about the further development of the UGKS with the implementation of the full Boltzmann collision term in the region where it is needed. The central ingredient of the UGKS is the coupled treatment of particle transport and collision in the flux evaluation across a cell interface, where a continuous flow dynamics from kinetic to hydrodynamic scales is modeled. The newly developed UGKS has the asymptotic preserving (AP) property of recovering the NS solutions in the continuum flow regime, and the full Boltzmann solution in the rarefied regime. In the mostly unexplored transition regime, the UGKS itself provides a valuable tool for the non-equilibrium flow study. The mathematical properties of the scheme, such as stability, accuracy, and the asymptotic preserving, will be analyzed in this paper as well.« less

One size fits all electronics for insole-based activity monitoring.

PubMed

Hegde, Nagaraj; Bries, Matthew; Melanson, Edward; Sazonov, Edward

2017-07-01

Footwear based wearable sensors are becoming prominent in many areas of monitoring health and wellness, such as gait and activity monitoring. In our previous research we introduced an insole based wearable system SmartStep, which is completely integrated in a socially acceptable package. From a manufacturing perspective, SmartStep's electronics had to be custom made for each shoe size, greatly complicating the manufacturing process. In this work we explore the possibility of making a universal electronics platform for SmartStep - SmartStep 3.0, which can be used in the most common insole sizes without modifications. A pilot human subject experiments were run to compare the accuracy between the one-size fits all (SmartStep 3.0) and custom size SmartStep 2.0. A total of ~10 hours of data was collected in the pilot study involving three participants performing different activities of daily living while wearing SmartStep 2.0 and SmartStep 3.0. Leave one out cross validation resulted in a 98.5% average accuracy from SmartStep 2.0, while SmartStep 3.0 resulted in 98.3% accuracy, suggesting that the SmartStep 3.0 can be as accurate as SmartStep 2.0, while fitting most common shoe sizes.

Fish mouths as engineering structures for vortical cross-step filtration

NASA Astrophysics Data System (ADS)

Sanderson, S. Laurie; Roberts, Erin; Lineburg, Jillian; Brooks, Hannah

2016-03-01

Suspension-feeding fishes such as goldfish and whale sharks retain prey without clogging their oral filters, whereas clogging is a major expense in industrial crossflow filtration of beer, dairy foods and biotechnology products. Fishes' abilities to retain particles that are smaller than the pore size of the gill-raker filter, including extraction of particles despite large holes in the filter, also remain unexplained. Here we show that unexplored combinations of engineering structures (backward-facing steps forming d-type ribs on the porous surface of a cone) cause fluid dynamic phenomena distinct from current biological and industrial filter operations. This vortical cross-step filtration model prevents clogging and explains the transport of tiny concentrated particles to the oesophagus using a hydrodynamic tongue. Mass transfer caused by vortices along d-type ribs in crossflow is applicable to filter-feeding duck beak lamellae and whale baleen plates, as well as the fluid mechanics of ventilation at fish gill filaments.

Determination of the coefficient of dynamic friction between coatings of alumina and metallic materials

NASA Astrophysics Data System (ADS)

Santos, A.; Córdoba, E.; Ramírez, Z.; Sierra, C.; Ortega, Y.

2017-12-01

This project aims to determine the coefficient of dynamic friction between micrometric size coatings of alumina and metallic materials (Steel and aluminium); the methodology used to achieve the proposed objective consisted of 4 phases, in the first one was developed a procedure that allowed, from a Pin on Disk machine built based on the specifications given by the ASTM G99-05 standard (Standard test method for wear tests with a Pin on Disk machine), to determine the coefficient of dynamic friction between two materials in contact; subsequently the methodology was verified through tests between steel-steel and steel-aluminium, due to these values are widely reported in the literature; as a third step, deposits of alumina particles of micrometric size were made on a steel substrate through thermal spraying by flame; finally, the tests were carried out between pins of steel of aluminium and alumina coating to determine the coefficients of dynamic friction between these two surfaces. The results of the project allowed to verify that the developed methodology is valid to obtain coefficients of dynamic friction between surfaces in contact since the percentages of error were of 3.5% and 2.1% for steel-steel and aluminium-steel, respectively; additionally, it was found that the coefficient of friction between steel-alumina coatings is 0.36 and aluminium-alumina coating is 0.25.

Generation of dense granular deposits for porosity analysis: assessment and application of large-scale non-smooth granular dynamics

NASA Astrophysics Data System (ADS)

Schruff, T.; Liang, R.; Rüde, U.; Schüttrumpf, H.; Frings, R. M.

2018-01-01

The knowledge of structural properties of granular materials such as porosity is highly important in many application-oriented and scientific fields. In this paper we present new results of computer-based packing simulations where we use the non-smooth granular dynamics (NSGD) method to simulate gravitational random dense packing of spherical particles with various particle size distributions and two types of depositional conditions. A bin packing scenario was used to compare simulation results to laboratory porosity measurements and to quantify the sensitivity of the NSGD regarding critical simulation parameters such as time step size. The results of the bin packing simulations agree well with laboratory measurements across all particle size distributions with all absolute errors below 1%. A large-scale packing scenario with periodic side walls was used to simulate the packing of up to 855,600 spherical particles with various particle size distributions (PSD). Simulation outcomes are used to quantify the effect of particle-domain-size ratio on the packing compaction. A simple correction model, based on the coordination number, is employed to compensate for this effect on the porosity and to determine the relationship between PSD and porosity. Promising accuracy and stability results paired with excellent computational performance recommend the application of NSGD for large-scale packing simulations, e.g. to further enhance the generation of representative granular deposits.

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

Shim, Yunsic; Amar, Jacques G.

While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N{sup 3} where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scalingmore » of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary “bottlenecks” to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N{sup 1/2}. Some additional possible methods to improve the scaling of TAD are also discussed.« less

One-step, low-temperature fabrication of CdS quantum dots by watermelon rind: a green approach

PubMed Central

Lakshmipathy, Rajasekhar; Sarada, Nallani Chakravarthula; Chidambaram, K; Pasha, Sk Khadeer

2015-01-01

We investigated the one-step synthesis of CdS nanoparticles via green synthesis that used aqueous extract of watermelon rind as a capping and stabilizing agent. Preliminary phytochemical analysis depicted the presence of carbohydrates which can act as capping and stabilizing agents. Synthesized CdS nanoparticles were characterized using UV-visible, Fourier transform infrared spectroscopy, X-ray diffraction, EDX, dynamic light scattering, transmission electron microscopy, and atomic force microscopy techniques. The CdS nanoparticles were found to be size- and shape-controlled and were stable even after 3 months of synthesis. The results suggest that watermelon rind, an agro-waste, can be used for synthesis of CdS nanoparticles without any addition of stabilizing and capping agents. PMID:26491319

Seed mediated synthesis of highly mono-dispersed gold nanoparticles in the presence of hydroquinone

NASA Astrophysics Data System (ADS)

Kumar, Dhiraj; Mutreja, Isha; Sykes, Peter

2016-09-01

Gold nanoparticles (AuNPs) are being studied for several biomedical applications, including drug delivery, biomedical imaging, contrast agents and tumor targeting. The synthesis of nanoparticles with a narrow size distribution is critical for these applications. We report the synthesis of highly mono-dispersed AuNPs by a seed mediated approach, in the presence of tri-sodium citrate and hydroquinone (HQ). AuNPs with an average size of 18 nm were used for the synthesis of highly mono-dispersed nanocrystals of an average size 40 nm, 60 nm, 80 nm and ˜100 nm; but the protocol is not limited to these sizes. The colloidal gold was subjected to UV-vis absorbance spectroscopy, showing a red shift in lambda max wavelength, peaks at 518.47 nm, 526.37 nm, 535.73 nm, 546.03 nm and 556.50 nm for AuNPs seed (18 nm), 40 nm, 60 nm, 80 nm and ˜100 nm respectively. The analysis was consistent with dynamic light scattering and electron microscopy. Hydrodynamic diameters measured were 17.6 nm, 40.8 nm, 59.8 nm, 74.1 nm, and 91.4 nm (size by dynamic light scattering—volume %); with an average poly dispersity index value of 0.088, suggesting mono-dispersity in the size distribution, which was also confirmed by transmission electron microscopy analysis. The advantage of a seed mediated approach is a multi-step growth of nanoparticle size that enables us to control the number of nanoparticles in the suspension, for size ranging from 24.5 nm to 95.8 nm. In addition, the HQ-based synthesis of colloidal nanocrystals allowed control of the particle size and size distribution by tailoring either the number of seeds, amount of gold precursor or reducing agent (HQ) in the final reaction mixture.

TEA CO 2 Laser Simulator: A software tool to predict the output pulse characteristics of TEA CO 2 laser

NASA Astrophysics Data System (ADS)

Abdul Ghani, B.

2005-09-01

"TEA CO 2 Laser Simulator" has been designed to simulate the dynamic emission processes of the TEA CO 2 laser based on the six-temperature model. The program predicts the behavior of the laser output pulse (power, energy, pulse duration, delay time, FWHM, etc.) depending on the physical and geometrical input parameters (pressure ratio of gas mixture, reflecting area of the output mirror, media length, losses, filling and decay factors, etc.). Program summaryTitle of program: TEA_CO2 Catalogue identifier: ADVW Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVW Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: P.IV DELL PC Setup: Atomic Energy Commission of Syria, Scientific Services Department, Mathematics and Informatics Division Operating system: MS-Windows 9x, 2000, XP Programming language: Delphi 6.0 No. of lines in distributed program, including test data, etc.: 47 315 No. of bytes in distributed program, including test data, etc.:7 681 109 Distribution format:tar.gz Classification: 15 Laser Physics Nature of the physical problem: "TEA CO 2 Laser Simulator" is a program that predicts the behavior of the laser output pulse by studying the effect of the physical and geometrical input parameters on the characteristics of the output laser pulse. The laser active medium consists of a CO 2-N 2-He gas mixture. Method of solution: Six-temperature model, for the dynamics emission of TEA CO 2 laser, has been adapted in order to predict the parameters of laser output pulses. A simulation of the laser electrical pumping was carried out using two approaches; empirical function equation (8) and differential equation (9). Typical running time: The program's running time mainly depends on both integration interval and step; for a 4 μs period of time and 0.001 μs integration step (defaults values used in the program), the running time will be about 4 seconds. Restrictions on the complexity: Using a very small integration step might leads to stop the program run due to the huge number of calculating points and to a small paging file size of the MS-Windows virtual memory. In such case, it is recommended to enlarge the paging file size to the appropriate size, or to use a bigger value of integration step.

N-terminus of Cardiac Myosin Essential Light Chain Modulates Myosin Step-Size

PubMed Central

Wang, Yihua; Ajtai, Katalin; Kazmierczak, Katarzyna; Szczesna-Cordary, Danuta; Burghardt, Thomas P.

2016-01-01

Muscle myosin cyclically hydrolyzes ATP to translate actin. Ventricular cardiac myosin (βmys) moves actin with three distinct unitary step-sizes resulting from its lever-arm rotation and with step-frequencies that are modulated in a myosin regulation mechanism. The lever-arm associated essential light chain (vELC) binds actin by its 43 residue N-terminal extension. Unitary steps were proposed to involve the vELC N-terminal extension with the 8 nm step engaging the vELC/actin bond facilitating an extra ~19 degrees of lever-arm rotation while the predominant 5 nm step forgoes vELC/actin binding. A minor 3 nm step is the unlikely conversion of the completed 5 to the 8 nm step. This hypothesis was tested using a 17 residue N-terminal truncated vELC in porcine βmys (Δ17βmys) and a 43 residue N-terminal truncated human vELC expressed in transgenic mouse heart (Δ43αmys). Step-size and step-frequency were measured using the Qdot motility assay. Both Δ17βmys and Δ43αmys had significantly increased 5 nm step-frequency and coincident loss in the 8 nm step-frequency compared to native proteins suggesting the vELC/actin interaction drives step-size preference. Step-size and step-frequency probability densities depend on the relative fraction of truncated vELC and relate linearly to pure myosin species concentrations in a mixture containing native vELC homodimer, two truncated vELCs in the modified homodimer, and one native and one truncated vELC in the heterodimer. Step-size and step-frequency, measured for native homodimer and at two or more known relative fractions of truncated vELC, are surmised for each pure species by using a new analytical method. PMID:26671638

An advection-diffusion-reaction size-structured fish population dynamics model combined with a statistical parameter estimation procedure: application to the Indian ocean skipjack tuna fishery.

PubMed

Faugeras, Blaise; Maury, Olivier

2005-10-01

We develop an advection-diffusion size-structured fish population dynamics model and apply it to simulate the skipjack tuna population in the Indian Ocean. The model is fully spatialized, and movements are parameterized with oceanographical and biological data; thus it naturally reacts to environment changes. We first formulate an initial-boundary value problem and prove existence of a unique positive solution. We then discuss the numerical scheme chosen for the integration of the simulation model. In a second step we address the parameter estimation problem for such a model. With the help of automatic differentiation, we derive the adjoint code which is used to compute the exact gradient of a Bayesian cost function measuring the distance between the outputs of the model and catch and length frequency data. A sensitivity analysis shows that not all parameters can be estimated from the data. Finally twin experiments in which pertubated parameters are recovered from simulated data are successfully conducted.

Quadratic adaptive algorithm for solving cardiac action potential models.

PubMed

Chen, Min-Hung; Chen, Po-Yuan; Luo, Ching-Hsing

2016-10-01

An adaptive integration method is proposed for computing cardiac action potential models accurately and efficiently. Time steps are adaptively chosen by solving a quadratic formula involving the first and second derivatives of the membrane action potential. To improve the numerical accuracy, we devise an extremum-locator (el) function to predict the local extremum when approaching the peak amplitude of the action potential. In addition, the time step restriction (tsr) technique is designed to limit the increase in time steps, and thus prevent the membrane potential from changing abruptly. The performance of the proposed method is tested using the Luo-Rudy phase 1 (LR1), dynamic (LR2), and human O'Hara-Rudy dynamic (ORd) ventricular action potential models, and the Courtemanche atrial model incorporating a Markov sodium channel model. Numerical experiments demonstrate that the action potential generated using the proposed method is more accurate than that using the traditional Hybrid method, especially near the peak region. The traditional Hybrid method may choose large time steps near to the peak region, and sometimes causes the action potential to become distorted. In contrast, the proposed new method chooses very fine time steps in the peak region, but large time steps in the smooth region, and the profiles are smoother and closer to the reference solution. In the test on the stiff Markov ionic channel model, the Hybrid blows up if the allowable time step is set to be greater than 0.1ms. In contrast, our method can adjust the time step size automatically, and is stable. Overall, the proposed method is more accurate than and as efficient as the traditional Hybrid method, especially for the human ORd model. The proposed method shows improvement for action potentials with a non-smooth morphology, and it needs further investigation to determine whether the method is helpful during propagation of the action potential. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Costa, Liborio I., E-mail: liborio78@gmail.com

A new Markov Chain Monte Carlo method for simulating the dynamics of particle systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is associated with minima in the energy landscape, in the proposed method, the state of the system is associated with the set of paths traveled by the atoms and the transition probabilities for an atom to be displaced are proportional to the corresponding velocities. In this way, the number of possible state-to-state transitions is reduced to a discrete set, and a direct link between the Montemore » Carlo time step and true physical time is naturally established. The resulting rejection-free algorithm is validated against event-driven molecular dynamics: the equilibrium and non-equilibrium dynamics of hard disks converge to the exact results with decreasing displacement size.« less

Dynamics of proteins aggregation. I. Universal scaling in unbounded media

NASA Astrophysics Data System (ADS)

Zheng, Size; Javidpour, Leili; Shing, Katherine S.; Sahimi, Muhammad

2016-10-01

It is well understood that in some cases proteins do not fold correctly and, depending on their environment, even properly-folded proteins change their conformation spontaneously, taking on a misfolded state that leads to protein aggregation and formation of large aggregates. An important factor that contributes to the aggregation is the interactions between the misfolded proteins. Depending on the aggregation environment, the aggregates may take on various shapes forming larger structures, such as protein plaques that are often toxic. Their deposition in tissues is a major contributing factor to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and prion. This paper represents the first part in a series devoted to molecular simulation of protein aggregation. We use the PRIME, a meso-scale model of proteins, together with extensive discontinuous molecular dynamics simulation to study the aggregation process in an unbounded fluid system, as the first step toward MD simulation of the same phenomenon in crowded cellular environments. Various properties of the aggregates have been computed, including dynamic evolution of aggregate-size distribution, mean aggregate size, number of peptides that contribute to the formation of β sheets, number of various types of hydrogen bonds formed in the system, radius of gyration of the aggregates, and the aggregates' diffusivity. We show that many of such quantities follow dynamic scaling, similar to those for aggregation of colloidal clusters. In particular, at long times the mean aggregate size S(t) grows with time as, S(t) ˜ tz, where z is the dynamic exponent. To our knowledge, this is the first time that the qualitative similarity between aggregation of proteins and colloidal aggregates has been pointed out.

Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

PubMed

Wang, Guanbo; Kaltashov, Igor A

2014-08-05

Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

Ocean regional circulation model sensitizes to resolution of the lateral boundary conditions

NASA Astrophysics Data System (ADS)

Pham, Van Sy; Hwang, Jin Hwan

2017-04-01

Dynamical downscaling with nested regional oceanographic models is an effective approach for forecasting operationally coastal weather and projecting long term climate on the ocean. Nesting procedures deliver the unwanted in dynamic downscaling due to the differences of numerical grid sizes and updating steps. Therefore, such unavoidable errors restrict the application of the Ocean Regional Circulation Model (ORCMs) in both short-term forecasts and long-term projections. The current work identifies the effects of errors induced by computational limitations during nesting procedures on the downscaled results of the ORCMs. The errors are quantitatively evaluated for each error source and its characteristics by the Big-Brother Experiments (BBE). The BBE separates identified errors from each other and quantitatively assess the amount of uncertainties employing the same model to simulate for both nesting and nested model. Here, we focus on discussing errors resulting from two main matters associated with nesting procedures. They should be the spatial grids' differences and the temporal updating steps. After the diverse cases from separately running of the BBE, a Taylor diagram was adopted to analyze the results and suggest an optimization intern of grid size and updating period and domain sizes. Key words: lateral boundary condition, error, ocean regional circulation model, Big-Brother Experiment. Acknowledgement: This research was supported by grants from the Korean Ministry of Oceans and Fisheries entitled "Development of integrated estuarine management system" and a National Research Foundation of Korea (NRF) Grant (No. 2015R1A5A 7037372) funded by MSIP of Korea. The authors thank the Integrated Research Institute of Construction and Environmental Engineering of Seoul National University for administrative support.

Formation and evolution of multimodal size distributions of InAs/GaAs quantum dots

NASA Astrophysics Data System (ADS)

Pohl, U. W.; Pötschke, K.; Schliwa, A.; Lifshits, M. B.; Shchukin, V. A.; Jesson, D. E.; Bimberg, D.

2006-05-01

Self-organized formation and evolution of quantum dot (QD) ensembles with a multimodal size distribution is reported. Such ensembles form after fast deposition near the critical thickness during a growth interruption (GRI) prior to cap layer growth and consist of pure InAs truncated pyramids with heights varying in steps of complete InAs monolayers, thereby creating well-distinguishable sub-ensembles. Ripening during GRI manifests itself by an increase of sub-ensembles of larger QDs at the expense of sub-ensembles of smaller ones, leaving the wetting layer unchanged. The dynamics of the multimodal QD size distribution is theoretically described using a kinetic approach. Starting from a broad distribution of flat QDs, a predominantly vertical growth is found due to strain-induced barriers for nucleation of a next atomic layer on different facets. QDs having initially a shorter base length attain a smaller height, accounting for the experimentally observed sub-ensemble structure. The evolution of the distribution is described by a master equation, which accounts for growth or dissolution of the QDs by mass exchange between the QDs and the adatom sea. The numerical solution is in good agreement with the measured dynamics.

Validation of a pretreatment delivery quality assurance method for the CyberKnife Synchrony system.

PubMed

Mastella, E; Vigorito, S; Rondi, E; Piperno, G; Ferrari, A; Strata, E; Rozza, D; Jereczek-Fossa, B A; Cattani, F

2016-08-01

To evaluate the geometric and dosimetric accuracies of the CyberKnife Synchrony respiratory tracking system (RTS) and to validate a method for pretreatment patient-specific delivery quality assurance (DQA). An EasyCube phantom was mounted on the ExacTrac gating phantom, which can move along the superior-inferior (SI) axis of a patient to simulate a moving target. The authors compared dynamic and static measurements. For each case, a Gafchromic EBT3 film was positioned between two slabs of the EasyCube, while a PinPoint ionization chamber was placed in the appropriate space. There were three steps to their evaluation: (1) the field size, the penumbra, and the symmetry of six secondary collimators were measured along the two main orthogonal axes. Dynamic measurements with deliberately simulated errors were also taken. (2) The delivered dose distributions (from step 1) were compared with the planned ones, using the gamma analysis method. The local gamma passing rates were evaluated using three acceptance criteria: 3% local dose difference (LDD)/3 mm, 2%LDD/2 mm, and 3%LDD/1 mm. (3) The DQA plans for six clinical patients were irradiated in different dynamic conditions, to give a total of 19 cases. The measured and planned dose distributions were evaluated with the same gamma-index criteria used in step 2 and the measured chamber doses were compared with the planned mean doses in the sensitive volume of the chamber. (1) A very slight enlargement of the field size and of the penumbra was observed in the SI direction (on average <1 mm), in line with the overall average CyberKnife system error for tracking treatments. (2) Comparison between the planned and the correctly delivered dose distributions confirmed the dosimetric accuracy of the RTS for simple plans. The multicriteria gamma analysis was able to detect the simulated errors, proving the robustness of their method of analysis. (3) All of the DQA clinical plans passed the tests, both in static and dynamic conditions. No statistically significant differences were found between static and dynamic cases, confirming the high degree of accuracy of the Synchrony RTS. The presented methods and measurements verified the mechanical and dosimetric accuracy of the Synchrony RTS. Their method confirms the fact that the RTS, if used properly, is able to treat a moving target with great precision. By combining PinPoint ion chamber, EBT3 films, and gamma evaluation of dose distributions, their DQA method robustly validated the effectiveness of CyberKnife and Synchrony system.

Molecular dynamics based enhanced sampling of collective variables with very large time steps.

PubMed

Chen, Pei-Yang; Tuckerman, Mark E

2018-01-14

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

NASA Astrophysics Data System (ADS)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Capillary fluctuations of surface steps: An atomistic simulation study for the model Cu(111) system

NASA Astrophysics Data System (ADS)

Freitas, Rodrigo; Frolov, Timofey; Asta, Mark

2017-10-01

Molecular dynamics (MD) simulations are employed to investigate the capillary fluctuations of steps on the surface of a model metal system. The fluctuation spectrum, characterized by the wave number (k ) dependence of the mean squared capillary-wave amplitudes and associated relaxation times, is calculated for 〈110 〉 and 〈112 〉 steps on the {111 } surface of elemental copper near the melting temperature of the classical potential model considered. Step stiffnesses are derived from the MD results, yielding values from the largest system sizes of (37 ±1 ) meV/A ˚ for the different line orientations, implying that the stiffness is isotropic within the statistical precision of the calculations. The fluctuation lifetimes are found to vary by approximately four orders of magnitude over the range of wave numbers investigated, displaying a k dependence consistent with kinetics governed by step-edge mediated diffusion. The values for step stiffness derived from these simulations are compared to step free energies for the same system and temperature obtained in a recent MD-based thermodynamic-integration (TI) study [Freitas, Frolov, and Asta, Phys. Rev. B 95, 155444 (2017), 10.1103/PhysRevB.95.155444]. Results from the capillary-fluctuation analysis and TI calculations yield statistically significant differences that are discussed within the framework of statistical-mechanical theories for configurational contributions to step free energies.

A highly accurate boundary integral equation method for surfactant-laden drops in 3D

NASA Astrophysics Data System (ADS)

Sorgentone, Chiara; Tornberg, Anna-Karin

2018-05-01

The presence of surfactants alters the dynamics of viscous drops immersed in an ambient viscous fluid. This is specifically true at small scales, such as in applications of droplet based microfluidics, where the interface dynamics become of increased importance. At such small scales, viscous forces dominate and inertial effects are often negligible. Considering Stokes flow, a numerical method based on a boundary integral formulation is presented for simulating 3D drops covered by an insoluble surfactant. The method is able to simulate drops with different viscosities and close interactions, automatically controlling the time step size and maintaining high accuracy also when substantial drop deformation appears. To achieve this, the drop surfaces as well as the surfactant concentration on each surface are represented by spherical harmonics expansions. A novel reparameterization method is introduced to ensure a high-quality representation of the drops also under deformation, specialized quadrature methods for singular and nearly singular integrals that appear in the formulation are evoked and the adaptive time stepping scheme for the coupled drop and surfactant evolution is designed with a preconditioned implicit treatment of the surfactant diffusion.

Ultrafast Transient Absorption Spectroscopy Investigation of Photoinduced Dynamics in Novel Donor-Acceptor Core-Shell Nanostructures for Organic Photovoltaics

NASA Astrophysics Data System (ADS)

Strain, Jacob; Jamhawi, Abdelqader; Abeywickrama, Thulitha M.; Loomis, Wendy; Rathnayake, Hemali; Liu, Jinjun

2016-06-01

Novel donor-acceptor nanostructures were synthesized via covalent synthesis and/or UV cross-linking method. Their photoinduced dynamics were investigated with ultrafast transient absorption (TA) spectroscopy. These new nanostructures are made with the strategy in mind to reduce manufacturing steps in the process of fabricating an organic photovoltaic cell. By imitating the heterojunction interface within a fixed particle domain, several fabrication steps can be bypassed reducing cost and giving more applicability to other film deposition methods. Such applications include aerosol deposition and ink-jet printing. The systems that were studied by TA spectroscopy include PDIB core, PDIB-P3HT core-shell, and PDIB-PANT core-shell which range in size from 60 to 130 nm. Within the experimentally accessible spectra range there resides a region of ground state bleaching, stimulated emission, and excited-state absorption of both neutrals and anions. Control experiments have been carried out to assign these features. At high pump fluences the TA spectra of PDIB core alone also indicate an intramolecular charge separation. The TA spectroscopy results thus far suggest that the core-shells resemble the photoinduced dynamics of a standard film although the particles are dispersed in solution, which indicates the desired outcome of the work.

An extension of the Saltykov method to quantify 3D grain size distributions in mylonites

NASA Astrophysics Data System (ADS)

Lopez-Sanchez, Marco A.; Llana-Fúnez, Sergio

2016-12-01

The estimation of 3D grain size distributions (GSDs) in mylonites is key to understanding the rheological properties of crystalline aggregates and to constraining dynamic recrystallization models. This paper investigates whether a common stereological method, the Saltykov method, is appropriate for the study of GSDs in mylonites. In addition, we present a new stereological method, named the two-step method, which estimates a lognormal probability density function describing the 3D GSD. Both methods are tested for reproducibility and accuracy using natural and synthetic data sets. The main conclusion is that both methods are accurate and simple enough to be systematically used in recrystallized aggregates with near-equant grains. The Saltykov method is particularly suitable for estimating the volume percentage of particular grain-size fractions with an absolute uncertainty of ±5 in the estimates. The two-step method is suitable for quantifying the shape of the actual 3D GSD in recrystallized rocks using a single value, the multiplicative standard deviation (MSD) parameter, and providing a precision in the estimate typically better than 5%. The novel method provides a MSD value in recrystallized quartz that differs from previous estimates based on apparent 2D GSDs, highlighting the inconvenience of using apparent GSDs for such tasks.

Some critical issues in the characterization of nanoscale thermal conductivity by molecular dynamics analysis

NASA Astrophysics Data System (ADS)

Ehsan Khaled, Mohammad; Zhang, Liangchi; Liu, Weidong

2018-07-01

The nanoscale thermal conductivity of a material can be significantly different from its value at the macroscale. Although a number of studies using the equilibrium molecular dynamics (EMD) with Green–Kubo (GK) formula have been conducted for nano-conductivity predictions, there are many problems in the analysis that have made the EMD results unreliable or misleading. This paper aims to clarify such critical issues through a thorough investigation on the effect and determination of the vital physical variables in the EMD-GK analysis, using the prediction of the nanoscale thermal conductivity of Si as an example. The study concluded that to have a reliable prediction, quantum correction, time step, simulation time, correlation time and system size are all crucial.

Scanning near-field optical microscopy.

PubMed

Vobornik, Dusan; Vobornik, Slavenka

2008-02-01

An average human eye can see details down to 0,07 mm in size. The ability to see smaller details of the matter is correlated with the development of the science and the comprehension of the nature. Today's science needs eyes for the nano-world. Examples are easily found in biology and medical sciences. There is a great need to determine shape, size, chemical composition, molecular structure and dynamic properties of nano-structures. To do this, microscopes with high spatial, spectral and temporal resolution are required. Scanning Near-field Optical Microscopy (SNOM) is a new step in the evolution of microscopy. The conventional, lens-based microscopes have their resolution limited by diffraction. SNOM is not subject to this limitation and can offer up to 70 times better resolution.

Effective size selection of MoS2 nanosheets by a novel liquid cascade centrifugation: Influences of the flakes dimensions on electrochemical and photoelectrochemical applications.

PubMed

Kajbafvala, Marzieh; Farbod, Mansoor

2018-05-14

Although liquid phase exfoliation is a powerful method to produce MoS 2 nanosheets in large scale, but its effectiveness is limited by the diversity of produced nanosheets sizes. Here a novel approach for separation of MoS 2 flakes having various lateral sizes and thicknesses based on the cascaded centrifugation has been introduced. This method involves a pre-separation step which is performed through low-speed centrifugation to avoid the deposition of large area single and few-layers by the heavier particles. The bulk MoS 2 powders were dispersed in an aqueous solution of sodium cholate (SC) and sonicated for 12 h. The main separation step was performed using different speed centrifugation intervals of 10-11, 8-10, 6-8, 4-6, 2-4 and 0.5-2 krpm by which nanosheets containing 2, 4, 7, 8, 14, 18 and 29 layers were obtained respectively. The samples were characterized using XRD, FESEM, AFM, TEM, DLS and also UV-vis, Raman and PL spectroscopy measurements. Dynamic light scattering (DLS) measurements have confirmed the existence of a larger number of single or few-layers MoS 2 nanosheets compared to when the pre-separation step was not used. Finally, Photocurrent and cyclic voltammetry of different samples were measured and found that the flakes with bigger surface area had larger CV loop area. Our results provide a method for the preparation of a MoS 2 monolayer enriched suspension which can be used for different applications. Copyright © 2018 Elsevier Inc. All rights reserved.

Crystal nucleation and metastable bcc phase in charged colloids: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Xinqiang; Sun, Zhiwei; Ouyang, Wenze; Xu, Shenghua

2018-05-01

The dynamic process of homogenous nucleation in charged colloids is investigated by brute-force molecular dynamics simulation. To check if the liquid-solid transition will pass through metastable bcc, simulations are performed at the state points that definitely lie in the phase region of thermodynamically stable fcc. The simulation results confirm that, in all of these cases, the preordered precursors, acting as the seeds of nucleation, always have predominant bcc symmetry consistent with Ostwald's step rule and the Alexander-McTague mechanism. However, the polymorph selection is not straightforward because the crystal structures formed are not often determined by the symmetry of intermediate precursors but have different characters under different state points. The region of the state point where bcc crystal structures of large enough size are formed during crystallization is narrow, which gives a reasonable explanation as to why the metastable bcc phase in charged colloidal suspensions is rarely detected in macroscopic experiments.

Non-Equlibrium Driven Dynamics of Continuous Attractors in Place Cell Networks

NASA Astrophysics Data System (ADS)

Zhong, Weishun; Kim, Hyun Jin; Schwab, David; Murugan, Arvind

Attractors have found much use in neuroscience as a means of information processing and decision making. Examples include associative memory with point and continuous attractors, spatial navigation and planning using place cell networks, dynamic pattern recognition among others. The functional use of such attractors requires the action of spatially and temporally varying external driving signals and yet, most theoretical work on attractors has been in the limit of small or no drive. We take steps towards understanding the non-equilibrium driven dynamics of continuous attractors in place cell networks. We establish an `equivalence principle' that relates fluctuations under a time-dependent external force to equilibrium fluctuations in a `co-moving' frame with only static forces, much like in Newtonian physics. Consequently, we analytically derive a network's capacity to encode multiple attractors as a function of the driving signal size and rate of change.

Predicting oscillatory dynamics in the movement of territorial animals.

PubMed

Giuggioli, L; Potts, J R; Harris, S

2012-07-07

Understanding ecological processes relies upon the knowledge of the dynamics of each individual component. In the context of animal population ecology, the way animals move and interact is of fundamental importance in explaining a variety of observed patterns. Here, we present a theoretical investigation on the movement dynamics of interacting scent-marking animals. We study how the movement statistics of territorial animals is responsible for the appearance of damped oscillations in the mean square displacement (MSD) of the animals. This non-monotonicity is shown to depend on one dimensionless parameter, given by the ratio of the correlation distance between successive steps to the size of the territory. As that parameter increases, the time dependence of the animal's MSD displays a transition from monotonic, characteristic of Brownian walks, to non-monotonic, characteristic of highly correlated walks. The results presented here represent a novel way of determining the degree of persistence in animal movement processes within confined regions.

Predicting oscillatory dynamics in the movement of territorial animals

PubMed Central

Giuggioli, L.; Potts, J. R.; Harris, S.

2012-01-01

Understanding ecological processes relies upon the knowledge of the dynamics of each individual component. In the context of animal population ecology, the way animals move and interact is of fundamental importance in explaining a variety of observed patterns. Here, we present a theoretical investigation on the movement dynamics of interacting scent-marking animals. We study how the movement statistics of territorial animals is responsible for the appearance of damped oscillations in the mean square displacement (MSD) of the animals. This non-monotonicity is shown to depend on one dimensionless parameter, given by the ratio of the correlation distance between successive steps to the size of the territory. As that parameter increases, the time dependence of the animal's MSD displays a transition from monotonic, characteristic of Brownian walks, to non-monotonic, characteristic of highly correlated walks. The results presented here represent a novel way of determining the degree of persistence in animal movement processes within confined regions. PMID:22262814

THz elastic dynamics in finite-size CoFeB-MgO phononic superlattices

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

Ulrichs, Henning, E-mail: hulrich@gwdg.de; Meyer, Dennis; Müller, Markus

2016-10-14

In this article, we present the observation of coherent elastic dynamics in a nano-scale phononic superlattice, which consists of only 4 bilayers. We demonstrate how ultra-short light pulses with a length of 40 fs can be utilized to excite a coherent elastic wave at 0.535 THz, which persist over about 20 ps. In later steps of the elastic dynamics, modes with frequency of 1.7 THz and above appear. All these modes are related to acoustic band gaps. Thus, the periodicity strongly manifests in the wave physics, although the system under investigation has only a small number of spatial periods. Tomore » further illustrate this, we show how by breaking the translational invariance of the superlattice, these features can be suppressed. Discussed in terms of phonon blocking and radiation, we elucidate in how far our structures can be considered as useful building blocks for phononic devices.« less

Prediction of flow dynamics using point processes

NASA Astrophysics Data System (ADS)

Hirata, Yoshito; Stemler, Thomas; Eroglu, Deniz; Marwan, Norbert

2018-01-01

Describing a time series parsimoniously is the first step to study the underlying dynamics. For a time-discrete system, a generating partition provides a compact description such that a time series and a symbolic sequence are one-to-one. But, for a time-continuous system, such a compact description does not have a solid basis. Here, we propose to describe a time-continuous time series using a local cross section and the times when the orbit crosses the local cross section. We show that if such a series of crossing times and some past observations are given, we can predict the system's dynamics with fine accuracy. This reconstructability neither depends strongly on the size nor the placement of the local cross section if we have a sufficiently long database. We demonstrate the proposed method using the Lorenz model as well as the actual measurement of wind speed.

Analyzing Dynamics of Cooperating Spacecraft

NASA Technical Reports Server (NTRS)

Hughes, Stephen P.; Folta, David C.; Conway, Darrel J.

2004-01-01

A software library has been developed to enable high-fidelity computational simulation of the dynamics of multiple spacecraft distributed over a region of outer space and acting with a common purpose. All of the modeling capabilities afforded by this software are available independently in other, separate software systems, but have not previously been brought together in a single system. A user can choose among several dynamical models, many high-fidelity environment models, and several numerical-integration schemes. The user can select whether to use models that assume weak coupling between spacecraft, or strong coupling in the case of feedback control or tethering of spacecraft to each other. For weak coupling, spacecraft orbits are propagated independently, and are synchronized in time by controlling the step size of the integration. For strong coupling, the orbits are integrated simultaneously. Among the integration schemes that the user can choose are Runge-Kutta Verner, Prince-Dormand, Adams-Bashforth-Moulton, and Bulirsh- Stoer. Comparisons of performance are included for both the weak- and strongcoupling dynamical models for all of the numerical integrators.

Investigation of stickiness influence in the anomalous transport and diffusion for a non-dissipative Fermi-Ulam model

NASA Astrophysics Data System (ADS)

Livorati, André L. P.; Palmero, Matheus S.; Díaz-I, Gabriel; Dettmann, Carl P.; Caldas, Iberê L.; Leonel, Edson D.

2018-02-01

We study the dynamics of an ensemble of non interacting particles constrained by two infinitely heavy walls, where one of them is moving periodically in time, while the other is fixed. The system presents mixed dynamics, where the accessible region for the particle to diffuse chaotically is bordered by an invariant spanning curve. Statistical analysis for the root mean square velocity, considering high and low velocity ensembles, leads the dynamics to the same steady state plateau for long times. A transport investigation of the dynamics via escape basins reveals that depending of the initial velocity ensemble, the decay rates of the survival probability present different shapes and bumps, in a mix of exponential, power law and stretched exponential decays. After an analysis of step-size averages, we found that the stable manifolds play the role of a preferential path for faster escape, being responsible for the bumps and different shapes of the survival probability.

Steepest descent method implementation on unconstrained optimization problem using C++ program

NASA Astrophysics Data System (ADS)

Napitupulu, H.; Sukono; Mohd, I. Bin; Hidayat, Y.; Supian, S.

2018-03-01

Steepest Descent is known as the simplest gradient method. Recently, many researches are done to obtain the appropriate step size in order to reduce the objective function value progressively. In this paper, the properties of steepest descent method from literatures are reviewed together with advantages and disadvantages of each step size procedure. The development of steepest descent method due to its step size procedure is discussed. In order to test the performance of each step size, we run a steepest descent procedure in C++ program. We implemented it to unconstrained optimization test problem with two variables, then we compare the numerical results of each step size procedure. Based on the numerical experiment, we conclude the general computational features and weaknesses of each procedure in each case of problem.

Decorrelation correction for nanoparticle tracking analysis of dilute polydisperse suspensions in bulk flow

NASA Astrophysics Data System (ADS)

Hartman, John; Kirby, Brian

2017-03-01

Nanoparticle tracking analysis, a multiprobe single particle tracking technique, is a widely used method to quickly determine the concentration and size distribution of colloidal particle suspensions. Many popular tools remove non-Brownian components of particle motion by subtracting the ensemble-average displacement at each time step, which is termed dedrifting. Though critical for accurate size measurements, dedrifting is shown here to introduce significant biasing error and can fundamentally limit the dynamic range of particle size that can be measured for dilute heterogeneous suspensions such as biological extracellular vesicles. We report a more accurate estimate of particle mean-square displacement, which we call decorrelation analysis, that accounts for correlations between individual and ensemble particle motion, which are spuriously introduced by dedrifting. Particle tracking simulation and experimental results show that this approach more accurately determines particle diameters for low-concentration polydisperse suspensions when compared with standard dedrifting techniques.

Sonoelectrochemical one-pot synthesis of Pt - Carbon black nanocomposite PEMFC electrocatalyst.

PubMed

Karousos, Dionysios S; Desdenakis, Kostantinos I; Sakkas, Petros M; Sourkouni, Georgia; Pollet, Bruno G; Argirusis, Christos

2017-03-01

Simultaneous electrocatalytic Pt-nanoparticle synthesis and decoration of Vulcan XC-72 carbon black substrate was achieved in a novel one-step-process, combining galvanostatic pulsed electrodeposition and pulsed ultrasonication with high power, low-frequency (20kHz) ultrasound. Aqueous chloroplatinic acid precursor baths, as well as carbon black suspensions in the former, were examined and decoration was proven by a combination of characterization methods, namely: dynamic light scattering, transmission electron microscopy, scanning electron microscopy with EDX-analysis and cyclic voltammetry. In particular, PVP was shown to have a beneficial stabilizing effect against free nanoparticle aggregation, ensuring narrow size distributions of the nanoparticles synthesized, but is also postulated to prevent the establishment of a strong metal-substrate interaction. Current pulse amplitude was identified as the most critical nanoparticle size-determining parameters, while only small size particles, under 10nm, appeared to be attached to carbon black. Copyright © 2016 Elsevier B.V. All rights reserved.

Finite size effects in epidemic spreading: the problem of overpopulated systems

NASA Astrophysics Data System (ADS)

Ganczarek, Wojciech

2013-12-01

In this paper we analyze the impact of network size on the dynamics of epidemic spreading. In particular, we investigate the pace of infection in overpopulated systems. In order to do that, we design a model for epidemic spreading on a finite complex network with a restriction to at most one contamination per time step, which can serve as a model for sexually transmitted diseases spreading in some student communes. Because of the highly discrete character of the process, the analysis cannot use the continuous approximation widely exploited for most models. Using a discrete approach, we investigate the epidemic threshold and the quasi-stationary distribution. The main results are two theorems about the mixing time for the process: it scales like the logarithm of the network size and it is proportional to the inverse of the distance from the epidemic threshold.

Dynamic modeling of photothermal interactions for laser-induced interstitial thermotherapy: parameter sensitivity analysis.

PubMed

Jiang, S C; Zhang, X X

2005-12-01

A two-dimensional model was developed to model the effects of dynamic changes in the physical properties on tissue temperature and damage to simulate laser-induced interstitial thermotherapy (LITT) treatment procedures with temperature monitoring. A modified Monte Carlo method was used to simulate photon transport in the tissue in the non-uniform optical property field with the finite volume method used to solve the Pennes bioheat equation to calculate the temperature distribution and the Arrhenius equation used to predict the thermal damage extent. The laser light transport and the heat transfer as well as the damage accumulation were calculated iteratively at each time step. The influences of different laser sources, different applicator sizes, and different irradiation modes on the final damage volume were analyzed to optimize the LITT treatment. The numerical results showed that damage volume was the smallest for the 1,064-nm laser, with much larger, similar damage volumes for the 980- and 850-nm lasers at normal blood perfusion rates. The damage volume was the largest for the 1,064-nm laser with significantly smaller, similar damage volumes for the 980- and 850-nm lasers with temporally interrupted blood perfusion. The numerical results also showed that the variations in applicator sizes, laser powers, heating durations and temperature monitoring ranges significantly affected the shapes and sizes of the thermal damage zones. The shapes and sizes of the thermal damage zones can be optimized by selecting different applicator sizes, laser powers, heating duration times, temperature monitoring ranges, etc.

Engineering multi-stage nanovectors for controlled degradation and tunable release kinetics

PubMed Central

Martinez, Jonathan O.; Chiappini, Ciro; Ziemys, Arturas; Faust, Ari M.; Kojic, Milos; Liu, Xuewu; Ferrari, Mauro; Tasciotti, Ennio

2013-01-01

Nanovectors hold substantial promise in abating the off-target effects of therapeutics by providing a means to selectively accumulate payloads at the target lesion, resulting in an increase in the therapeutic index. A sophisticated understanding of the factors that govern the degradation and release dynamics of these nanovectors is imperative to achieve these ambitious goals. In this work, we elucidate the relationship that exists between variations in pore size and the impact on the degradation, loading, and release of multistage nanovectors. Larger pored vectors displayed faster degradation and higher loading of nanoparticles, while exhibiting the slowest release rate. The degradation of these particles was characterized to occur in a multi-step progression where they initially decreased in size leaving the porous core isolated, while the pores gradually increased in size. Empirical loading and release studies of nanoparticles along with diffusion modeling revealed that this prolonged release was modulated by the penetration within the porous core of the vectors regulated by their pore size. PMID:23911070

Equivalent model construction for a non-linear dynamic system based on an element-wise stiffness evaluation procedure and reduced analysis of the equivalent system

NASA Astrophysics Data System (ADS)

Kim, Euiyoung; Cho, Maenghyo

2017-11-01

In most non-linear analyses, the construction of a system matrix uses a large amount of computation time, comparable to the computation time required by the solving process. If the process for computing non-linear internal force matrices is substituted with an effective equivalent model that enables the bypass of numerical integrations and assembly processes used in matrix construction, efficiency can be greatly enhanced. A stiffness evaluation procedure (STEP) establishes non-linear internal force models using polynomial formulations of displacements. To efficiently identify an equivalent model, the method has evolved such that it is based on a reduced-order system. The reduction process, however, makes the equivalent model difficult to parameterize, which significantly affects the efficiency of the optimization process. In this paper, therefore, a new STEP, E-STEP, is proposed. Based on the element-wise nature of the finite element model, the stiffness evaluation is carried out element-by-element in the full domain. Since the unit of computation for the stiffness evaluation is restricted by element size, and since the computation is independent, the equivalent model can be constructed efficiently in parallel, even in the full domain. Due to the element-wise nature of the construction procedure, the equivalent E-STEP model is easily characterized by design parameters. Various reduced-order modeling techniques can be applied to the equivalent system in a manner similar to how they are applied in the original system. The reduced-order model based on E-STEP is successfully demonstrated for the dynamic analyses of non-linear structural finite element systems under varying design parameters.

Dynamic gamma knife radiosurgery

NASA Astrophysics Data System (ADS)

Luan, Shuang; Swanson, Nathan; Chen, Zhe; Ma, Lijun

2009-03-01

Gamma knife has been the treatment of choice for various brain tumors and functional disorders. Current gamma knife radiosurgery is planned in a 'ball-packing' approach and delivered in a 'step-and-shoot' manner, i.e. it aims to 'pack' the different sized spherical high-dose volumes (called 'shots') into a tumor volume. We have developed a dynamic scheme for gamma knife radiosurgery based on the concept of 'dose-painting' to take advantage of the new robotic patient positioning system on the latest Gamma Knife C™ and Perfexion™ units. In our scheme, the spherical high dose volume created by the gamma knife unit will be viewed as a 3D spherical 'paintbrush', and treatment planning reduces to finding the best route of this 'paintbrush' to 'paint' a 3D tumor volume. Under our dose-painting concept, gamma knife radiosurgery becomes dynamic, where the patient moves continuously under the robotic positioning system. We have implemented a fully automatic dynamic gamma knife radiosurgery treatment planning system, where the inverse planning problem is solved as a traveling salesman problem combined with constrained least-square optimizations. We have also carried out experimental studies of dynamic gamma knife radiosurgery and showed the following. (1) Dynamic gamma knife radiosurgery is ideally suited for fully automatic inverse planning, where high quality radiosurgery plans can be obtained in minutes of computation. (2) Dynamic radiosurgery plans are more conformal than step-and-shoot plans and can maintain a steep dose gradient (around 13% per mm) between the target tumor volume and the surrounding critical structures. (3) It is possible to prescribe multiple isodose lines with dynamic gamma knife radiosurgery, so that the treatment can cover the periphery of the target volume while escalating the dose for high tumor burden regions. (4) With dynamic gamma knife radiosurgery, one can obtain a family of plans representing a tradeoff between the delivery time and the dose distributions, thus giving the clinician one more dimension of flexibility of choosing a plan based on the clinical situations.

In Vitro and In Vivo Single Myosin Step-Sizes in Striated Muscle a

PubMed Central

Burghardt, Thomas P.; Sun, Xiaojing; Wang, Yihua; Ajtai, Katalin

2016-01-01

Myosin in muscle transduces ATP free energy into the mechanical work of moving actin. It has a motor domain transducer containing ATP and actin binding sites, and, mechanical elements coupling motor impulse to the myosin filament backbone providing transduction/mechanical-coupling. The mechanical coupler is a lever-arm stabilized by bound essential and regulatory light chains. The lever-arm rotates cyclically to impel bound filamentous actin. Linear actin displacement due to lever-arm rotation is the myosin step-size. A high-throughput quantum dot labeled actin in vitro motility assay (Qdot assay) measures motor step-size in the context of an ensemble of actomyosin interactions. The ensemble context imposes a constant velocity constraint for myosins interacting with one actin filament. In a cardiac myosin producing multiple step-sizes, a “second characterization” is step-frequency that adjusts longer step-size to lower frequency maintaining a linear actin velocity identical to that from a shorter step-size and higher frequency actomyosin cycle. The step-frequency characteristic involves and integrates myosin enzyme kinetics, mechanical strain, and other ensemble affected characteristics. The high-throughput Qdot assay suits a new paradigm calling for wide surveillance of the vast number of disease or aging relevant myosin isoforms that contrasts with the alternative model calling for exhaustive research on a tiny subset myosin forms. The zebrafish embryo assay (Z assay) performs single myosin step-size and step-frequency assaying in vivo combining single myosin mechanical and whole muscle physiological characterizations in one model organism. The Qdot and Z assays cover “bottom-up” and “top-down” assaying of myosin characteristics. PMID:26728749

Role of step size and max dwell time in anatomy based inverse optimization for prostate implants

PubMed Central

Manikandan, Arjunan; Sarkar, Biplab; Rajendran, Vivek Thirupathur; King, Paul R.; Sresty, N.V. Madhusudhana; Holla, Ragavendra; Kotur, Sachin; Nadendla, Sujatha

2013-01-01

In high dose rate (HDR) brachytherapy, the source dwell times and dwell positions are vital parameters in achieving a desirable implant dose distribution. Inverse treatment planning requires an optimal choice of these parameters to achieve the desired target coverage with the lowest achievable dose to the organs at risk (OAR). This study was designed to evaluate the optimum source step size and maximum source dwell time for prostate brachytherapy implants using an Ir-192 source. In total, one hundred inverse treatment plans were generated for the four patients included in this study. Twenty-five treatment plans were created for each patient by varying the step size and maximum source dwell time during anatomy-based, inverse-planned optimization. Other relevant treatment planning parameters were kept constant, including the dose constraints and source dwell positions. Each plan was evaluated for target coverage, urethral and rectal dose sparing, treatment time, relative target dose homogeneity, and nonuniformity ratio. The plans with 0.5 cm step size were seen to have clinically acceptable tumor coverage, minimal normal structure doses, and minimum treatment time as compared with the other step sizes. The target coverage for this step size is 87% of the prescription dose, while the urethral and maximum rectal doses were 107.3 and 68.7%, respectively. No appreciable difference in plan quality was observed with variation in maximum source dwell time. The step size plays a significant role in plan optimization for prostate implants. Our study supports use of a 0.5 cm step size for prostate implants. PMID:24049323

2-Step scalar deadzone quantization for bitplane image coding.

PubMed

Auli-Llinas, Francesc

2013-12-01

Modern lossy image coding systems generate a quality progressive codestream that, truncated at increasing rates, produces an image with decreasing distortion. Quality progressivity is commonly provided by an embedded quantizer that employs uniform scalar deadzone quantization (USDQ) together with a bitplane coding strategy. This paper introduces a 2-step scalar deadzone quantization (2SDQ) scheme that achieves same coding performance as that of USDQ while reducing the coding passes and the emitted symbols of the bitplane coding engine. This serves to reduce the computational costs of the codec and/or to code high dynamic range images. The main insights behind 2SDQ are the use of two quantization step sizes that approximate wavelet coefficients with more or less precision depending on their density, and a rate-distortion optimization technique that adjusts the distortion decreases produced when coding 2SDQ indexes. The integration of 2SDQ in current codecs is straightforward. The applicability and efficiency of 2SDQ are demonstrated within the framework of JPEG2000.

The accuracy of matrix population model projections for coniferous trees in the Sierra Nevada, California

USGS Publications Warehouse

van Mantgem, P.J.; Stephenson, N.L.

2005-01-01

1 We assess the use of simple, size-based matrix population models for projecting population trends for six coniferous tree species in the Sierra Nevada, California. We used demographic data from 16 673 trees in 15 permanent plots to create 17 separate time-invariant, density-independent population projection models, and determined differences between trends projected from initial surveys with a 5-year interval and observed data during two subsequent 5-year time steps. 2 We detected departures from the assumptions of the matrix modelling approach in terms of strong growth autocorrelations. We also found evidence of observation errors for measurements of tree growth and, to a more limited degree, recruitment. Loglinear analysis provided evidence of significant temporal variation in demographic rates for only two of the 17 populations. 3 Total population sizes were strongly predicted by model projections, although population dynamics were dominated by carryover from the previous 5-year time step (i.e. there were few cases of recruitment or death). Fractional changes to overall population sizes were less well predicted. Compared with a null model and a simple demographic model lacking size structure, matrix model projections were better able to predict total population sizes, although the differences were not statistically significant. Matrix model projections were also able to predict short-term rates of survival, growth and recruitment. Mortality frequencies were not well predicted. 4 Our results suggest that simple size-structured models can accurately project future short-term changes for some tree populations. However, not all populations were well predicted and these simple models would probably become more inaccurate over longer projection intervals. The predictive ability of these models would also be limited by disturbance or other events that destabilize demographic rates. ?? 2005 British Ecological Society.

Dynamic behaviors of cavitation bubble for the steady cavitating flow

NASA Astrophysics Data System (ADS)

Cai, Jun; Huai, Xiulan; Li, Xunfeng

2009-12-01

In this paper, by introducing the flow velocity item into the classical Rayleigh-Plesset dynamic equation, a new equation, which does not involve the time term and can describe the motion of cavitation bubble in the steady cavitating flow, has been obtained. By solving the new motion equation using Runge-Kutta fourth order method with adaptive step size control, the dynamic behaviors of cavitation bubble driven by the varying pressure field downstream of a venturi cavitation reactor are numerically simulated. The effects of liquid temperature (corresponding to the saturated vapor pressure of liquid), cavitation number and inlet pressure of venturi on radial motion of bubble and pressure pulse due to the radial motion are analyzed and discussed in detail. Some dynamic behaviors of bubble different from those in previous papers are displayed. In addition, the internal relationship between bubble dynamics and process intensification is also discussed. The simulation results reported in this work reveal the variation laws of cavitation intensity with the flow conditions of liquid, and will lay a foundation for the practical application of hydrodynamic cavitation technology.

Simulation of localized heavy precipitation in South Korea on 20 June 2014: sensitivity test of integration time-step size and an effect of topographic resolution using WRF model

NASA Astrophysics Data System (ADS)

Roh, Joon-Woo; Jee, Joon-Bum; Lim, A.-Young; Choi, Young-Jean

2015-04-01

Korean warm-season rainfall, accounting for about three-fourths of the annual precipitation, is primarily caused by Changma front, which is a kind of the East Asian summer monsoon, and localized heavy rainfall with convective instability. Various physical mechanisms potentially exert influences on heavy precipitation over South Korea. Representatively, the middle latitude and subtropical weather fronts, associated with a quasi-stationary moisture convergence zone among varying air masses, make up one of the main rain-bearing synoptic scale systems. Localized heavy rainfall events in South Korea generally arise from mesoscale convective systems embedded in these synoptic scale disturbances along the Changma front or convective instabilities resulted from unstable air mass including the direct or indirect effect of typhoons. In recent years, torrential rainfalls, which are more than 30mm/hour of precipitation amount, in warm-season has increased threefold in Seoul, which is a metropolitan city in South Korea. In order to investigate multiple potential causes of warm-season localized heavy precipitation in South Korea, a localized heavy precipitation case took place on 20 June 2014 at Seoul. This case was mainly seen to be caused by short-wave trough, which is associated with baroclinic instability in the northwest of Korea, and a thermal low, which has high moist and warm air through analysis. This structure showed convective scale torrential rain was embedded in the dynamic and in the thermodynamic structures. In addition to, a sensitivity of rainfall amount and maximum rainfall location to the integration time-step sizes was investigated in the simulations of a localized heavy precipitation case using Weather Research and Forecasting model. The simulation of time-step sizes of 9-27s corresponding to a horizontal resolution of 4.5km and 1.5km varied slightly difference of the maximum rainfall amount. However, the sensitivity of spatial patterns and temporal variations in rainfall were relatively small for the time-step sizes. The effect of topography was also important in the localized heavy precipitation simulation.

Coral population dynamics across consecutive mass mortality events.

PubMed

Riegl, Bernhard; Purkis, Sam

2015-11-01

Annual coral mortality events due to increased atmospheric heat may occur regularly from the middle of the century and are considered apocalyptic for coral reefs. In the Arabian/Persian Gulf, this situation has already occurred and population dynamics of four widespread corals (Acropora downingi, Porites harrisoni, Dipsastrea pallida, Cyphastrea micropthalma) were examined across the first-ever occurrence of four back-to-back mass mortality events (2009-2012). Mortality was driven by diseases in 2009, bleaching and subsequent diseases in 2010/2011/2012. 2009 reduced P. harrisoni cover and size, the other events increasingly reduced overall cover (2009: -10%; 2010: -20%; 2011: -20%; 2012: -15%) and affected all examined species. Regeneration was only observed after the first disturbance. P. harrisoni and A. downingi severely declined from 2010 due to bleaching and subsequent white syndromes, while D. pallida and P. daedalea declined from 2011 due to bleaching and black-band disease. C. microphthalma cover was not affected. In all species, most large corals were lost while fission due to partial tissue mortality bolstered small size classes. This general shrinkage led to a decrease of coral cover and a dramatic reduction of fecundity. Transition matrices for disturbed and undisturbed conditions were evaluated as Life Table Response Experiment and showed that C. microphthalma changed the least in size-class dynamics and fecundity, suggesting they were 'winners'. In an ordered 'degradation cascade', impacts decreased from the most common to the least common species, leading to step-wise removal of previously dominant species. A potentially permanent shift from high- to low-coral cover with different coral community and size structure can be expected due to the demographic dynamics resultant from the disturbances. Similarities to degradation of other Caribbean and Pacific reefs are discussed. As comparable environmental conditions and mortality patterns must be expected worldwide, demographic collapse of many other coral populations may soon be widespread. © 2015 John Wiley & Sons Ltd.

Dynamic fiber Bragg gratings based health monitoring system of composite aerospace structures

NASA Astrophysics Data System (ADS)

Panopoulou, A.; Loutas, T.; Roulias, D.; Fransen, S.; Kostopoulos, V.

2011-09-01

The main purpose of the current work is to develop a new system for structural health monitoring of composite aerospace structures based on real-time dynamic measurements, in order to identify the structural state condition. Long-gauge Fibre Bragg Grating (FBG) optical sensors were used for monitoring the dynamic response of the composite structure. The algorithm that was developed for structural damage detection utilizes the collected dynamic response data, analyzes them in various ways and through an artificial neural network identifies the damage state and its location. Damage was simulated by slightly varying locally the mass of the structure (by adding a known mass) at different zones of the structure. Lumped masses in different locations upon the structure alter the eigen-frequencies in a way similar to actual damage. The structural dynamic behaviour has been numerically simulated and experimentally verified by means of modal testing on two different composite aerospace structures. Advanced digital signal processing techniques, e.g. the wavelet transform (WT), were used for the analysis of the dynamic response for feature extraction. WT's capability of separating the different frequency components in the time domain without loosing frequency information makes it a versatile tool for demanding signal processing applications. The use of WT is also suggested by the no-stationary nature of dynamic response signals and the opportunity of evaluating the temporal evolution of their frequency contents. Feature extraction is the first step of the procedure. The extracted features are effective indices of damage size and location. The classification step comprises of a feed-forward back propagation network, whose output determines the simulated damage location. Finally, dedicated training and validation activities were carried out by means of numerical simulations and experimental procedures. Experimental validation was performed initially on a flat stiffened panel, representing a section of a typical aeronautical structure, manufactured and tested in the lab and, as a second step, on a scaled up space oriented structure, which is a composite honeycomb plate, used as a deployment base for antenna arrays. An integrated FBG sensor network, based on the advantage of multiplexing, was mounted on both structures and different excitation positions and boundary conditions were used. The analysis of operational dynamic responses was employed to identify both the damage and its position. The system that was designed and tested initially on the thin composite panel, was successfully validated on the larger honeycomb structure. Numerical simulation of both structures was used as a support tool at all the steps of the work providing among others the location of the optical sensors used. The proposed work will be the base for the whole system qualification and validation on an antenna reflector in future work.

Dynamic Model of the BIO-Plex Air Revitalization System

NASA Technical Reports Server (NTRS)

Finn, Cory; Meyers, Karen; Duffield, Bruce; Luna, Bernadette (Technical Monitor)

2000-01-01

The BIO-Plex facility will need to support a variety of life support system designs and operation strategies. These systems will be tested and evaluated in the BIO-Plex facility. An important goal of the life support program is to identify designs that best meet all size and performance constraints for a variety of possible future missions. Integrated human testing is a necessary step in reaching this goal. System modeling and analysis will also play an important role in this endeavor. Currently, simulation studies are being used to estimate air revitalization buffer and storage requirements in order to develop the infrastructure requirements of the BIO-Plex facility. Simulation studies are also being used to verify that the envisioned operation strategy will be able to meet all performance criteria. In this paper, a simulation study is presented for a nominal BIO-Plex scenario with a high-level of crop growth. A general description of the dynamic mass flow model is provided, along with some simulation results. The paper also discusses sizing and operations issues and describes plans for future simulation studies.

Conformation and Dynamics of a Flexible Sheet in Solvent Media by Monte Carlo Simulations

NASA Astrophysics Data System (ADS)

Pandey, Ras; Anderson, Kelly; Heinz, Hendrik; Farmer, Barry

2005-03-01

Flexibility of the clay sheet is limited even in the ex-foliated state in some solvent media. A coarse grained model is used to investigate dynamics and conformation of a flexible sheet to model such a clay platelet in an effective solvent medium on a cubic lattice of size L^3 with lattice constant a. The undeformed sheet is described by a square lattice of size Ls^2, where, each node of the sheet is represented by the unit cube of the cubic lattice and 2a is the minimum distance between the nearest neighbor nodes to incorporate the excluded volume constraints. Additionally, each node interacts with neighboring nodes and solvent (empty) sites within a range ri. Each node execute their stochastic motion with the Metropolis algorithm subject to bond length fluctuation and excluded volume constraints. Mean square displacements of the center node and that of its center of mass are investigated as a function of time step for a set of these parameters. The radius of gyration (Rg) is also examined concurrently to understand its relaxation. Multi-scale segmental dynamics of the sheet is studied by identifying the power-law dependence in various time regimes. Relaxation of Rg and its dependence of temperature are planned to be discussed.

Auxotonic to isometric contraction transitioning in a beating heart causes myosin step-size to down shift

PubMed Central

Sun, Xiaojing; Wang, Yihua; Ajtai, Katalin

2017-01-01

Myosin motors in cardiac ventriculum convert ATP free energy to the work of moving blood volume under pressure. The actin bound motor cyclically rotates its lever-arm/light-chain complex linking motor generated torque to the myosin filament backbone and translating actin against resisting force. Previous research showed that the unloaded in vitro motor is described with high precision by single molecule mechanical characteristics including unitary step-sizes of approximately 3, 5, and 8 nm and their relative step-frequencies of approximately 13, 50, and 37%. The 3 and 8 nm unitary step-sizes are dependent on myosin essential light chain (ELC) N-terminus actin binding. Step-size and step-frequency quantitation specifies in vitro motor function including duty-ratio, power, and strain sensitivity metrics. In vivo, motors integrated into the muscle sarcomere form the more complex and hierarchically functioning muscle machine. The goal of the research reported here is to measure single myosin step-size and step-frequency in vivo to assess how tissue integration impacts motor function. A photoactivatable GFP tags the ventriculum myosin lever-arm/light-chain complex in the beating heart of a live zebrafish embryo. Detected single GFP emission reports time-resolved myosin lever-arm orientation interpreted as step-size and step-frequency providing single myosin mechanical characteristics over the active cycle. Following step-frequency of cardiac ventriculum myosin transitioning from low to high force in relaxed to auxotonic to isometric contraction phases indicates that the imposition of resisting force during contraction causes the motor to down-shift to the 3 nm step-size accounting for >80% of all the steps in the near-isometric phase. At peak force, the ATP initiated actomyosin dissociation is the predominant strain inhibited transition in the native myosin contraction cycle. The proposed model for motor down-shifting and strain sensing involves ELC N-terminus actin binding. Overall, the approach is a unique bottom-up single molecule mechanical characterization of a hierarchically functional native muscle myosin. PMID:28423017

Generalised Sandpile Dynamics on Artificial and Real-World Directed Networks

PubMed Central

Zachariou, Nicky; Expert, Paul; Takayasu, Misako; Christensen, Kim

2015-01-01

The main finding of this paper is a novel avalanche-size exponent τ ≈ 1.87 when the generalised sandpile dynamics evolves on the real-world Japanese inter-firm network. The topology of this network is non-layered and directed, displaying the typical bow tie structure found in real-world directed networks, with cycles and triangles. We show that one can move from a strictly layered regular lattice to a more fluid structure of the inter-firm network in a few simple steps. Relaxing the regular lattice structure by introducing an interlayer distribution for the interactions, forces the scaling exponent of the avalanche-size probability density function τ out of the two-dimensional directed sandpile universality class τ = 4/3, into the mean field universality class τ = 3/2. Numerical investigation shows that these two classes are the only that exist on the directed sandpile, regardless of the underlying topology, as long as it is strictly layered. Randomly adding a small proportion of links connecting non adjacent layers in an otherwise layered network takes the system out of the mean field regime to produce non-trivial avalanche-size probability density function. Although these do not display proper scaling, they closely reproduce the behaviour observed on the Japanese inter-firm network. PMID:26606143

Generalised Sandpile Dynamics on Artificial and Real-World Directed Networks.

PubMed

Zachariou, Nicky; Expert, Paul; Takayasu, Misako; Christensen, Kim

2015-01-01

The main finding of this paper is a novel avalanche-size exponent τ ≈ 1.87 when the generalised sandpile dynamics evolves on the real-world Japanese inter-firm network. The topology of this network is non-layered and directed, displaying the typical bow tie structure found in real-world directed networks, with cycles and triangles. We show that one can move from a strictly layered regular lattice to a more fluid structure of the inter-firm network in a few simple steps. Relaxing the regular lattice structure by introducing an interlayer distribution for the interactions, forces the scaling exponent of the avalanche-size probability density function τ out of the two-dimensional directed sandpile universality class τ = 4/3, into the mean field universality class τ = 3/2. Numerical investigation shows that these two classes are the only that exist on the directed sandpile, regardless of the underlying topology, as long as it is strictly layered. Randomly adding a small proportion of links connecting non adjacent layers in an otherwise layered network takes the system out of the mean field regime to produce non-trivial avalanche-size probability density function. Although these do not display proper scaling, they closely reproduce the behaviour observed on the Japanese inter-firm network.

Large Eddy Simulation including population dynamics model for polydisperse droplet evolution

NASA Astrophysics Data System (ADS)

Aiyer, Aditya; Yang, Di; Chamecki, Marcelo; Meneveau, Charles

2017-11-01

Previous studies have shown that dispersion patterns of oil droplets in the ocean following a deep sea oil spill depend critically on droplet diameter. Hence predicting the evolution of the droplet size distribution is of critical importance for predicting macroscopic features of dispersion in the ocean. We adopt a population dynamics model of polydisperse droplet distributions for use in LES. We generalize a breakup model from Reynolds averaging approaches to LES in which the breakup is modeled as due to bombardment of droplets by turbulent eddies of various sizes. The breakage rate is expressed as an integral of a collision frequency times a breakage efficiency over all eddy sizes. An empirical fit to the integral is proposed in order to avoid having to recalculate the integral at every LES grid point and time step. The fit is tested by comparison with various stirred tank experiments. As a flow application for LES we consider a jet of bubbles and large droplets injected at the bottom of the tank. The advected velocity and concentration fields of the drops are described using an Eulerian approach. We study the change of the oil droplet distribution due to breakup caused by interaction of turbulence with the oil droplets. This research was made possible by a Grant from the Gulf of Mexico Research Initiative.

A Variable Step-Size Proportionate Affine Projection Algorithm for Identification of Sparse Impulse Response

NASA Astrophysics Data System (ADS)

Liu, Ligang; Fukumoto, Masahiro; Saiki, Sachio; Zhang, Shiyong

2009-12-01

Proportionate adaptive algorithms have been proposed recently to accelerate convergence for the identification of sparse impulse response. When the excitation signal is colored, especially the speech, the convergence performance of proportionate NLMS algorithms demonstrate slow convergence speed. The proportionate affine projection algorithm (PAPA) is expected to solve this problem by using more information in the input signals. However, its steady-state performance is limited by the constant step-size parameter. In this article we propose a variable step-size PAPA by canceling the a posteriori estimation error. This can result in high convergence speed using a large step size when the identification error is large, and can then considerably decrease the steady-state misalignment using a small step size after the adaptive filter has converged. Simulation results show that the proposed approach can greatly improve the steady-state misalignment without sacrificing the fast convergence of PAPA.

4D measurements of biological and synthetic structures using a dynamic interferometer

NASA Astrophysics Data System (ADS)

Toto-Arellano, Noel-Ivan

2017-12-01

Considering the deficiency of time elapsed for phase-stepping interferometric techniques and the need of developing non-contact and on-line measurement with high accuracy, a single-shot phase-shifting triple-interferometer (PSTI) is developed for analysis of characteristics of transparent structures and optical path difference (OPD) measurements. In the proposed PSTI, coupled three interferometers which generate four interference patterns, and a polarizer array is used as phase shifters to produce four spatially separated interferograms with π/2-phase shifts, which are recorded in a single capture by a camera. The configuration of the PSTI allows dynamic measurements (4D measurements) and does not require vibration isolation. We have applied the developed system to examine the size and OPD of cells, and the slope of thin films

Stability analysis of the Euler discretization for SIR epidemic model

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

Suryanto, Agus

2014-06-19

In this paper we consider a discrete SIR epidemic model obtained by the Euler method. For that discrete model, existence of disease free equilibrium and endemic equilibrium is established. Sufficient conditions on the local asymptotical stability of both disease free equilibrium and endemic equilibrium are also derived. It is found that the local asymptotical stability of the existing equilibrium is achieved only for a small time step size h. If h is further increased and passes the critical value, then both equilibriums will lose their stability. Our numerical simulations show that a complex dynamical behavior such as bifurcation or chaosmore » phenomenon will appear for relatively large h. Both analytical and numerical results show that the discrete SIR model has a richer dynamical behavior than its continuous counterpart.« less

The primary case is not enough: Variation among individuals, groups and social networks modify bacterial transmission dynamics.

PubMed

Keiser, Carl N; Pinter-Wollman, Noa; Ziemba, Michael J; Kothamasu, Krishna S; Pruitt, Jonathan N

2018-03-01

The traits of the primary case of an infectious disease outbreak, and the circumstances for their aetiology, potentially influence the trajectory of transmission dynamics. However, these dynamics likely also depend on the traits of the individuals with whom the primary case interacts. We used the social spider Stegodyphus dumicola to test how the traits of the primary case, group phenotypic composition and group size interact to facilitate the transmission of a GFP-labelled cuticular bacterium. We also compared bacterial transmission across experimentally generated "daisy-chain" vs. "star" networks of social interactions. Finally, we compared social network structure across groups of different sizes. Groups of 10 spiders experienced more bacterial transmission events compared to groups of 30 spiders, regardless of groups' behavioural composition. Groups containing only one bold spider experienced the lowest levels of bacterial transmission regardless of group size. We found no evidence for the traits of the primary case influencing any transmission dynamics. In a second experiment, bacteria were transmitted to more individuals in experimentally induced star networks than in daisy-chains, on which transmission never exceeded three steps. In both experimental network types, transmission success depended jointly on the behavioural traits of the interacting individuals; however, the behavioural traits of the primary case were only important for transmission on star networks. Larger social groups exhibited lower interaction density (i.e. had a low ratio of observed to possible connections) and were more modular, i.e. they had more connections between nodes within a subgroup and fewer connections across subgroups. Thus, larger groups may restrict transmission by forming fewer interactions and by isolating subgroups that interacted with the primary case. These findings suggest that accounting for the traits of single exposed hosts has less power in predicting transmission dynamics compared to the larger scale factors of the social groups in which they reside. Factors like group size and phenotypic composition appear to alter social interaction patterns, which leads to differential transmission of microbes. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Dynamic Obstacle Avoidance for Unmanned Underwater Vehicles Based on an Improved Velocity Obstacle Method

PubMed Central

Zhang, Wei; Wei, Shilin; Teng, Yanbin; Zhang, Jianku; Wang, Xiufang; Yan, Zheping

2017-01-01

In view of a dynamic obstacle environment with motion uncertainty, we present a dynamic collision avoidance method based on the collision risk assessment and improved velocity obstacle method. First, through the fusion optimization of forward-looking sonar data, the redundancy of the data is reduced and the position, size and velocity information of the obstacles are obtained, which can provide an accurate decision-making basis for next-step collision avoidance. Second, according to minimum meeting time and the minimum distance between the obstacle and unmanned underwater vehicle (UUV), this paper establishes the collision risk assessment model, and screens key obstacles to avoid collision. Finally, the optimization objective function is established based on the improved velocity obstacle method, and a UUV motion characteristic is used to calculate the reachable velocity sets. The optimal collision speed of UUV is searched in velocity space. The corresponding heading and speed commands are calculated, and outputted to the motion control module. The above is the complete dynamic obstacle avoidance process. The simulation results show that the proposed method can obtain a better collision avoidance effect in the dynamic environment, and has good adaptability to the unknown dynamic environment. PMID:29186878

Dynamic characteristics of hydrocarbon fuel within the channel at supercritical and pyrolysis condition

NASA Astrophysics Data System (ADS)

Yu, Bin; Zhou, Weixing; Qin, Jiang; Bao, Wen

2017-12-01

Regenerative cooling with fuel as the coolant is used in the scramjet engine. In order to grasp the dynamic characteristics of engine fuel supply processes, this article studies the dynamic characteristics of hydrocarbon fuel within the channel. A one-dimensional dynamic model was proved, the thermal energy storage effect, fuel volume effect and chemical dynamic effect have been considered in the model, the ordinary differential equations were solved using a 4th order Runge-Kutta method. The precision of the model was validated by three groups of experimental data. The effects of input signal, working condition, tube size on the dynamic characteristics of pressure, flow rate, temperature have been simulated. It is found that cracking reaction increased the compressibility of the fuel pyrolysis mixture and lead to longer responding time of outlet flow. The responding time of outlet flow can reach 3s when tube is 5m long which will greatly influence the control performance of the engine thrust system. Meanwhile, when the inlet flow rate appears the step change, the inlet pressure leads to overshoot, the overshoot can reach as much as 100%, such highly transient impulse will result in detrimental effect on fuel pump.

The role of telomere dynamics in aging and cancer

NASA Astrophysics Data System (ADS)

Blagoev, Krastan; Goodwin, Edwin

2006-03-01

Telomere length changes are far more dynamic than previously thought. In addition to a gradual loss of ˜100 base pairs per telomere in each cell division, losses as well as gains may occur within a single cell cycle. We are investigating how telomere exchange, extension, and deletion affect the proliferative potential of telomerase-negative somatic cells. Experimental techniques are being devised to detect dynamic telomere processes and quantify both the frequency and length changes of each. In parallel, a ``dynamic telomere model'' is being used that incorporates telomere dynamics to study how the telomere size distribution evolves with time. This is an essential step towards understanding the role that telomere dynamics play in the normal aging of tissues and organisms. The model casts light on relationships not otherwise easily explained by a deterministic ``mitotic clock,'' or to what extent the shortest initial telomere determines the onset of senescence. We also expect to identify biomarkers that will correlate with aging better than average telomere length and to shed light on the transition to unlimited growth found in telomerase-negative tumor cells having the ALT (alternative lengthening of telomeres) phenotype, and to evaluate strategies to suppress the growth of these tumors.

SCANNING NEAR-FIELD OPTICAL MICROSCOPY

PubMed Central

Vobornik, Dušan; Vobornik, Slavenka

2008-01-01

An average human eye can see details down to 0,07 mm in size. The ability to see smaller details of the matter is correlated with the development of the science and the comprehension of the nature. Today’s science needs eyes for the nano-world. Examples are easily found in biology and medical sciences. There is a great need to determine shape, size, chemical composition, molecular structure and dynamic properties of nano-structures. To do this, microscopes with high spatial, spectral and temporal resolution are required. Scanning Near-field Optical Microscopy (SNOM) is a new step in the evolution of microscopy. The conventional, lens-based microscopes have their resolution limited by diffraction. SNOM is not subject to this limitation and can offer up to 70 times better resolution. PMID:18318675

Frequency analysis of a step dynamic pressure calibrator.

PubMed

Choi, In-Mook; Yang, Inseok; Yang, Tae-Heon

2012-09-01

A dynamic high pressure standard is becoming more essential in the fields of mobile engines, space science, and especially the area of defense such as long-range missile development. However, a complication arises when a dynamic high pressure sensor is compared with a reference dynamic pressure gauge calibrated in static mode. Also, it is difficult to determine a reference dynamic pressure signal from the calibrator because a dynamic high pressure calibrator generates unnecessary oscillations in a positive-going pressure step method. A dynamic high pressure calibrator, using a quick-opening ball valve, generates a fast step pressure change within 1 ms; however, the calibrator also generates a big impulse force that can lead to a short life-time of the system and to oscillating characteristics in response to the dynamic sensor to be calibrated. In this paper, unnecessary additional resonant frequencies besides those of the step function are characterized using frequency analysis. Accordingly, the main sources of resonance are described. In order to remove unnecessary frequencies, the post processing results, obtained by a filter, are given; also, a method for the modification of the dynamic calibration system is proposed.

Frequency analysis of a step dynamic pressure calibrator

NASA Astrophysics Data System (ADS)

Choi, In-Mook; Yang, Inseok; Yang, Tae-Heon

2012-09-01

A dynamic high pressure standard is becoming more essential in the fields of mobile engines, space science, and especially the area of defense such as long-range missile development. However, a complication arises when a dynamic high pressure sensor is compared with a reference dynamic pressure gauge calibrated in static mode. Also, it is difficult to determine a reference dynamic pressure signal from the calibrator because a dynamic high pressure calibrator generates unnecessary oscillations in a positive-going pressure step method. A dynamic high pressure calibrator, using a quick-opening ball valve, generates a fast step pressure change within 1 ms; however, the calibrator also generates a big impulse force that can lead to a short life-time of the system and to oscillating characteristics in response to the dynamic sensor to be calibrated. In this paper, unnecessary additional resonant frequencies besides those of the step function are characterized using frequency analysis. Accordingly, the main sources of resonance are described. In order to remove unnecessary frequencies, the post processing results, obtained by a filter, are given; also, a method for the modification of the dynamic calibration system is proposed.

Dynamics of upper mantle rocks decompression melting above hot spots under continental plates

NASA Astrophysics Data System (ADS)

Perepechko, Yury; Sorokin, Konstantin; Sharapov, Victor

2014-05-01

Numeric 2D simulation of the decompression melting above the hot spots (HS) was accomplished under the following conditions: initial temperature within crust mantle section was postulated; thickness of the metasomatized lithospheric mantle is determined by the mantle rheology and position of upper asthenosphere boundary; upper and lower boundaries were postulated to be not permeable and the condition for adhesion and the distribution of temperature (1400-2050°C); lateral boundaries imitated infinity of layer. Sizes and distribution of lateral points, their symmetry, and maximum temperature varied between the thermodynamic condition for existences of perovskite - majorite transition and its excess above transition temperature. Problem was solved numerically a cell-vertex finite volume method for thermo hydrodynamic problems. For increasing convergence of iterative process the method of lower relaxation with different value of relaxation parameter for each equation was used. The method of through calculation was used for the increase in the computing rate for the two-layered upper mantle - lithosphere system. Calculated region was selected as 700 x (2100-4900) km. The time step for the study of the asthenosphere dynamics composed 0.15-0.65 Ma. The following factors controlling the sizes and melting degree of the convective upper mantle, are shown: a) the initial temperature distribution along the section of upper mantleb) sizes and the symmetry of HS, c) temperature excess within the HS above the temperature on the upper and lower mantle border TB=1500-2000oC with 5-15% deviation but not exceed 2350oC. It is found, that appearance of decompression melting with HS presence initiate primitive mantle melting at TB > of 1600oC. Initial upper mantle heating influence on asthenolens dimensions with a constant HS size is controlled mainly by decompression melting degree. Thus, with lateral sizes of HS = 400 km the decompression melting appears at TB > 1600oC and HS temperature (THS) > 1900oC asthenolens size ~700 km. When THS = of 2000oC the maximum melting degree of the primitive mantle is near 40%. An increase in the TB > 1900oC the maximum degree of melting could rich 100% with the same size of decompression melting zone (700 km). We examined decompression melting above the HS having LHS = 100 km - 780 km at a TB 1850- 2100oC with the thickness of lithosphere = 100 km.It is shown that asthenolens size (Lln) does not change substantially: Lln=700 km at LHS = of 100 km; Lln= 800 km at LHS = of 780 km. In presence of asymmetry of large HS the region of advection is developed above the HS maximum with the formation of asymmetrical cell. Influence of lithospheric plate thicknesses on appearance and evolution of asthenolens above the HS were investigated for the model stepped profile for the TB ≤ of 1750oS with Lhs = 100km and maximum of THS =2350oC. With an increase of TB the Lln difference beneath lithospheric steps is leveled with retention of a certain difference to melting degrees and time of the melting appearance a top of the HS. RFBR grant 12-05-00625.

Model reduction of dynamical systems by proper orthogonal decomposition: Error bounds and comparison of methods using snapshots from the solution and the time derivatives [Proper orthogonal decomposition model reduction of dynamical systems: error bounds and comparison of methods using snapshots from the solution and the time derivatives

DOE PAGES

Kostova-Vassilevska, Tanya; Oxberry, Geoffrey M.

2017-09-17

In this study, we consider two proper orthogonal decomposition (POD) methods for dimension reduction of dynamical systems. The first method (M1) uses only time snapshots of the solution, while the second method (M2) augments the snapshot set with time-derivative snapshots. The goal of the paper is to analyze and compare the approximation errors resulting from the two methods by using error bounds. We derive several new bounds of the error from POD model reduction by each of the two methods. The new error bounds involve a multiplicative factor depending on the time steps between the snapshots. For method M1 themore » factor depends on the second power of the time step, while for method 2 the dependence is on the fourth power of the time step, suggesting that method M2 can be more accurate for small between-snapshot intervals. However, three other factors also affect the size of the error bounds. These include (i) the norm of the second (for M1) and fourth derivatives (M2); (ii) the first neglected singular value and (iii) the spectral properties of the projection of the system’s Jacobian in the reduced space. Because of the interplay of these factors neither method is more accurate than the other in all cases. Finally, we present numerical examples demonstrating that when the number of collected snapshots is small and the first neglected singular value has a value of zero, method M2 results in a better approximation.« less

Model reduction of dynamical systems by proper orthogonal decomposition: Error bounds and comparison of methods using snapshots from the solution and the time derivatives [Proper orthogonal decomposition model reduction of dynamical systems: error bounds and comparison of methods using snapshots from the solution and the time derivatives

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

Kostova-Vassilevska, Tanya; Oxberry, Geoffrey M.

In this study, we consider two proper orthogonal decomposition (POD) methods for dimension reduction of dynamical systems. The first method (M1) uses only time snapshots of the solution, while the second method (M2) augments the snapshot set with time-derivative snapshots. The goal of the paper is to analyze and compare the approximation errors resulting from the two methods by using error bounds. We derive several new bounds of the error from POD model reduction by each of the two methods. The new error bounds involve a multiplicative factor depending on the time steps between the snapshots. For method M1 themore » factor depends on the second power of the time step, while for method 2 the dependence is on the fourth power of the time step, suggesting that method M2 can be more accurate for small between-snapshot intervals. However, three other factors also affect the size of the error bounds. These include (i) the norm of the second (for M1) and fourth derivatives (M2); (ii) the first neglected singular value and (iii) the spectral properties of the projection of the system’s Jacobian in the reduced space. Because of the interplay of these factors neither method is more accurate than the other in all cases. Finally, we present numerical examples demonstrating that when the number of collected snapshots is small and the first neglected singular value has a value of zero, method M2 results in a better approximation.« less

Numerical research of dynamic characteristics in tower solar cavity receiver based on step-change radiation flux

NASA Astrophysics Data System (ADS)

Chen, Zhengwei; Wang, Yueshe; Hao, Yun; Wang, Qizhi

2013-07-01

The solar cavity receiver is an important light-energy to thermal-energy convector in the tower solar thermal power plant system. The heat flux in the inner surface of the cavity will show the characteristics of non-continuous step change especially in non-normal and transient weather conditions, which may result in a continuous dynamic variation of the characteristic parameters. Therefore, the research of dynamic characteristics of the receiver plays a very important role in the operation and the control safely in solar cavity receiver system. In this paper, based on the non-continuous step change of radiation flux, a non-linear dynamic model is put forward to obtain the effects of the non-continuous step change radiation flux and step change feed water flow on the receiver performance by sequential modular approach. The subject investigated in our study is a 1MW solar power station constructed in Yanqing County, Beijing. This study has obtained the dynamic responses of the characteristic parameters in the cavity receiver, such as drum pressure, drum water level, main steam flow and main steam enthalpy under step change radiation flux. And the influence law of step-change feed water flow to the dynamic characteristics in the receiver also has been analyzed. The results have a reference value for the safe operation and the control in solar cavity receiver system.

Integrating Thermodynamic Models in Geodynamic Simulations: The Example of the Community Software ASPECT

NASA Astrophysics Data System (ADS)

Dannberg, J.; Heister, T.; Grove, R. R.; Gassmoeller, R.; Spiegelman, M. W.; Bangerth, W.

2017-12-01

Earth's surface shows many features whose genesis can only be understood through the interplay of geodynamic and thermodynamic models. This is particularly important in the context of melt generation and transport: Mantle convection determines the distribution of temperature and chemical composition, the melting process itself is then controlled by the thermodynamic relations and in turn influences the properties and the transport of melt. Here, we present our extension of the community geodynamics code ASPECT, which solves the equations of coupled magma/mantle dynamics, and allows to integrate different parametrizations of reactions and phase transitions: They may alternatively be implemented as simple analytical expressions, look-up tables, or computed by a thermodynamics software. As ASPECT uses a variety of numerical methods and solvers, this also gives us the opportunity to compare different approaches of modelling the melting process. In particular, we will elaborate on the spatial and temporal resolution that is required to accurately model phase transitions, and show the potential of adaptive mesh refinement when applied to melt generation and transport. We will assess the advantages and disadvantages of iterating between fluid dynamics and chemical reactions derived from thermodynamic models within each time step, or decoupling them, allowing for different time step sizes. Beyond that, we will expand on the functionality required for an interface between computational thermodynamics and fluid dynamics models from the geodynamics side. Finally, using a simple example of melting of a two-phase, two-component system, we compare different time-stepping and solver schemes in terms of accuracy and efficiency, in dependence of the time scales of fluid flow and chemical reactions relative to each other. Our software provides a framework to integrate thermodynamic models in high resolution, 3d simulations of coupled magma/mantle dynamics, and can be used as a tool to study links between physical processes and geochemical signals in the Earth.

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

PubMed

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

2016-12-28

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

On the use of finite difference matrix-vector products in Newton-Krylov solvers for implicit climate dynamics with spectral elements

DOE PAGES

Woodward, Carol S.; Gardner, David J.; Evans, Katherine J.

2015-01-01

Efficient solutions of global climate models require effectively handling disparate length and time scales. Implicit solution approaches allow time integration of the physical system with a step size governed by accuracy of the processes of interest rather than by stability of the fastest time scales present. Implicit approaches, however, require the solution of nonlinear systems within each time step. Usually, a Newton's method is applied to solve these systems. Each iteration of the Newton's method, in turn, requires the solution of a linear model of the nonlinear system. This model employs the Jacobian of the problem-defining nonlinear residual, but thismore » Jacobian can be costly to form. If a Krylov linear solver is used for the solution of the linear system, the action of the Jacobian matrix on a given vector is required. In the case of spectral element methods, the Jacobian is not calculated but only implemented through matrix-vector products. The matrix-vector multiply can also be approximated by a finite difference approximation which may introduce inaccuracy in the overall nonlinear solver. In this paper, we review the advantages and disadvantages of finite difference approximations of these matrix-vector products for climate dynamics within the spectral element shallow water dynamical core of the Community Atmosphere Model.« less

Short-Term Adaptive Modification of Dynamic Ocular Accommodation

PubMed Central

Bharadwaj, Shrikant R.; Vedamurthy, Indu; Schor, Clifton M.

2009-01-01

Purpose Indirect observations suggest that the neural control of accommodation may undergo adaptive recalibration in response to age-related biomechanical changes in the accommodative system. However, there has been no direct demonstration of such an adaptive capability. This investigation was conducted to demonstrate short-term adaptation of accommodative step response dynamics to optically induced changes in neuromuscular demands. Methods Repetitive changes in accommodative effort were induced in 15 subjects (18–34 years) with a double-step adaptation paradigm wherein an initial 2-D step change in blur was followed 350 ms later by either a 2-D step increase in blur (increasing-step paradigm) or a 1.75-D step decrease in blur (decreasing-step paradigm). Peak velocity, peak acceleration, and latency of 2-D single-step test responses were assessed before and after 1.5 hours of training with these paradigms. Results Peak velocity and peak acceleration of 2-D step responses increased after adaptation to the increasing-step paradigm (9/12 subjects), and they decreased after adaptation to the decreasing-step paradigm (4/9 subjects). Adaptive changes in peak velocity and peak acceleration generalized to responses that were smaller (1 D) and larger (3 D) than the 2-D adaptation stimulus. The magnitude of adaptation correlated poorly with the subject's age, but it was significantly negatively correlated with the preadaptation dynamics. Response latency decreased after adaptation, irrespective of the direction of adaptation. Conclusions Short-term adaptive changes in accommodative step response dynamics could be induced, at least in some of our subjects between 18 and 34 years, with a directional bias toward increasing rather than decreasing the dynamics. PMID:19255153

Finite element model updating using the shadow hybrid Monte Carlo technique

NASA Astrophysics Data System (ADS)

Boulkaibet, I.; Mthembu, L.; Marwala, T.; Friswell, M. I.; Adhikari, S.

2015-02-01

Recent research in the field of finite element model updating (FEM) advocates the adoption of Bayesian analysis techniques to dealing with the uncertainties associated with these models. However, Bayesian formulations require the evaluation of the Posterior Distribution Function which may not be available in analytical form. This is the case in FEM updating. In such cases sampling methods can provide good approximations of the Posterior distribution when implemented in the Bayesian context. Markov Chain Monte Carlo (MCMC) algorithms are the most popular sampling tools used to sample probability distributions. However, the efficiency of these algorithms is affected by the complexity of the systems (the size of the parameter space). The Hybrid Monte Carlo (HMC) offers a very important MCMC approach to dealing with higher-dimensional complex problems. The HMC uses the molecular dynamics (MD) steps as the global Monte Carlo (MC) moves to reach areas of high probability where the gradient of the log-density of the Posterior acts as a guide during the search process. However, the acceptance rate of HMC is sensitive to the system size as well as the time step used to evaluate the MD trajectory. To overcome this limitation we propose the use of the Shadow Hybrid Monte Carlo (SHMC) algorithm. The SHMC algorithm is a modified version of the Hybrid Monte Carlo (HMC) and designed to improve sampling for large-system sizes and time steps. This is done by sampling from a modified Hamiltonian function instead of the normal Hamiltonian function. In this paper, the efficiency and accuracy of the SHMC method is tested on the updating of two real structures; an unsymmetrical H-shaped beam structure and a GARTEUR SM-AG19 structure and is compared to the application of the HMC algorithm on the same structures.

Effects of annealing on the physical properties of therapeutic proteins during freeze drying process.

PubMed

Lim, Jun Yeul; Lim, Dae Gon; Kim, Ki Hyun; Park, Sang-Koo; Jeong, Seong Hoon

2018-02-01

Effects of annealing steps during the freeze drying process on etanercept, model protein, were evaluated using various analytical methods. The annealing was introduced in three different ways depending on time and temperature. Residual water contents of dried cakes varied from 2.91% to 6.39% and decreased when the annealing step was adopted, suggesting that they are directly affected by the freeze drying methods Moreover, the samples were more homogenous when annealing was adopted. Transition temperatures of the excipients (sucrose, mannitol, and glycine) were dependent on the freeze drying steps. Size exclusion chromatography showed that monomer contents were high when annealing was adopted and also they decreased less after thermal storage at 60°C. Dynamic light scattering results exhibited that annealing can be helpful in inhibiting aggregation and that thermal storage of freeze-dried samples preferably induced fragmentation over aggregation. Shift of circular dichroism spectrum and of the contents of etanercept secondary structure was observed with different freeze drying steps and thermal storage conditions. All analytical results suggest that the physicochemical properties of etanercept formulation can differ in response to different freeze drying steps and that annealing is beneficial for maintaining stability of protein and reducing the time of freeze drying process. Copyright © 2017 Elsevier B.V. All rights reserved.

Lab-on-a-disc agglutination assay for protein detection by optomagnetic readout and optical imaging using nano- and micro-sized magnetic beads.

PubMed

Uddin, Rokon; Burger, Robert; Donolato, Marco; Fock, Jeppe; Creagh, Michael; Hansen, Mikkel Fougt; Boisen, Anja

2016-11-15

We present a biosensing platform for the detection of proteins based on agglutination of aptamer coated magnetic nano- or microbeads. The assay, from sample to answer, is integrated on an automated, low-cost microfluidic disc platform. This ensures fast and reliable results due to a minimum of manual steps involved. The detection of the target protein was achieved in two ways: (1) optomagnetic readout using magnetic nanobeads (MNBs); (2) optical imaging using magnetic microbeads (MMBs). The optomagnetic readout of agglutination is based on optical measurement of the dynamics of MNB aggregates whereas the imaging method is based on direct visualization and quantification of the average size of MMB aggregates. By enhancing magnetic particle agglutination via application of strong magnetic field pulses, we obtained identical limits of detection of 25pM with the same sample-to-answer time (15min 30s) using the two differently sized beads for the two detection methods. In both cases a sample volume of only 10µl is required. The demonstrated automation, low sample-to-answer time and portability of both detection instruments as well as integration of the assay on a low-cost disc are important steps for the implementation of these as portable tools in an out-of-lab setting. Copyright © 2016 Elsevier B.V. All rights reserved.

Ultrafast axial scanning for two-photon microscopy via a digital micromirror device and binary holography.

PubMed

Cheng, Jiyi; Gu, Chenglin; Zhang, Dapeng; Wang, Dien; Chen, Shih-Chi

2016-04-01

In this Letter, we present an ultrafast nonmechanical axial scanning method for two-photon excitation (TPE) microscopy based on binary holography using a digital micromirror device (DMD), achieving a scanning rate of 4.2 kHz, scanning range of ∼180  μm, and scanning resolution (minimum step size) of ∼270  nm. Axial scanning is achieved by projecting the femtosecond laser to a DMD programmed with binary holograms of spherical wavefronts of increasing/decreasing radii. To guide the scanner design, we have derived the parametric relationships between the DMD parameters (i.e., aperture and pixel size), and the axial scanning characteristics, including (1) maximum optical power, (2) minimum step size, and (3) scan range. To verify the results, the DMD scanner is integrated with a custom-built TPE microscope that operates at 60 frames per second. In the experiment, we scanned a pollen sample via both the DMD scanner and a precision z-stage. The results show the DMD scanner generates images of equal quality throughout the scanning range. The overall efficiency of the TPE system was measured to be ∼3%. With the high scanning rate, the DMD scanner may find important applications in random-access imaging or high-speed volumetric imaging that enables visualization of highly dynamic biological processes in 3D with submillisecond temporal resolution.

Bitwise efficiency in chaotic models

PubMed Central

Düben, Peter; Palmer, Tim

2017-01-01

Motivated by the increasing energy consumption of supercomputing for weather and climate simulations, we introduce a framework for investigating the bit-level information efficiency of chaotic models. In comparison with previous explorations of inexactness in climate modelling, the proposed and tested information metric has three specific advantages: (i) it requires only a single high-precision time series; (ii) information does not grow indefinitely for decreasing time step; and (iii) information is more sensitive to the dynamics and uncertainties of the model rather than to the implementation details. We demonstrate the notion of bit-level information efficiency in two of Edward Lorenz’s prototypical chaotic models: Lorenz 1963 (L63) and Lorenz 1996 (L96). Although L63 is typically integrated in 64-bit ‘double’ floating point precision, we show that only 16 bits have significant information content, given an initial condition uncertainty of approximately 1% of the size of the attractor. This result is sensitive to the size of the uncertainty but not to the time step of the model. We then apply the metric to the L96 model and find that a 16-bit scaled integer model would suffice given the uncertainty of the unresolved sub-grid-scale dynamics. We then show that, by dedicating computational resources to spatial resolution rather than numeric precision in a field programmable gate array (FPGA), we see up to 28.6% improvement in forecast accuracy, an approximately fivefold reduction in the number of logical computing elements required and an approximately 10-fold reduction in energy consumed by the FPGA, for the L96 model. PMID:28989303

Bitwise efficiency in chaotic models

NASA Astrophysics Data System (ADS)

Jeffress, Stephen; Düben, Peter; Palmer, Tim

2017-09-01

Motivated by the increasing energy consumption of supercomputing for weather and climate simulations, we introduce a framework for investigating the bit-level information efficiency of chaotic models. In comparison with previous explorations of inexactness in climate modelling, the proposed and tested information metric has three specific advantages: (i) it requires only a single high-precision time series; (ii) information does not grow indefinitely for decreasing time step; and (iii) information is more sensitive to the dynamics and uncertainties of the model rather than to the implementation details. We demonstrate the notion of bit-level information efficiency in two of Edward Lorenz's prototypical chaotic models: Lorenz 1963 (L63) and Lorenz 1996 (L96). Although L63 is typically integrated in 64-bit `double' floating point precision, we show that only 16 bits have significant information content, given an initial condition uncertainty of approximately 1% of the size of the attractor. This result is sensitive to the size of the uncertainty but not to the time step of the model. We then apply the metric to the L96 model and find that a 16-bit scaled integer model would suffice given the uncertainty of the unresolved sub-grid-scale dynamics. We then show that, by dedicating computational resources to spatial resolution rather than numeric precision in a field programmable gate array (FPGA), we see up to 28.6% improvement in forecast accuracy, an approximately fivefold reduction in the number of logical computing elements required and an approximately 10-fold reduction in energy consumed by the FPGA, for the L96 model.

Dynamic contrast-enhanced diffuse optical tomography (DCE-DOT): experimental validation with a dynamic phantom

NASA Astrophysics Data System (ADS)

Burcin Unlu, Mehmet; Lin, Yuting; Gulsen, Gultekin

2009-11-01

Dynamic contrast-enhanced diffuse optical tomography (DCE-DOT) can provide spatially resolved enhancement kinetics of an optical contrast agent. We undertook a systematic phantom study to evaluate the effects of the geometrical parameters such as the depth and size of the inclusion as well as the optical parameters of the background on the recovered enhancement kinetics of the most commonly used optical contrast agent, indocyanine green (ICG). For this purpose a computer-controlled dynamic phantom was constructed. An ICG-intralipid-water mixture was circulated through the inclusions while the DCE-DOT measurements were acquired with a temporal resolution of 16 s. The same dynamic study was repeated using inclusions of different sizes located at different depths. In addition to this, the effect of non-scattering regions was investigated by placing a second inclusion filled with water in the background. The phantom studies confirmed that although the peak enhancement varied substantially for each case, the recovered injection and dilution rates obtained from the percentage enhancement maps agreed within 15% independent of not only the depth and the size of the inclusion but also the presence of a non-scattering region in the background. Although no internal structural information was used in these phantom studies, it may be necessary to use it for small objects buried deep in tissue. However, the different contrast mechanisms of optical and other imaging modalities as well as imperfect co-registration between both modalities may lead to potential errors in the structural a priori. Therefore, the effect of erroneous selection of structural priors was investigated as the final step. Again, the injection and dilution rates obtained from the percentage enhancement maps were also immune to the systematic errors introduced by erroneous selection of the structural priors, e.g. choosing the diameter of the inclusion 20% smaller increased the peak enhancement 60% but changed the injection and dilution rates only less than 10%.

Concepts in gravel beach dynamics

NASA Astrophysics Data System (ADS)

Buscombe, Daniel; Masselink, Gerhard

2006-11-01

The dominant processes in gravel beach dynamics are reviewed, highlighting some common themes which unify the various components of the gravel beach system, the repercussions of which impart on how gravel beach dynamics might be understood conceptually. In particular, gravel beach dynamics are thought to be highly dependent on the temporal and spatial variation in grain size, and the continual adjustments made by an active beach step, both of which act not only as the expression of changing morphodynamic conditions, but also as a controlling influence. Morphodynamics, the notion that the exchanges on beaches between the hydrodynamics, sediment transport, and morphological change takes the form of reciprocal relationships which are mediated through feedback mechanisms (in such a way that they cannot be thought of or studied independently) is not a new one. Yet it appears that for the gravel beach, morphodynamics must be re-defined to describe conditions where variations in sediment size are thought to deserve parity, rather than as merely a sequent entity or boundary condition. 'Morpho-sedimentary-dynamics' is a phrase coined to intuit such cause and effect, detailing the co-evolution of morphology, hydro-hydraulics and sediment properties whilst acknowledging causative pluralism, feedbacks and multiplier effects. This is the recommended conceptual framework within which to crystallise thought and organise further research for the gravel beach. Essentially, it increases the minimum number of parameters needed to describe the state of the gravel beach as a physical system. Therefore, it is advised that simplicity will be most expedient in our future modelling efforts, if complexity is to be adequately encapsulated.

Refined BCF-type boundary conditions for mesoscale surface step dynamics

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

Zhao, Renjie; Ackerman, David M.; Evans, James W.

Deposition on a vicinal surface with alternating rough and smooth steps is described by a solid-on-solid model with anisotropic interactions. Kinetic Monte Carlo (KMC) simulations of the model reveal step pairing in the absence of any additional step attachment barriers. We explore the description of this behavior within an analytic Burton-Cabrera-Frank (BCF)-type step dynamics treatment. Without attachment barriers, conventional kinetic coefficients for the rough and smooth steps are identical, as are the predicted step velocities for a vicinal surface with equal terrace widths. However, we determine refined kinetic coefficients from a two-dimensional discrete deposition-diffusion equation formalism which accounts for stepmore » structure. These coefficients are generally higher for rough steps than for smooth steps, reflecting a higher propensity for capture of diffusing terrace adatoms due to a higher kink density. Such refined coefficients also depend on the local environment of the step and can even become negative (corresponding to net detachment despite an excess adatom density) for a smooth step in close proximity to a rough step. Incorporation of these refined kinetic coefficients into a BCF-type step dynamics treatment recovers quantitatively the mesoscale step-pairing behavior observed in the KMC simulations.« less

Refined BCF-type boundary conditions for mesoscale surface step dynamics

DOE PAGES

Zhao, Renjie; Ackerman, David M.; Evans, James W.

2015-06-24

Deposition on a vicinal surface with alternating rough and smooth steps is described by a solid-on-solid model with anisotropic interactions. Kinetic Monte Carlo (KMC) simulations of the model reveal step pairing in the absence of any additional step attachment barriers. We explore the description of this behavior within an analytic Burton-Cabrera-Frank (BCF)-type step dynamics treatment. Without attachment barriers, conventional kinetic coefficients for the rough and smooth steps are identical, as are the predicted step velocities for a vicinal surface with equal terrace widths. However, we determine refined kinetic coefficients from a two-dimensional discrete deposition-diffusion equation formalism which accounts for stepmore » structure. These coefficients are generally higher for rough steps than for smooth steps, reflecting a higher propensity for capture of diffusing terrace adatoms due to a higher kink density. Such refined coefficients also depend on the local environment of the step and can even become negative (corresponding to net detachment despite an excess adatom density) for a smooth step in close proximity to a rough step. Incorporation of these refined kinetic coefficients into a BCF-type step dynamics treatment recovers quantitatively the mesoscale step-pairing behavior observed in the KMC simulations.« less

Role of step stiffness and kinks in the relaxation of vicinal (001) with zigzag [110] steps

NASA Astrophysics Data System (ADS)

Mahjoub, B.; Hamouda, Ajmi BH.; Einstein, TL.

2017-08-01

We present a kinetic Monte Carlo study of the relaxation dynamics and steady state configurations of 〈110〉 steps on a vicinal (001) simple cubic surface. This system is interesting because 〈110〉 (fully kinked) steps have different elementary excitation energetics and favor step diffusion more than 〈100〉 (nominally straight) steps. In this study we show how this leads to different relaxation dynamics as well as to different steady state configurations, including that 2-bond breaking processes are rate determining for 〈110〉 steps in contrast to 3-bond breaking processes for 〈100〉-steps found in previous work [Surface Sci. 602, 3569 (2008)]. The analysis of the terrace-width distribution (TWD) shows a significant role of kink-generation-annihilation processes during the relaxation of steps: the kinetic of relaxation, toward the steady state, is much faster in the case of 〈110〉-zigzag steps, with a higher standard deviation of the TWD, in agreement with a decrease of step stiffness due to orientation. We conclude that smaller step stiffness leads inexorably to faster step dynamics towards the steady state. The step-edge anisotropy slows the relaxation of steps and increases the strength of step-step effective interactions.

Implicit flux-split Euler schemes for unsteady aerodynamic analysis involving unstructured dynamic meshes

NASA Technical Reports Server (NTRS)

Batina, John T.

1990-01-01

Improved algorithms for the solution of the time-dependent Euler equations are presented for unsteady aerodynamic analysis involving unstructured dynamic meshes. The improvements have been developed recently to the spatial and temporal discretizations used by unstructured grid flow solvers. The spatial discretization involves a flux-split approach which is naturally dissipative and captures shock waves sharply with at most one grid point within the shock structure. The temporal discretization involves an implicit time-integration shceme using a Gauss-Seidel relaxation procedure which is computationally efficient for either steady or unsteady flow problems. For example, very large time steps may be used for rapid convergence to steady state, and the step size for unsteady cases may be selected for temporal accuracy rather than for numerical stability. Steady and unsteady flow results are presented for the NACA 0012 airfoil to demonstrate applications of the new Euler solvers. The unsteady results were obtained for the airfoil pitching harmonically about the quarter chord. The resulting instantaneous pressure distributions and lift and moment coefficients during a cycle of motion compare well with experimental data. The paper presents a description of the Euler solvers along with results and comparisons which assess the capability.

Dynamic load balancing for petascale quantum Monte Carlo applications: The Alias method

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

Sudheer, C. D.; Krishnan, S.; Srinivasan, A.

Diffusion Monte Carlo is the most accurate widely used Quantum Monte Carlo method for the electronic structure of materials, but it requires frequent load balancing or population redistribution steps to maintain efficiency and avoid accumulation of systematic errors on parallel machines. The load balancing step can be a significant factor affecting performance, and will become more important as the number of processing elements increases. We propose a new dynamic load balancing algorithm, the Alias Method, and evaluate it theoretically and empirically. An important feature of the new algorithm is that the load can be perfectly balanced with each process receivingmore » at most one message. It is also optimal in the maximum size of messages received by any process. We also optimize its implementation to reduce network contention, a process facilitated by the low messaging requirement of the algorithm. Empirical results on the petaflop Cray XT Jaguar supercomputer at ORNL showing up to 30% improvement in performance on 120,000 cores. The load balancing algorithm may be straightforwardly implemented in existing codes. The algorithm may also be employed by any method with many near identical computational tasks that requires load balancing.« less

Implicit flux-split Euler schemes for unsteady aerodynamic analysis involving unstructured dynamic meshes

NASA Technical Reports Server (NTRS)

Batina, John T.

1990-01-01

Improved algorithm for the solution of the time-dependent Euler equations are presented for unsteady aerodynamic analysis involving unstructured dynamic meshes. The improvements were developed recently to the spatial and temporal discretizations used by unstructured grid flow solvers. The spatial discretization involves a flux-split approach which is naturally dissipative and captures shock waves sharply with at most one grid point within the shock structure. The temporal discretization involves an implicit time-integration scheme using a Gauss-Seidel relaxation procedure which is computationally efficient for either steady or unsteady flow problems. For example, very large time steps may be used for rapid convergence to steady state, and the step size for unsteady cases may be selected for temporal accuracy rather than for numerical stability. Steady and unsteady flow results are presented for the NACA 0012 airfoil to demonstrate applications of the new Euler solvers. The unsteady results were obtained for the airfoil pitching harmonically about the quarter chord. The resulting instantaneous pressure distributions and lift and moment coefficients during a cycle of motion compare well with experimental data. A description of the Euler solvers is presented along with results and comparisons which assess the capability.

Physical modeling of Tibetan bowls

NASA Astrophysics Data System (ADS)

Antunes, Jose; Inacio, Octavio

2004-05-01

Tibetan bowls produce rich penetrating sounds, used in musical contexts and to induce a state of relaxation for meditation or therapy purposes. To understand the dynamics of these instruments under impact and rubbing excitation, we developed a simulation method based on the modal approach, following our previous papers on physical modeling of plucked/bowed strings and impacted/bowed bars. This technique is based on a compact representation of the system dynamics, in terms of the unconstrained bowl modes. Nonlinear contact/friction interaction forces, between the exciter (puja) and the bowl, are computed at each time step and projected on the bowl modal basis, followed by step integration of the modal equations. We explore the behavior of two different-sized bowls, for extensive ranges of excitation conditions (contact/friction parameters, normal force, and tangential puja velocity). Numerical results and experiments show that various self-excited motions may arise depending on the playing conditions and, mainly, on the contact/friction interaction parameters. Indeed, triggering of a given bowl modal frequency mainly depends on the puja material. Computed animations and experiments demonstrate that self-excited modes spin, following the puja motion. Accordingly, the sensed pressure field pulsates, with frequency controlled by the puja spinning velocity and the spatial pattern of the singing mode.

Modeling of Abrasion and Crushing of Unbound Granular Materials During Compaction

NASA Astrophysics Data System (ADS)

Ocampo, Manuel S.; Caicedo, Bernardo

2009-06-01

Unbound compacted granular materials are commonly used in engineering structures as layers in road pavements, railroad beds, highway embankments, and foundations. These structures are generally subjected to dynamic loading by construction operations, traffic and wheel loads. These repeated or cyclic loads cause abrasion and crushing of the granular materials. Abrasion changes a particle's shape, and crushing divides the particle into a mixture of many small particles of varying sizes. Particle breakage is important because the mechanical and hydraulic properties of these materials depend upon their grain size distribution. Therefore, it is important to evaluate the evolution of the grain size distribution of these materials. In this paper an analytical model for unbound granular materials is proposed in order to evaluate particle crushing of gravels and soils subjected to cyclic loads. The model is based on a Markov chain which describes the development of grading changes in the material as a function of stress levels. In the model proposed, each particle size is a state in the system, and the evolution of the material is the movement of particles from one state to another in n steps. Each step is a load cycle, and movement between states is possible with a transition probability. The crushing of particles depends on the mechanical properties of each grain and the packing density of the granular material. The transition probability was calculated using both the survival probability defined by Weibull and the compressible packing model developed by De Larrard. Material mechanical properties are considered using the Weibull probability theory. The size and shape of the grains, as well as the method of processing the packing density are considered using De Larrard's model. Results of the proposed analytical model show a good agreement with the experimental tests carried out using the gyratory compaction test.

Modeling behavior dynamics using computational psychometrics within virtual worlds.

PubMed

Cipresso, Pietro

2015-01-01

In case of fire in a building, how will people behave in the crowd? The behavior of each individual affects the behavior of others and, conversely, each one behaves considering the crowd as a whole and the individual others. In this article, I propose a three-step method to explore a brand new way to study behavior dynamics. The first step relies on the creation of specific situations with standard techniques (such as mental imagery, text, video, and audio) and an advanced technique [Virtual Reality (VR)] to manipulate experimental settings. The second step concerns the measurement of behavior in one, two, or many individuals focusing on parameters extractions to provide information about the behavior dynamics. Finally, the third step, which uses the parameters collected and measured in the previous two steps in order to simulate possible scenarios to forecast through computational models, understand, and explain behavior dynamics at the social level. An experimental study was also included to demonstrate the three-step method and a possible scenario.

Fishing-induced changes in adult length are mediated by skipped-spawning.

PubMed

Wang, Hui-Yu; Chen, Ying-Shiuan; Hsu, Chien-Chung; Shen, Sheng-Feng

2017-01-01

Elucidating fishing effects on fish population dynamics is a critical step toward sustainable fisheries management. Despite previous studies that have suggested age or size truncation in exploited fish populations, other aspects of fishing effects on population demography, e.g., via altering life histories and density, have received less attention. Here, we investigated the fishing effects altering adult demography via shifting reproductive trade-offs in the iconic, overexploited, Pacific bluefin tuna Thunnus orientalis. We found that, contrary to our expectation, mean lengths of catch increased over time in longline fisheries. On the other hand, mean catch lengths for purse seine fisheries did not show such increasing trends. We hypothesized that the size-dependent energetic cost of the spawning migration and elevated fishing mortality on the spawning grounds potentially drive size-dependent skipped spawning for adult tuna, mediating the observed changes in the catch lengths. Using eco-genetic individual-based modeling, we demonstrated that fishing-induced evolution of skipped spawning and size truncation interacted to shape the observed temporal changes in mean catch lengths for tuna. Skipped spawning of the small adults led to increased mean catch lengths for the longline fisheries, while truncation of small adults by the purse seines could offset such a pattern. Our results highlight the eco-evolutionary dynamics of fishing effects on population demography and caution against using demographic traits as a basis for fisheries management of the Pacific bluefin tuna as well as other migratory species. © 2016 by the Ecological Society of America.

Modeling the Dynamics of Soil Structure and Water in Agricultural Soil

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2017-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Future Carbon Dynamics of the Northern Rockies Ecoregion due to Climate Impacts and Fire Effects

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2016-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Methodological aspects of an adaptive multidirectional pattern search to optimize speech perception using three hearing-aid algorithms

NASA Astrophysics Data System (ADS)

Franck, Bas A. M.; Dreschler, Wouter A.; Lyzenga, Johannes

2004-12-01

In this study we investigated the reliability and convergence characteristics of an adaptive multidirectional pattern search procedure, relative to a nonadaptive multidirectional pattern search procedure. The procedure was designed to optimize three speech-processing strategies. These comprise noise reduction, spectral enhancement, and spectral lift. The search is based on a paired-comparison paradigm, in which subjects evaluated the listening comfort of speech-in-noise fragments. The procedural and nonprocedural factors that influence the reliability and convergence of the procedure are studied using various test conditions. The test conditions combine different tests, initial settings, background noise types, and step size configurations. Seven normal hearing subjects participated in this study. The results indicate that the reliability of the optimization strategy may benefit from the use of an adaptive step size. Decreasing the step size increases accuracy, while increasing the step size can be beneficial to create clear perceptual differences in the comparisons. The reliability also depends on starting point, stop criterion, step size constraints, background noise, algorithms used, as well as the presence of drifting cues and suboptimal settings. There appears to be a trade-off between reliability and convergence, i.e., when the step size is enlarged the reliability improves, but the convergence deteriorates. .

A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size

PubMed Central

Ovchinnikov, V.; Cecchini, M.; Vanden-Eijnden, E.; Karplus, M.

2011-01-01

Myosin VI (MVI) is a dimeric molecular motor that translocates backwards on actin filaments with a surprisingly large and variable step size, given its short lever arm. A recent x-ray structure of MVI indicates that the large step size can be explained in part by a novel conformation of the converter subdomain in the prepowerstroke state, in which a 53-residue insert, unique to MVI, reorients the lever arm nearly parallel to the actin filament. To determine whether the existence of the novel converter conformation could contribute to the step-size variability, we used a path-based free-energy simulation tool, the string method, to show that there is a small free-energy difference between the novel converter conformation and the conventional conformation found in other myosins. This result suggests that MVI can bind to actin with the converter in either conformation. Models of MVI/MV chimeric dimers show that the variability in the tilting angle of the lever arm that results from the two converter conformations can lead to step-size variations of ∼12 nm. These variations, in combination with other proposed mechanisms, could explain the experimentally determined step-size variability of ∼25 nm for wild-type MVI. Mutations to test the findings by experiment are suggested. PMID:22098742

Microgravity Foam Structure and Rheology

NASA Technical Reports Server (NTRS)

Durian, Douglas J.

1997-01-01

To exploit rheological and multiple-light scattering techniques, and ultimately microgravity conditions, in order to quantify and elucidate the unusual elastic character of foams in terms of their underlying microscopic structure and dynamics. Special interest is in determining how this elastic character vanishes, i.e. how the foam melts into a simple viscous liquid, as a function of both increasing liquid content and shear strain rate. The unusual elastic character of foams will be quantified macroscopically by measurement of the shear stress as a function of static shear strain, shear strain rate, and time following a step strain; such data will be analyzed in terms of a yield stress, a static shear modulus, and dynamical time scales. Microscopic information about bubble packing and rearrangement dynamics, from which these macroscopic non-Newtonian properties presumably arise, will be obtained non-invasively by novel multiple-light scattering diagnostics such as Diffusing-Wave Spectroscopy (DWS). Quantitative trends with materials parameters, such as average bubble size, and liquid content, will be sought in order to elucidate the fundamental connection between the microscopic structure and dynamics and the macroscopic rheology.

Effects of homogenization treatment on recrystallization behavior of 7150 aluminum sheet during post-rolling annealing

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

Guo, Zhanying; Department of Applied Science, University of Québec at Chicoutimi, Saguenay, QC G7H 2B1; Zhao, Gang

2016-04-15

The effects of two homogenization treatments applied to the direct chill (DC) cast billet on the recrystallization behavior in 7150 aluminum alloy during post-rolling annealing have been investigated using the electron backscatter diffraction (EBSD) technique. Following hot and cold rolling to the sheet, measured orientation maps, the recrystallization fraction and grain size, the misorientation angle and the subgrain size were used to characterize the recovery and recrystallization processes at different annealing temperatures. The results were compared between the conventional one-step homogenization and the new two-step homogenization, with the first step being pretreated at 250 °C. Al{sub 3}Zr dispersoids with highermore » densities and smaller sizes were obtained after the two-step homogenization, which strongly retarded subgrain/grain boundary mobility and inhibited recrystallization. Compared with the conventional one-step homogenized samples, a significantly lower recrystallized fraction and a smaller recrystallized grain size were obtained under all annealing conditions after cold rolling in the two-step homogenized samples. - Highlights: • Effects of two homogenization treatments on recrystallization in 7150 Al sheets • Quantitative study on the recrystallization evolution during post-rolling annealing • Al{sub 3}Zr dispersoids with higher densities and smaller sizes after two-step treatment • Higher recrystallization resistance of 7150 sheets with two-step homogenization.« less

Size distribution of extracellular vesicles by optical correlation techniques.

PubMed

Montis, Costanza; Zendrini, Andrea; Valle, Francesco; Busatto, Sara; Paolini, Lucia; Radeghieri, Annalisa; Salvatore, Annalisa; Berti, Debora; Bergese, Paolo

2017-10-01

Understanding the colloidal properties of extracellular vesicles (EVs) is key to advance fundamental knowledge in this field and to develop effective EV-based diagnostics, therapeutics and devices. Determination of size distribution and of colloidal stability of purified EVs resuspended in buffered media is a complex and challenging issue - because of the wide range of EV diameters (from 30 to 2000nm), concentrations of interest and membrane properties, and the possible presence of co-isolated contaminants with similar size and densities, such as protein aggregates and fat globules - which is still waiting to be fully addressed. We report here a fully detailed protocol for accurate and robust determination of the size distribution and stability of EV samples which leverages a dedicated combination of Fluorescence Correlation Spectroscopy (FCS) and Dynamic Light Scattering (DLS). The theoretical background, critical experimental steps and data analysis procedures are thoroughly presented and finally illustrated through the representative case study of EV formulations obtained from culture media of B16 melanoma cells, a murine tumor cell line used as a model for human skin cancers. Copyright © 2017 Elsevier B.V. All rights reserved.

Anticipatory Postural Adjustment During Self-Initiated, Cued, and Compensatory Stepping in Healthy Older Adults and Patients With Parkinson Disease.

PubMed

Schlenstedt, Christian; Mancini, Martina; Horak, Fay; Peterson, Daniel

2017-07-01

To characterize anticipatory postural adjustments (APAs) across a variety of step initiation tasks in people with Parkinson disease (PD) and healthy subjects. Cross-sectional study. Step initiation was analyzed during self-initiated gait, perceptual cued gait, and compensatory forward stepping after platform perturbation. People with PD were assessed on and off levodopa. University research laboratory. People (N=31) with PD (n=19) and healthy aged-matched subjects (n=12). Not applicable. Mediolateral (ML) size of APAs (calculated from center of pressure recordings), step kinematics, and body alignment. With respect to self-initiated gait, the ML size of APAs was significantly larger during the cued condition and significantly smaller during the compensatory condition (P<.001). Healthy subjects and patients with PD did not differ in body alignment during the stance phase prior to stepping. No significant group effect was found for ML size of APAs between healthy subjects and patients with PD. However, the reduction in APA size from cued to compensatory stepping was significantly less pronounced in PD off medication compared with healthy subjects, as indicated by a significant group by condition interaction effect (P<.01). No significant differences were found comparing patients with PD on and off medications. Specific stepping conditions had a significant effect on the preparation and execution of step initiation. Therefore, APA size should be interpreted with respect to the specific stepping condition. Across-task changes in people with PD were less pronounced compared with healthy subjects. Antiparkinsonian medication did not significantly improve step initiation in this mildly affected PD cohort. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Protein analysis by time-resolved measurements with an electro-switchable DNA chip

PubMed Central

Langer, Andreas; Hampel, Paul A.; Kaiser, Wolfgang; Knezevic, Jelena; Welte, Thomas; Villa, Valentina; Maruyama, Makiko; Svejda, Matej; Jähner, Simone; Fischer, Frank; Strasser, Ralf; Rant, Ulrich

2013-01-01

Measurements in stationary or mobile phases are fundamental principles in protein analysis. Although the immobilization of molecules on solid supports allows for the parallel analysis of interactions, properties like size or shape are usually inferred from the molecular mobility under the influence of external forces. However, as these principles are mutually exclusive, a comprehensive characterization of proteins usually involves a multi-step workflow. Here we show how these measurement modalities can be reconciled by tethering proteins to a surface via dynamically actuated nanolevers. Short DNA strands, which are switched by alternating electric fields, are employed as capture probes to bind target proteins. By swaying the proteins over nanometre amplitudes and comparing their motional dynamics to a theoretical model, the protein diameter can be quantified with Angström accuracy. Alterations in the tertiary protein structure (folding) and conformational changes are readily detected, and even post-translational modifications are revealed by time-resolved molecular dynamics measurements. PMID:23839273

Dynamical traps in Wang-Landau sampling of continuous systems: Mechanism and solution

NASA Astrophysics Data System (ADS)

Koh, Yang Wei; Sim, Adelene Y. L.; Lee, Hwee Kuan

2015-08-01

We study the mechanism behind dynamical trappings experienced during Wang-Landau sampling of continuous systems reported by several authors. Trapping is caused by the random walker coming close to a local energy extremum, although the mechanism is different from that of the critical slowing-down encountered in conventional molecular dynamics or Monte Carlo simulations. When trapped, the random walker misses the entire or even several stages of Wang-Landau modification factor reduction, leading to inadequate sampling of the configuration space and a rough density of states, even though the modification factor has been reduced to very small values. Trapping is dependent on specific systems, the choice of energy bins, and the Monte Carlo step size, making it highly unpredictable. A general, simple, and effective solution is proposed where the configurations of multiple parallel Wang-Landau trajectories are interswapped to prevent trapping. We also explain why swapping frees the random walker from such traps. The efficacy of the proposed algorithm is demonstrated.

Two-color single-photon emission from InAs quantum dots: toward logic information management using quantum light.

PubMed

Rivas, David; Muñoz-Matutano, Guillermo; Canet-Ferrer, Josep; García-Calzada, Raúl; Trevisi, Giovanna; Seravalli, Luca; Frigeri, Paola; Martínez-Pastor, Juan P

2014-02-12

In this work, we propose the use of the Hanbury-Brown and Twiss interferometric technique and a switchable two-color excitation method for evaluating the exciton and noncorrelated electron-hole dynamics associated with single photon emission from indium arsenide (InAs) self-assembled quantum dots (QDs). Using a microstate master equation model we demonstrate that our single QDs are described by nonlinear exciton dynamics. The simultaneous detection of two-color, single photon emission from InAs QDs using these nonlinear dynamics was used to design a NOT AND logic transference function. This computational functionality combines the advantages of working with light/photons as input/output device parameters (all-optical system) and that of a nanodevice (QD size of ∼ 20 nm) while also providing high optical sensitivity (ultralow optical power operational requirements). These system features represent an important and interesting step toward the development of new prototypes for the incoming quantum information technologies.

Competing Classical and Quantum Effects in Shape Relaxation of a Metallic Island

NASA Technical Reports Server (NTRS)

Okamoto, Rowland H.; Chen, D.; Yamada, T.

2002-01-01

Pb islands grown on a silicon substrate transform at room temperature from the initially flattop facet geometry into an unusual ring, shape with a volume-preserving mass transport process catalysed by the tip electrical field of a scanning tunnelling microscope. The formation of such ring shape morphology results from the competing classical and quantum effects in the shape relaxation. The latter also leads to a sequential regrowth on alternating, strips of the same facet defined by the underlying substrate steps, showing for the first time the dynamical impact of the quantum size effect on the stability of a nanostructure.

Event-driven Monte Carlo: Exact dynamics at all time scales for discrete-variable models

NASA Astrophysics Data System (ADS)

Mendoza-Coto, Alejandro; Díaz-Méndez, Rogelio; Pupillo, Guido

2016-06-01

We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found, with no need to define any other phase-space construction. However, unlike existing methods, the present algorithm does not assume any particular statistical distribution to perform moves or to advance the time, and thus is a unique tool for the numerical exploration of fast and ultra-fast dynamical regimes. By decomposing the problem in a set of two-level subsystems, we find a natural variable step size, that is well defined from the normalization condition of the transition probabilities between the levels. We successfully test the algorithm with known exact solutions for non-equilibrium dynamics and equilibrium thermodynamical properties of Ising-spin models in one and two dimensions, and compare to standard implementations of kinetic Monte Carlo methods. The present algorithm is directly applicable to the study of the real-time dynamics of a large class of classical Markovian chains, and particularly to short-time situations where the exact evolution is relevant.

Imaging dynamic fingerprints of competing E2 and SN2 reactions.

PubMed

Carrascosa, Eduardo; Meyer, Jennifer; Zhang, Jiaxu; Stei, Martin; Michaelsen, Tim; Hase, William L; Yang, Li; Wester, Roland

2017-06-21

The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X -  + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity. This characteristic fingerprint is also confirmed by direct dynamics simulations for ethyl as residue and attributed to the dynamics of elimination reactions. This work opens the door to a detailed atomistic understanding of transformation reactions in even larger systems.The competition between chemical reactions critically affects our natural environment and the synthesis of new materials. Here, the authors present an approach to directly image distinct fingerprints of essential organic reactions and monitor their competition as a function of steric substitution.

Combining gas-phase electrophoretic mobility molecular analysis (GEMMA), light scattering, field flow fractionation and cryo electron microscopy in a multidimensional approach to characterize liposomal carrier vesicles

PubMed Central

Gondikas, Andreas; von der Kammer, Frank; Hofmann, Thilo; Marchetti-Deschmann, Martina; Allmaier, Günter; Marko-Varga, György; Andersson, Roland

2017-01-01

For drug delivery, characterization of liposomes regarding size, particle number concentrations, occurrence of low-sized liposome artefacts and drug encapsulation are of importance to understand their pharmacodynamic properties. In our study, we aimed to demonstrate the applicability of nano Electrospray Gas-Phase Electrophoretic Mobility Molecular Analyser (nES GEMMA) as a suitable technique for analyzing these parameters. We measured number-based particle concentrations, identified differences in size between nominally identical liposomal samples, and detected the presence of low-diameter material which yielded bimodal particle size distributions. Subsequently, we compared these findings to dynamic light scattering (DLS) data and results from light scattering experiments coupled to Asymmetric Flow-Field Flow Fractionation (AF4), the latter improving the detectability of smaller particles in polydisperse samples due to a size separation step prior detection. However, the bimodal size distribution could not be detected due to method inherent limitations. In contrast, cryo transmission electron microscopy corroborated nES GEMMA results. Hence, gas-phase electrophoresis proved to be a versatile tool for liposome characterization as it could analyze both vesicle size and size distribution. Finally, a correlation of nES GEMMA results with cell viability experiments was carried out to demonstrate the importance of liposome batch-to-batch control as low-sized sample components possibly impact cell viability. PMID:27639623

In situ UV curable 3D printing of multi-material tri-legged soft bot with spider mimicked multi-step forward dynamic gait

NASA Astrophysics Data System (ADS)

Zeb Gul, Jahan; Yang, Bong-Su; Yang, Young Jin; Chang, Dong Eui; Choi, Kyung Hyun

2016-11-01

Soft bots have the expedient ability of adopting intricate postures and fitting in complex shapes compared to mechanical robots. This paper presents a unique in situ UV curing three-dimensional (3D) printed multi-material tri-legged soft bot with spider mimicked multi-step dynamic forward gait using commercial bio metal filament (BMF) as an actuator. The printed soft bot can produce controllable forward motion in response to external signals. The fundamental properties of BMF, including output force, contractions at different frequencies, initial loading rate, and displacement-rate are verified. The tri-pedal soft bot CAD model is designed inspired by spider’s legged structure and its locomotion is assessed by simulating strain and displacement using finite element analysis. A customized rotational multi-head 3D printing system assisted with multiple wavelength’s curing lasers is used for in situ fabrication of tri-pedal soft-bot using two flexible materials (epoxy and polyurethane) in three layered steps. The size of tri-pedal soft-bot is 80 mm in diameter and each pedal’s width and depth is 5 mm × 5 mm respectively. The maximum forward speed achieved is 2.7 mm s-1 @ 5 Hz with input voltage of 3 V and 250 mA on a smooth surface. The fabricated tri-pedal soft bot proved its power efficiency and controllable locomotion at three input signal frequencies (1, 2, 5 Hz).

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

DOE PAGES

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; ...

2017-06-09

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of “KMC stiffness” (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps / cpu-time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order tomore » achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events -- allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm designed for use in achieving and simulating steady-state conditions in KMC simulations. Lastly, as shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.« less

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; Savara, Aditya

2017-10-01

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of "KMC stiffness" (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps/CPU time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order to achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events-allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm is designed for use in achieving and simulating steady-state conditions in KMC simulations. As shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.

Interplay between structure, stoichiometry, and electron transfer dynamics in SILAR-based quantum dot-sensitized oxides.

PubMed

Wang, Hai; Barceló, Irene; Lana-Villarreal, Teresa; Gómez, Roberto; Bonn, Mischa; Cánovas, Enrique

2014-10-08

We quantify the rate and efficiency of picosecond electron transfer (ET) from PbS nanocrystals, grown by successive ionic layer adsorption and reaction (SILAR), into a mesoporous SnO2 support. Successive SILAR deposition steps allow for stoichiometry- and size-variation of the QDs, characterized using transmission electron microscopy. Whereas for sulfur-rich (p-type) QD surfaces substantial electron trapping at the QD surface occurs, for lead-rich (n-type) QD surfaces, the QD trapping channel is suppressed and the ET efficiency is boosted. The ET efficiency increase achieved by lead-rich QD surfaces is found to be QD-size dependent, increasing linearly with QD surface area. On the other hand, ET rates are found to be independent of both QD size and surface stoichiometry, suggesting that the donor-acceptor energetics (constituting the driving force for ET) are fixed due to Fermi level pinning at the QD/oxide interface. Implications of our results for QD-sensitized solar cell design are discussed.

Influence of system size and solvent flow on the distribution of wormlike micelles in a contraction-expansion geometry

NASA Astrophysics Data System (ADS)

Stukan, M. R.; Boek, E. S.; Padding, J. T.; Crawshaw, J. P.

2008-05-01

Viscoelastic wormlike micelles are formed by surfactants assembling into elongated cylindrical structures. These structures respond to flow by aligning, breaking and reforming. Their response to the complex flow fields encountered in porous media is particularly rich. Here we use a realistic mesoscopic Brownian Dynamics model to investigate the flow of a viscoelastic surfactant (VES) fluid through individual pores idealized as a step expansion-contraction of size around one micron. In a previous study, we assumed the flow field to be Newtonian. Here we extend the work to include the non-Newtonian flow field previously obtained by experiment. The size of the simulations is also increased so that the pore is much larger than the radius of gyration of the micelles. For the non-Newtonian flow field at the higher flow rates in relatively large pores, the density of the micelles becomes markedly non-uniform. In this case, we find that the density in the large, slowly moving entry corner regions is substantially increased.

Size Control of Porous Silicon-Based Nanoparticles via Pore-Wall Thinning.

PubMed

Secret, Emilie; Leonard, Camille; Kelly, Stefan J; Uhl, Amanda; Cozzan, Clayton; Andrew, Jennifer S

2016-02-02

Photoluminescent silicon nanocrystals are very attractive for biomedical and electronic applications. Here a new process is presented to synthesize photoluminescent silicon nanocrystals with diameters smaller than 6 nm from a porous silicon template. These nanoparticles are formed using a pore-wall thinning approach, where the as-etched porous silicon layer is partially oxidized to silica, which is dissolved by a hydrofluoric acid solution, decreasing the pore-wall thickness. This decrease in pore-wall thickness leads to a corresponding decrease in the size of the nanocrystals that make up the pore walls, resulting in the formation of smaller nanoparticles during sonication of the porous silicon. Particle diameters were measured using dynamic light scattering, and these values were compared with the nanocrystallite size within the pore wall as determined from X-ray diffraction. Additionally, an increase in the quantum confinement effect is observed for these particles through an increase in the photoluminescence intensity of the nanoparticles compared with the as-etched nanoparticles, without the need for a further activation step by oxidation after synthesis.

Statistical processing of large image sequences.

PubMed

Khellah, F; Fieguth, P; Murray, M J; Allen, M

2005-01-01

The dynamic estimation of large-scale stochastic image sequences, as frequently encountered in remote sensing, is important in a variety of scientific applications. However, the size of such images makes conventional dynamic estimation methods, for example, the Kalman and related filters, impractical. In this paper, we present an approach that emulates the Kalman filter, but with considerably reduced computational and storage requirements. Our approach is illustrated in the context of a 512 x 512 image sequence of ocean surface temperature. The static estimation step, the primary contribution here, uses a mixture of stationary models to accurately mimic the effect of a nonstationary prior, simplifying both computational complexity and modeling. Our approach provides an efficient, stable, positive-definite model which is consistent with the given correlation structure. Thus, the methods of this paper may find application in modeling and single-frame estimation.

High-Order Implicit-Explicit Multi-Block Time-stepping Method for Hyperbolic PDEs

NASA Technical Reports Server (NTRS)

Nielsen, Tanner B.; Carpenter, Mark H.; Fisher, Travis C.; Frankel, Steven H.

2014-01-01

This work seeks to explore and improve the current time-stepping schemes used in computational fluid dynamics (CFD) in order to reduce overall computational time. A high-order scheme has been developed using a combination of implicit and explicit (IMEX) time-stepping Runge-Kutta (RK) schemes which increases numerical stability with respect to the time step size, resulting in decreased computational time. The IMEX scheme alone does not yield the desired increase in numerical stability, but when used in conjunction with an overlapping partitioned (multi-block) domain significant increase in stability is observed. To show this, the Overlapping-Partition IMEX (OP IMEX) scheme is applied to both one-dimensional (1D) and two-dimensional (2D) problems, the nonlinear viscous Burger's equation and 2D advection equation, respectively. The method uses two different summation by parts (SBP) derivative approximations, second-order and fourth-order accurate. The Dirichlet boundary conditions are imposed using the Simultaneous Approximation Term (SAT) penalty method. The 6-stage additive Runge-Kutta IMEX time integration schemes are fourth-order accurate in time. An increase in numerical stability 65 times greater than the fully explicit scheme is demonstrated to be achievable with the OP IMEX method applied to 1D Burger's equation. Results from the 2D, purely convective, advection equation show stability increases on the order of 10 times the explicit scheme using the OP IMEX method. Also, the domain partitioning method in this work shows potential for breaking the computational domain into manageable sizes such that implicit solutions for full three-dimensional CFD simulations can be computed using direct solving methods rather than the standard iterative methods currently used.

Assembly, growth, and catalytic activity of gold nanoparticles in hollow carbon nanofibers.

PubMed

La Torre, Alessandro; Giménez-López, Maria del Carmen; Fay, Michael W; Rance, Graham A; Solomonsz, William A; Chamberlain, Thomas W; Brown, Paul D; Khlobystov, Andrei N

2012-03-27

Graphitized carbon nanofibers (GNFs) act as efficient templates for the growth of gold nanoparticles (AuNPs) adsorbed on the interior (and exterior) of the tubular nanostructures. Encapsulated AuNPs are stabilized by interactions with the step-edges of the individual graphitic nanocones, of which GNFs are composed, and their size is limited to approximately 6 nm, while AuNPs adsorbed on the atomically flat graphitic surfaces of the GNF exterior continue their growth to 13 nm and beyond under the same heat treatment conditions. The corrugated structure of the GNF interior imposes a significant barrier for the migration of AuNPs, so that their growth mechanism is restricted to Ostwald ripening. Conversely, nanoparticles adsorbed on smooth GNF exterior surfaces are more likely to migrate and coalesce into larger nanoparticles, as revealed by in situ transmission electron microscopy imaging. The presence of alkyl thiol surfactant within the GNF channels changes the dynamics of the AuNP transformations, as surfactant molecules adsorbed on the surface of the AuNPs diminished the stabilization effect of the step-edges, thus allowing nanoparticles to grow until their diameters reach the internal diameter of the host nanofiber. Nanoparticles thermally evolved within the GNF channel exhibit alignment, perpendicular to the GNF axis due to interactions with the step-edges and parallel to the axis because of graphitic facets of the nanocones. Despite their small size, AuNPs in GNF possess high stability and remain unchanged at temperatures up to 300 °C in ambient atmosphere. Nanoparticles immobilized at the step-edges within GNF are shown to act as effective catalysts promoting the transformation of dimethylphenylsilane to bis(dimethylphenyl)disiloxane with a greater than 10-fold enhancement of selectivity as compared to free-standing or surface-adsorbed nanoparticles. © 2012 American Chemical Society

Design of a side coupled standing wave accelerating tube for NSTRI e-Linac

NASA Astrophysics Data System (ADS)

Zarei, S.; Abbasi Davani, F.; Lamehi Rachti, M.; Ghasemi, F.

2017-09-01

The design and construction of a 6 MeV electron linear accelerator (e-Linac) was defined in the Institute of Nuclear Science and Technology (NSTRI) for cargo inspection and medical applications. For this accelerator, a side coupled standing wave tube resonant at a frequency of 2998.5 MHZ in π/2 mode was selected. In this article, the authors provide a step-by-step explanation of the process of the design for this tube. The design and simulation of the accelerating and coupling cavities were carried out in five steps; (1) separate design of the accelerating and coupling cavities, (2) design of the coupling aperture between the cavities, (3) design of the entire structure for resonance at the nominal frequency, (4) design of the buncher, and (5) design of the power coupling port. At all design stages, in addition to finding the dimensions of the cavity, the impact of construction tolerances and simulation errors on the electromagnetic parameters were investigated. The values obtained for the coupling coefficient, coupling constant, quality factor and capture efficiency are 2.11, 0.011, 16203 and 36%, respectively. The results of beam dynamics study of the simulated tube in ASTRA have yielded a value of 5.14 π-mm-mrad for the horizontal emittance, 5.06 π-mm-mrad for the vertical emittance, 1.17 mm for the horizontal beam size, 1.16 mm for the vertical beam size and 1090 keV for the energy spread of the output beam.

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales

NASA Astrophysics Data System (ADS)

Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

2005-10-01

Time series models, which are constructed from the projections of the molecular-dynamics (MD) runs on principal components (modes), are used to mimic the dynamics of two proteins: tendamistat and immunity protein of colicin E7 (ImmE7). Four independent MD runs of tendamistat and three independent runs of ImmE7 protein in vacuum are used to investigate the energy landscapes of these proteins. It is found that mean-square displacements of residues along the modes in different time scales can be mimicked by time series models, which are utilized in dividing protein dynamics into different regimes with respect to the dominating motion type. The first two regimes constitute the dominance of intraminimum motions during the first 5ps and the random walk motion in a hierarchically higher-level energy minimum, which comprise the initial time period of the trajectories up to 20-40ps for tendamistat and 80-120ps for ImmE7. These are also the time ranges within which the linear nonstationary time series are completely satisfactory in explaining protein dynamics. Encountering energy barriers enclosing higher-level energy minima constrains the random walk motion of the proteins, and pseudorelaxation processes at different levels of minima are detected in tendamistat, depending on the sampling window size. Correlation (relaxation) times of 30-40ps and 150-200ps are detected for two energy envelopes of successive levels for tendamistat, which gives an overall idea about the hierarchical structure of the energy landscape. However, it should be stressed that correlation times of the modes are highly variable with respect to conformational subspaces and sampling window sizes, indicating the absence of an actual relaxation. The random-walk step sizes and the time length of the second regime are used to illuminate an important difference between the dynamics of the two proteins, which cannot be clarified by the investigation of relaxation times alone: ImmE7 has lower-energy barriers enclosing the higher-level energy minimum, preventing the protein to relax and letting it move in a random-walk fashion for a longer period of time.

Supramolecular "Step Polymerization" of Preassembled Micelles: A Study of "Polymerization" Kinetics.

PubMed

Yang, Chaoying; Ma, Xiaodong; Lin, Jiaping; Wang, Liquan; Lu, Yingqing; Zhang, Liangshun; Cai, Chunhua; Gao, Liang

2018-03-01

In nature, sophisticated functional materials are created through hierarchical self-assembly of nanoscale motifs, which has inspired the fabrication of man-made materials with complex architectures for a variety of applications. Herein, a kinetic study on the self-assembly of spindle-like micelles preassembled from polypeptide graft copolymers is reported. The addition of dimethylformamide and, subsequently, a selective solvent (water) can generate a "reactive point" at both ends of the spindles as a result of the existence of structural defects, which induces the "polymerization" of the spindles into nanowires. Experimental results combined with dissipative particle dynamics simulations show that the polymerization of the micellar subunits follows a step-growth polymerization mechanism with a second-order reaction characteristic. The assembly rate of the micelles is dependent on the subunit concentration and on the activity of the reactive points. The present work reveals a law governing the self-assembly kinetics of micelles with structural defects and opens the door for the construction of hierarchical structures with a controllable size through supramolecular step polymerization. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stable and pH-responsive core-shell nanoparticles based on HEC and PMAA networks via template copolymerization

NASA Astrophysics Data System (ADS)

Zhang, Y.; Jin, Q.; Chen, Y.; Zhao, J.

2011-10-01

Taking advantage of the specific hydrogen bonding interactions, stable and pH-responsive core-shell nanoparticles based on hydroxyethyl cellulose (HEC) and polymethacrylic acid (PMAA) networks, with a < D h > size ranging from 190 to 250 nm, can be efficiently prepared via facile one-step co-polymerization of methacrylic acid (MAA) and N, N'-methylenebisacrylamide (MBA) on HEC template in water. Using dynamic light scattering, electrophoretic light scattering, fluorescence spectrometry, thermo-gravimetric analysis, TEM, and AFM observations, the influence of crosslinker MBA as well as the reaction parameters were studied. The results show that after the introduction of crosslinker MBA, the nanoparticles became less compact; their size exhibited a smaller pH sensitivity, and their stability against pH value was improved greatly. Furthermore, the size, structure, and pH response of the nanoparticles can be adjusted via varying the reaction parameters: nanoparticles of smaller size, more compact structure, and higher swelling capacity were produced as pH value of the reaction medium increased or the HEC/MAA ratio decreased; while nanoparticles of smaller size, less compact structure and smaller swelling capacity were produced as the total feeding concentration increased.

The melting mechanism in binary Pd0.25Ni0.75 nanoparticles: molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Domekeli, U.; Sengul, S.; Celtek, M.; Canan, C.

2018-02-01

The melting mechanism for Pd0.25Ni0.75 alloy nanoparticles (NPs) was investigated using molecular dynamics (MD) simulations with quantum Sutton-Chen many-body potentials. NPs of six different sizes ranging from 682 to 22,242 atoms were studied to observe the effect of size on the melting point. The melting temperatures of the NPs were estimated by following the changes in both the thermodynamic and structural quantities such as the total energy, heat capacity and Lindemann index. We also used a thermodynamics model to better estimate the melting point and to check the accuracy of MD simulations. We observed that the melting points of the NPs decreased as their sizes decreased. Although the MD simulations for the bulk system yielded higher melting temperatures because of the lack of a seed for the liquid phase, the melting temperatures determined for both the bulk material and the NPs are in good agreement with those predicted from the thermodynamics model. The melting mechanism proceeds in two steps: firstly, a liquid-like shell is formed in the outer regions of the NP with increasing temperature. The thickness of the liquid-like shell increases with increasing temperature until the shell reaches a critical thickness. Then, the entire Pd-Ni NP including core-related solid-like regions melts at once.

Wettability behavior of water droplet on organic-polluted fused quartz surfaces of pillar-type nanostructures applying molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Chen, Jiaxuan; Chen, Wenyang; Xie, Yajing; Wang, Zhiguo; Qin, Jianbo

2017-02-01

Molecular dynamics (MD) is applied to research the wettability behaviors of different scale of water clusters absorbed on organic-polluted fused quartz (FQ) surface and different surface structures. The wettability of water clusters is studied under the effect of organic pollutant. With the combined influence of pillar height and interval, the stair-step Wenzel-Cassie transition critical line is obtained by analyzing stable state of water clusters on different surface structures. The results also show that when interval of pillars and the height of pillars keep constant respectively, the changing rules are exactly the opposite and these are termed as the "waterfall" rules. The substrate models of water clusters at Cassie-Baxter state which are at the vicinity of critical line are chosen to analyze the relationship of HI (refers to the pillar height/interval) ratio and scale of water cluster. The study has found that there is a critical changing threshold in the wettability changing process. When the HI ratio keeps constant, the wettability decreases first and then increase as the size of cluster increases; on the contrary, when the size of cluster keeps constant, the wettability decreases and then increase with the decrease of HI ratio, but when the size of water cluster is close to the threshold the HI ratio has little effect on the wettability.

Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD–DNA complexes

PubMed Central

Carter, Ashley R.; Seaberg, Maasa H.; Fan, Hsiu-Fang; Sun, Gang; Wilds, Christopher J.; Li, Hung-Wen; Perkins, Thomas T.

2016-01-01

RecBCD is a multifunctional enzyme that possesses both helicase and nuclease activities. To gain insight into the mechanism of its helicase function, RecBCD unwinding at low adenosine triphosphate (ATP) (2–4 μM) was measured using an optical-trapping assay featuring 1 base-pair (bp) precision. Instead of uniformly sized steps, we observed forward motion convolved with rapid, large-scale (∼4 bp) variations in DNA length. We interpret this motion as conformational dynamics of the RecBCD–DNA complex in an unwinding-competent state, arising, in part, by an enzyme-induced, back-and-forth motion relative to the dsDNA that opens and closes the duplex. Five observations support this interpretation. First, these dynamics were present in the absence of ATP. Second, the onset of the dynamics was coupled to RecBCD entering into an unwinding-competent state that required a sufficiently long 5′ strand to engage the RecD helicase. Third, the dynamics were modulated by the GC-content of the dsDNA. Fourth, the dynamics were suppressed by an engineered interstrand cross-link in the dsDNA that prevented unwinding. Finally, these dynamics were suppressed by binding of a specific non-hydrolyzable ATP analog. Collectively, these observations show that during unwinding, RecBCD binds to DNA in a dynamic mode that is modulated by the nucleotide state of the ATP-binding pocket. PMID:27220465

Adaptive step-size algorithm for Fourier beam-propagation method with absorbing boundary layer of auto-determined width.

PubMed

Learn, R; Feigenbaum, E

2016-06-01

Two algorithms that enhance the utility of the absorbing boundary layer are presented, mainly in the framework of the Fourier beam-propagation method. One is an automated boundary layer width selector that chooses a near-optimal boundary size based on the initial beam shape. The second algorithm adjusts the propagation step sizes based on the beam shape at the beginning of each step in order to reduce aliasing artifacts.

Adaptive step-size algorithm for Fourier beam-propagation method with absorbing boundary layer of auto-determined width

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

Learn, R.; Feigenbaum, E.

Two algorithms that enhance the utility of the absorbing boundary layer are presented, mainly in the framework of the Fourier beam-propagation method. One is an automated boundary layer width selector that chooses a near-optimal boundary size based on the initial beam shape. Furthermore, the second algorithm adjusts the propagation step sizes based on the beam shape at the beginning of each step in order to reduce aliasing artifacts.

Adaptive step-size algorithm for Fourier beam-propagation method with absorbing boundary layer of auto-determined width

DOE PAGES

Learn, R.; Feigenbaum, E.

2016-05-27

Two algorithms that enhance the utility of the absorbing boundary layer are presented, mainly in the framework of the Fourier beam-propagation method. One is an automated boundary layer width selector that chooses a near-optimal boundary size based on the initial beam shape. Furthermore, the second algorithm adjusts the propagation step sizes based on the beam shape at the beginning of each step in order to reduce aliasing artifacts.

Drying step optimization to obtain large-size transparent magnesium-aluminate spinel samples

NASA Astrophysics Data System (ADS)

Petit, Johan; Lallemant, Lucile

2017-05-01

In the transparent ceramics processing, the green body elaboration step is probably the most critical one. Among the known techniques, wet shaping processes are particularly interesting because they enable the particles to find an optimum position on their own. Nevertheless, the presence of water molecules leads to drying issues. During the water removal, its concentration gradient induces cracks limiting the sample size: laboratory samples are generally less damaged because of their small size but upscaling the samples for industrial applications lead to an increasing cracking probability. Thanks to the drying step optimization, large size spinel samples were obtained.

Simulation and experimental design of a new advanced variable step size Incremental Conductance MPPT algorithm for PV systems.

PubMed

Loukriz, Abdelhamid; Haddadi, Mourad; Messalti, Sabir

2016-05-01

Improvement of the efficiency of photovoltaic system based on new maximum power point tracking (MPPT) algorithms is the most promising solution due to its low cost and its easy implementation without equipment updating. Many MPPT methods with fixed step size have been developed. However, when atmospheric conditions change rapidly , the performance of conventional algorithms is reduced. In this paper, a new variable step size Incremental Conductance IC MPPT algorithm has been proposed. Modeling and simulation of different operational conditions of conventional Incremental Conductance IC and proposed methods are presented. The proposed method was developed and tested successfully on a photovoltaic system based on Flyback converter and control circuit using dsPIC30F4011. Both, simulation and experimental design are provided in several aspects. A comparative study between the proposed variable step size and fixed step size IC MPPT method under similar operating conditions is presented. The obtained results demonstrate the efficiency of the proposed MPPT algorithm in terms of speed in MPP tracking and accuracy. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

40 CFR 141.81 - Applicability of corrosion control treatment steps to small, medium-size and large water systems.

Code of Federal Regulations, 2011 CFR

2011-07-01

... treatment steps to small, medium-size and large water systems. 141.81 Section 141.81 Protection of... to small, medium-size and large water systems. (a) Systems shall complete the applicable corrosion...) or (b)(3) of this section. (2) A small system (serving ≤3300 persons) and a medium-size system...

40 CFR 141.81 - Applicability of corrosion control treatment steps to small, medium-size and large water systems.

Code of Federal Regulations, 2013 CFR

2013-07-01

... treatment steps to small, medium-size and large water systems. 141.81 Section 141.81 Protection of... to small, medium-size and large water systems. (a) Systems shall complete the applicable corrosion...) or (b)(3) of this section. (2) A small system (serving ≤3300 persons) and a medium-size system...

40 CFR 141.81 - Applicability of corrosion control treatment steps to small, medium-size and large water systems.

Code of Federal Regulations, 2012 CFR

2012-07-01

... treatment steps to small, medium-size and large water systems. 141.81 Section 141.81 Protection of... to small, medium-size and large water systems. (a) Systems shall complete the applicable corrosion...) or (b)(3) of this section. (2) A small system (serving ≤3300 persons) and a medium-size system...

40 CFR 141.81 - Applicability of corrosion control treatment steps to small, medium-size and large water systems.

Code of Federal Regulations, 2010 CFR

2010-07-01

... treatment steps to small, medium-size and large water systems. 141.81 Section 141.81 Protection of... to small, medium-size and large water systems. (a) Systems shall complete the applicable corrosion...) or (b)(3) of this section. (2) A small system (serving ≤3300 persons) and a medium-size system...

Dynamics of nonlinear feedback control.

PubMed

Snippe, H P; van Hateren, J H

2007-05-01

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

Dynamics of neural cryptography

NASA Astrophysics Data System (ADS)

Ruttor, Andreas; Kinzel, Wolfgang; Kanter, Ido

2007-05-01

Synchronization of neural networks has been used for public channel protocols in cryptography. In the case of tree parity machines the dynamics of both bidirectional synchronization and unidirectional learning is driven by attractive and repulsive stochastic forces. Thus it can be described well by a random walk model for the overlap between participating neural networks. For that purpose transition probabilities and scaling laws for the step sizes are derived analytically. Both these calculations as well as numerical simulations show that bidirectional interaction leads to full synchronization on average. In contrast, successful learning is only possible by means of fluctuations. Consequently, synchronization is much faster than learning, which is essential for the security of the neural key-exchange protocol. However, this qualitative difference between bidirectional and unidirectional interaction vanishes if tree parity machines with more than three hidden units are used, so that those neural networks are not suitable for neural cryptography. In addition, the effective number of keys which can be generated by the neural key-exchange protocol is calculated using the entropy of the weight distribution. As this quantity increases exponentially with the system size, brute-force attacks on neural cryptography can easily be made unfeasible.

Dynamics of neural cryptography.

PubMed

Ruttor, Andreas; Kinzel, Wolfgang; Kanter, Ido

2007-05-01

Synchronization of neural networks has been used for public channel protocols in cryptography. In the case of tree parity machines the dynamics of both bidirectional synchronization and unidirectional learning is driven by attractive and repulsive stochastic forces. Thus it can be described well by a random walk model for the overlap between participating neural networks. For that purpose transition probabilities and scaling laws for the step sizes are derived analytically. Both these calculations as well as numerical simulations show that bidirectional interaction leads to full synchronization on average. In contrast, successful learning is only possible by means of fluctuations. Consequently, synchronization is much faster than learning, which is essential for the security of the neural key-exchange protocol. However, this qualitative difference between bidirectional and unidirectional interaction vanishes if tree parity machines with more than three hidden units are used, so that those neural networks are not suitable for neural cryptography. In addition, the effective number of keys which can be generated by the neural key-exchange protocol is calculated using the entropy of the weight distribution. As this quantity increases exponentially with the system size, brute-force attacks on neural cryptography can easily be made unfeasible.

Efficient compression of molecular dynamics trajectory files.

PubMed

Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James

2012-10-15

We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases. Copyright © 2012 Wiley Periodicals, Inc.

Thermal conductivity of silicon using reverse non-equilibrium molecular dynamics

NASA Astrophysics Data System (ADS)

El-Genk, Mohamed S.; Talaat, Khaled; Cowen, Benjamin J.

2018-05-01

Simulations are performed using the reverse non-equilibrium molecular dynamics (rNEMD) method and the Stillinger-Weber (SW) potential to determine the input parameters for achieving ±1% convergence of the calculated thermal conductivity of silicon. These parameters are then used to investigate the effects of the interatomic potentials of SW, Tersoff II, Environment Dependent Interatomic Potential (EDIP), Second Nearest Neighbor, Modified Embedded-Atom Method (MEAM), and Highly Optimized Empirical Potential MEAM on determining the bulk thermal conductivity as a function of temperature (400-1000 K). At temperatures > 400 K, data collection and swap periods of 15 ns and 150 fs, system size ≥6 × 6 UC2 and system lengths ≥192 UC are adequate for ±1% convergence with all potentials, regardless of the time step size (0.1-0.5 fs). This is also true at 400 K, except for the SW potential, which requires a data collection period ≥30 ns. The calculated bulk thermal conductivities using the rNEMD method and the EDIP potential are close to, but lower than experimental values. The 10% difference at 400 K increases gradually to 20% at 1000 K.

Dynamics of neural cryptography

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

Ruttor, Andreas; Kinzel, Wolfgang; Kanter, Ido

2007-05-15

Synchronization of neural networks has been used for public channel protocols in cryptography. In the case of tree parity machines the dynamics of both bidirectional synchronization and unidirectional learning is driven by attractive and repulsive stochastic forces. Thus it can be described well by a random walk model for the overlap between participating neural networks. For that purpose transition probabilities and scaling laws for the step sizes are derived analytically. Both these calculations as well as numerical simulations show that bidirectional interaction leads to full synchronization on average. In contrast, successful learning is only possible by means of fluctuations. Consequently,more » synchronization is much faster than learning, which is essential for the security of the neural key-exchange protocol. However, this qualitative difference between bidirectional and unidirectional interaction vanishes if tree parity machines with more than three hidden units are used, so that those neural networks are not suitable for neural cryptography. In addition, the effective number of keys which can be generated by the neural key-exchange protocol is calculated using the entropy of the weight distribution. As this quantity increases exponentially with the system size, brute-force attacks on neural cryptography can easily be made unfeasible.« less

Real-time feedback control of twin-screw wet granulation based on image analysis.

PubMed

Madarász, Lajos; Nagy, Zsombor Kristóf; Hoffer, István; Szabó, Barnabás; Csontos, István; Pataki, Hajnalka; Démuth, Balázs; Szabó, Bence; Csorba, Kristóf; Marosi, György

2018-06-04

The present paper reports the first dynamic image analysis-based feedback control of continuous twin-screw wet granulation process. Granulation of the blend of lactose and starch was selected as a model process. The size and size distribution of the obtained particles were successfully monitored by a process camera coupled with an image analysis software developed by the authors. The validation of the developed system showed that the particle size analysis tool can determine the size of the granules with an error of less than 5 µm. The next step was to implement real-time feedback control of the process by controlling the liquid feeding rate of the pump through a PC, based on the real-time determined particle size results. After the establishment of the feedback control, the system could correct different real-life disturbances, creating a Process Analytically Controlled Technology (PACT), which guarantees the real-time monitoring and controlling of the quality of the granules. In the event of changes or bad tendencies in the particle size, the system can automatically compensate the effect of disturbances, ensuring proper product quality. This kind of quality assurance approach is especially important in the case of continuous pharmaceutical technologies. Copyright © 2018 Elsevier B.V. All rights reserved.

Dynamical Chaos in the Wisdom-Holman Integrator: Origins and Solutions

NASA Technical Reports Server (NTRS)

Rauch, Kevin P.; Holman, Matthew

1999-01-01

We examine the nonlinear stability of the Wisdom-Holman (WH) symplectic mapping applied to the integration of perturbed, highly eccentric (e-0.9) two-body orbits. We find that the method is unstable and introduces artificial chaos into the computed trajectories for this class of problems, unless the step size chosen 1s small enough that PeriaPse is always resolved, in which case the method is generically stable. This 'radial orbit instability' persists even for weakly perturbed systems. Using the Stark problem as a fiducial test case, we investigate the dynamical origin of this instability and argue that the numerical chaos results from the overlap of step-size resonances; interestingly, for the Stark-problem many of these resonances appear to be absolutely stable. We similarly examine the robustness of several alternative integration methods: a time-regularized version of the WH mapping suggested by Mikkola; the potential-splitting (PS) method of Duncan, Levison, Lee; and two original methods incorporating approximations based on Stark motion instead of Keplerian motion. The two fixed point problem and a related, more general problem are used to conduct a comparative test of the various methods for several types of motion. Among the algorithms tested, the time-transformed WH mapping is clearly the most efficient and stable method of integrating eccentric, nearly Keplerian orbits in the absence of close encounters. For test particles subject to both high eccentricities and very close encounters, we find an enhanced version of the PS method-incorporating time regularization, force-center switching, and an improved kernel function-to be both economical and highly versatile. We conclude that Stark-based methods are of marginal utility in N-body type integrations. Additional implications for the symplectic integration of N-body systems are discussed.

Effects of an aft facing step on the surface of a laminar flow glider wing

NASA Technical Reports Server (NTRS)

Sandlin, Doral R.; Saiki, Neal

1993-01-01

A motor glider was used to perform a flight test study on the effects of aft facing steps in a laminar boundary layer. This study focuses on two dimensional aft facing steps oriented spanwise to the flow. The size and location of the aft facing steps were varied in order to determine the critical size that will force premature transition. Transition over a step was found to be primarily a function of Reynolds number based on step height. Both of the step height Reynolds numbers for premature and full transition were determined. A hot film anemometry system was used to detect transition.

Kinesin Steps Do Not Alternate in Size☆

PubMed Central

Fehr, Adrian N.; Asbury, Charles L.; Block, Steven M.

2008-01-01

Abstract Kinesin is a two-headed motor protein that transports cargo inside cells by moving stepwise on microtubules. Its exact trajectory along the microtubule is unknown: alternative pathway models predict either uniform 8-nm steps or alternating 7- and 9-nm steps. By analyzing single-molecule stepping traces from “limping” kinesin molecules, we were able to distinguish alternate fast- and slow-phase steps and thereby to calculate the step sizes associated with the motions of each of the two heads. We also compiled step distances from nonlimping kinesin molecules and compared these distributions against models predicting uniform or alternating step sizes. In both cases, we find that kinesin takes uniform 8-nm steps, a result that strongly constrains the allowed models. PMID:18083906

Growth of group II-VI semiconductor quantum dots with strong quantum confinement and low size dispersion

NASA Astrophysics Data System (ADS)

Pandey, Praveen K.; Sharma, Kriti; Nagpal, Swati; Bhatnagar, P. K.; Mathur, P. C.

2003-11-01

CdTe quantum dots embedded in glass matrix are grown using two-step annealing method. The results for the optical transmission characterization are analysed and compared with the results obtained from CdTe quantum dots grown using conventional single-step annealing method. A theoretical model for the absorption spectra is used to quantitatively estimate the size dispersion in the two cases. In the present work, it is established that the quantum dots grown using two-step annealing method have stronger quantum confinement, reduced size dispersion and higher volume ratio as compared to the single-step annealed samples. (

Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction

PubMed Central

Abdallah, Bahige G.; Zatsepin, Nadia A.; Roy-Chowdhury, Shatabdi; Coe, Jesse; Conrad, Chelsie E.; Dörner, Katerina; Sierra, Raymond G.; Stevenson, Hilary P.; Camacho-Alanis, Fernanda; Grant, Thomas D.; Nelson, Garrett; James, Daniel; Calero, Guillermo; Wachter, Rebekka M.; Spence, John C. H.; Weierstall, Uwe; Fromme, Petra; Ros, Alexandra

2015-01-01

The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size. PMID:26798818

Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction

DOE PAGES

Abdallah, Bahige G.; Zatsepin, Nadia A.; Roy-Chowdhury, Shatabdi; ...

2015-08-19

We report that the advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles canmore » be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ~4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. Ultimately, this method will also permit an analysis of the dependence of crystal quality on crystal size.« less

Modeling ultrasound propagation through material of increasing geometrical complexity.

PubMed

Odabaee, Maryam; Odabaee, Mostafa; Pelekanos, Matthew; Leinenga, Gerhard; Götz, Jürgen

2018-06-01

Ultrasound is increasingly being recognized as a neuromodulatory and therapeutic tool, inducing a broad range of bio-effects in the tissue of experimental animals and humans. To achieve these effects in a predictable manner in the human brain, the thick cancellous skull presents a problem, causing attenuation. In order to overcome this challenge, as a first step, the acoustic properties of a set of simple bone-modeling resin samples that displayed an increasing geometrical complexity (increasing step sizes) were analyzed. Using two Non-Destructive Testing (NDT) transducers, we found that Wiener deconvolution predicted the Ultrasound Acoustic Response (UAR) and attenuation caused by the samples. However, whereas the UAR of samples with step sizes larger than the wavelength could be accurately estimated, the prediction was not accurate when the sample had a smaller step size. Furthermore, a Finite Element Analysis (FEA) performed in ANSYS determined that the scattering and refraction of sound waves was significantly higher in complex samples with smaller step sizes compared to simple samples with a larger step size. Together, this reveals an interaction of frequency and geometrical complexity in predicting the UAR and attenuation. These findings could in future be applied to poro-visco-elastic materials that better model the human skull. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

A real-time extension of density matrix embedding theory for non-equilibrium electron dynamics

NASA Astrophysics Data System (ADS)

Kretchmer, Joshua S.; Chan, Garnet Kin-Lic

2018-02-01

We introduce real-time density matrix embedding theory (DMET), a dynamical quantum embedding theory for computing non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static DMET, real-time DMET partitions the system into an impurity corresponding to the region of interest coupled to the surrounding environment, which is efficiently represented by a quantum bath of the same size as the impurity. In this work, we focus on a simplified single-impurity time-dependent formulation as a first step toward a multi-impurity theory. The equations of motion of the coupled impurity and bath embedding problem are derived using the time-dependent variational principle. The accuracy of real-time DMET is compared to that of time-dependent complete active space self-consistent field (TD-CASSCF) theory and time-dependent Hartree-Fock (TDHF) theory for a variety of quantum quenches in the single impurity Anderson model (SIAM), in which the Hamiltonian is suddenly changed (quenched) to induce a non-equilibrium state. Real-time DMET shows a marked improvement over the mean-field TDHF, converging to the exact answer even in the non-trivial Kondo regime of the SIAM. However, as expected from analogous behavior in static DMET, the constrained structure of the real-time DMET wavefunction leads to a slower convergence with respect to active space size, in the single-impurity formulation, relative to TD-CASSCF. Our initial results suggest that real-time DMET provides a promising framework to simulate non-equilibrium electron dynamics in which strong electron correlation plays an important role, and lays the groundwork for future multi-impurity formulations.

A real-time extension of density matrix embedding theory for non-equilibrium electron dynamics.

PubMed

Kretchmer, Joshua S; Chan, Garnet Kin-Lic

2018-02-07

We introduce real-time density matrix embedding theory (DMET), a dynamical quantum embedding theory for computing non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static DMET, real-time DMET partitions the system into an impurity corresponding to the region of interest coupled to the surrounding environment, which is efficiently represented by a quantum bath of the same size as the impurity. In this work, we focus on a simplified single-impurity time-dependent formulation as a first step toward a multi-impurity theory. The equations of motion of the coupled impurity and bath embedding problem are derived using the time-dependent variational principle. The accuracy of real-time DMET is compared to that of time-dependent complete active space self-consistent field (TD-CASSCF) theory and time-dependent Hartree-Fock (TDHF) theory for a variety of quantum quenches in the single impurity Anderson model (SIAM), in which the Hamiltonian is suddenly changed (quenched) to induce a non-equilibrium state. Real-time DMET shows a marked improvement over the mean-field TDHF, converging to the exact answer even in the non-trivial Kondo regime of the SIAM. However, as expected from analogous behavior in static DMET, the constrained structure of the real-time DMET wavefunction leads to a slower convergence with respect to active space size, in the single-impurity formulation, relative to TD-CASSCF. Our initial results suggest that real-time DMET provides a promising framework to simulate non-equilibrium electron dynamics in which strong electron correlation plays an important role, and lays the groundwork for future multi-impurity formulations.

Human dynamic closed-loop accommodation augmented by sympathetic inhibition.

PubMed

Culhane, H M; Winn, B; Gilmartin, B

1999-05-01

A ciliary alpha-adrenoceptor accommodative effect has been proposed, caused by a small population of alpha1-inhibitory receptors in excised human ciliary muscle. This study was intended to investigate the effect on the closed-loop dynamic accommodative process of modulating alpha1-adrenoceptor activity by topical instillation of the alpha1-adrenergic agonist, phenylephrine hydrochloride. A group of 10 visually normal subjects viewed a photopic (30 candela/m2) high-contrast Maltese cross, which was modulated sinusoidally (0.05-0.6Hz) and stepwise over a 2-D range (2-4 D). Monocular temporal accommodation responses were measured using a continuously recording dynamic tracking infrared optometer under two trial conditions: after instillation of saline control solution and 50 minutes subsequent to the instillation of 0.27 microl 0.4% benoxinate hydrochloride and 0.27 microl 2.5% phenylephrine hydrochloride. Pupil size and accommodative amplitude were measured at 90-second intervals for 50 minutes after drug instillation. All accommodative measurements were recorded through a fixed 4-mm pupil. A significant reduction in accommodative amplitude (11%; P < 0.05) was recorded, whereas pupil size showed a significant increase (33%; P < 0.05). No significant change in step-response dynamics was observed. However, phenylephrine hydrochloride caused a significant increase in accommodative gain in the low and midtemporal frequency ranges compared with the effect of a saline control treatment. No significant variation in phase lag was observed. For the first time in humans, this study shows that augmentation of the alpha1-inhibitory sympathetic contribution results in increased accommodative gain at low and midtemporal frequencies, which is consistent with findings in animal studies.

Controlling dental enamel-cavity ablation depth with optimized stepping parameters along the focal plane normal using a three axis, numerically controlled picosecond laser.

PubMed

Yuan, Fusong; Lv, Peijun; Wang, Dangxiao; Wang, Lei; Sun, Yuchun; Wang, Yong

2015-02-01

The purpose of this study was to establish a depth-control method in enamel-cavity ablation by optimizing the timing of the focal-plane-normal stepping and the single-step size of a three axis, numerically controlled picosecond laser. Although it has been proposed that picosecond lasers may be used to ablate dental hard tissue, the viability of such a depth-control method in enamel-cavity ablation remains uncertain. Forty-two enamel slices with approximately level surfaces were prepared and subjected to two-dimensional ablation by a picosecond laser. The additive-pulse layer, n, was set to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70. A three-dimensional microscope was then used to measure the ablation depth, d, to obtain a quantitative function relating n and d. Six enamel slices were then subjected to three dimensional ablation to produce 10 cavities, respectively, with additive-pulse layer and single-step size set to corresponding values. The difference between the theoretical and measured values was calculated for both the cavity depth and the ablation depth of a single step. These were used to determine minimum-difference values for both the additive-pulse layer (n) and single-step size (d). When the additive-pulse layer and the single-step size were set 5 and 45, respectively, the depth error had a minimum of 2.25 μm, and 450 μm deep enamel cavities were produced. When performing three-dimensional ablating of enamel with a picosecond laser, adjusting the timing of the focal-plane-normal stepping and the single-step size allows for the control of ablation-depth error to the order of micrometers.

Flow dynamics in bioreactors containing tissue engineering scaffolds.

PubMed

Lawrence, Benjamin J; Devarapalli, Mamatha; Madihally, Sundararajan V

2009-02-15

Bioreactors are widely used in tissue engineering as a way to distribute nutrients within porous materials and provide physical stimulus required by many tissues. However, the fluid dynamics within the large porous structure are not well understood. In this study, we explored the effect of reactor geometry by using rectangular and circular reactors with three different inlet and outlet patterns. Geometries were simulated with and without the porous structure using the computational fluid dynamics software Comsol Multiphysics 3.4 and/or ANSYS CFX 11 respectively. Residence time distribution analysis using a step change of a tracer within the reactor revealed non-ideal fluid distribution characteristics within the reactors. The Brinkman equation was used to model the permeability characteristics with in the chitosan porous structure. Pore size was varied from 10 to 200 microm and the number of pores per unit area was varied from 15 to 1,500 pores/mm(2). Effect of cellular growth and tissue remodeling on flow distribution was also assessed by changing the pore size (85-10 microm) while keeping the number of pores per unit area constant. These results showed significant increase in pressure with reduction in pore size, which could limit the fluid flow and nutrient transport. However, measured pressure drop was marginally higher than the simulation results. Maximum shear stress was similar in both reactors and ranged approximately 0.2-0.3 dynes/cm(2). The simulations were validated experimentally using both a rectangular and circular bioreactor, constructed in-house. Porous structures for the experiments were formed using 0.5% chitosan solution freeze-dried at -80 degrees C, and the pressure drop across the reactor was monitored.

Dynamics of aesthetic appreciation

NASA Astrophysics Data System (ADS)

Carbon, Claus-Christian

2012-03-01

Aesthetic appreciation is a complex cognitive processing with inherent aspects of cold as well as hot cognition. Research from the last decades of empirical has shown that evaluations of aesthetic appreciation are highly reliable. Most frequently, facial attractiveness was used as the corner case for investigating aesthetic appreciation. Evaluating facial attractiveness shows indeed high internal consistencies and impressively high inter-rater reliabilities, even across cultures. Although this indicates general and stable mechanisms underlying aesthetic appreciation, it is also obvious that our taste for specific objects changes dynamically. Aesthetic appreciation on artificial object categories, such as fashion, design or art is inherently very dynamic. Gaining insights into the cognitive mechanisms that trigger and enable corresponding changes of aesthetic appreciation is of particular interest for research as this will provide possibilities to modeling aesthetic appreciation for longer durations and from a dynamic perspective. The present paper refers to a recent two-step model ("the dynamical two-step-model of aesthetic appreciation"), dynamically adapting itself, which accounts for typical dynamics of aesthetic appreciation found in different research areas such as art history, philosophy and psychology. The first step assumes singular creative sources creating and establishing innovative material towards which, in a second step, people adapt by integrating it into their visual habits. This inherently leads to dynamic changes of the beholders' aesthetic appreciation.

Effect of Target Location on Dynamic Visual Acuity During Passive Horizontal Rotation

NASA Technical Reports Server (NTRS)

Appelbaum, Meghan; DeDios, Yiri; Kulecz, Walter; Peters, Brian; Wood, Scott

2010-01-01

The vestibulo-ocular reflex (VOR) generates eye rotation to compensate for potential retinal slip in the specific plane of head movement. Dynamic visual acuity (DVA) has been utilized as a functional measure of the VOR. The purpose of this study was to examine changes in accuracy and reaction time when performing a DVA task with targets offset from the plane of rotation, e.g. offset vertically during horizontal rotation. Visual acuity was measured in 12 healthy subjects as they moved a hand-held joystick to indicate the orientation of a computer-generated Landolt C "as quickly and accurately as possible." Acuity thresholds were established with optotypes presented centrally on a wall-mounted LCD screen at 1.3 m distance, first without motion (static condition) and then while oscillating at 0.8 Hz (DVA, peak velocity 60 deg/s). The effect of target location was then measured during horizontal rotation with the optotypes randomly presented in one of nine different locations on the screen (offset up to 10 deg). The optotype size (logMar 0, 0.2 or 0.4, corresponding to Snellen range 20/20 to 20/50) and presentation duration (150, 300 and 450 ms) were counter-balanced across five trials, each utilizing horizontal rotation at 0.8 Hz. Dynamic acuity was reduced relative to static acuity in 7 of 12 subjects by one step size. During the random target trials, both accuracy and reaction time improved proportional to optotype size. Accuracy and reaction time also improved between 150 ms and 300 ms presentation durations. The main finding was that both accuracy and reaction time varied as a function of target location, with greater performance decrements when acquiring vertical targets. We conclude that dynamic visual acuity varies with target location, with acuity optimized for targets in the plane of motion. Both reaction time and accuracy are functionally relevant DVA parameters of VOR function.

A Dynamic Pathway for Stone-Wales Bond Rotation on Carbon Nanotubes through Diamond-Like Bonds

NASA Technical Reports Server (NTRS)

Wei, Chen-Yu; Srivastava, Deepak; Cho, Kyeong-Jae; Menon, Madhu

2003-01-01

A new lower energy barrier with a two-step pathway of Stone-Wales (SW) ,ond rotation on carbon nanotubes (CNTs) is found through molecular dynamics (MD) simulations of CNTs under tension. The first step involves going over to a stable sp3-like metastable configuration with half rotated and partially tilted C-C bond. The second step involves going over to the fully rotated C-C bond with the formation of a SW defect in the nanotube. The energy barrier for this two-step dynamic pathway is significantly lower than the previously known static barrier for in-plane rotation of the C-C bond on a tensile strained (> 4%) CNT.

Do protein crystals nucleate within dense liquid clusters?

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

Maes, Dominique, E-mail: dommaes@vub.ac.be; Vorontsova, Maria A.; Potenza, Marco A. C.

2015-06-27

The evolution of protein-rich clusters and nucleating crystals were characterized by dynamic light scattering (DLS), confocal depolarized dynamic light scattering (cDDLS) and depolarized oblique illumination dark-field microscopy. Newly nucleated crystals within protein-rich clusters were detected directly. These observations indicate that the protein-rich clusters are locations for crystal nucleation. Protein-dense liquid clusters are regions of high protein concentration that have been observed in solutions of several proteins. The typical cluster size varies from several tens to several hundreds of nanometres and their volume fraction remains below 10{sup −3} of the solution. According to the two-step mechanism of nucleation, the protein-rich clustersmore » serve as locations for and precursors to the nucleation of protein crystals. While the two-step mechanism explained several unusual features of protein crystal nucleation kinetics, a direct observation of its validity for protein crystals has been lacking. Here, two independent observations of crystal nucleation with the proteins lysozyme and glucose isomerase are discussed. Firstly, the evolutions of the protein-rich clusters and nucleating crystals were characterized simultaneously by dynamic light scattering (DLS) and confocal depolarized dynamic light scattering (cDDLS), respectively. It is demonstrated that protein crystals appear following a significant delay after cluster formation. The cDDLS correlation functions follow a Gaussian decay, indicative of nondiffusive motion. A possible explanation is that the crystals are contained inside large clusters and are driven by the elasticity of the cluster surface. Secondly, depolarized oblique illumination dark-field microscopy reveals the evolution from liquid clusters without crystals to newly nucleated crystals contained in the clusters to grown crystals freely diffusing in the solution. Collectively, the observations indicate that the protein-rich clusters in lysozyme and glucose isomerase solutions are locations for crystal nucleation.« less

Fluid transport properties by equilibrium molecular dynamics. I. Methodology at extreme fluid states

NASA Astrophysics Data System (ADS)

Dysthe, D. K.; Fuchs, A. H.; Rousseau, B.

1999-02-01

The Green-Kubo formalism for evaluating transport coefficients by molecular dynamics has been applied to flexible, multicenter models of linear and branched alkanes in the gas phase and in the liquid phase from ambient conditions to close to the triple point. The effects of integration time step, potential cutoff and system size have been studied and shown to be small compared to the computational precision except for diffusion in gaseous n-butane. The RATTLE algorithm is shown to give accurate transport coefficients for time steps up to a limit of 8 fs. The different relaxation mechanisms in the fluids have been studied and it is shown that the longest relaxation time of the system governs the statistical precision of the results. By measuring the longest relaxation time of a system one can obtain a reliable error estimate from a single trajectory. The accuracy of the Green-Kubo method is shown to be as good as the precision for all states and models used in this study even when the system relaxation time becomes very long. The efficiency of the method is shown to be comparable to nonequilibrium methods. The transport coefficients for two recently proposed potential models are presented, showing deviations from experiment of 0%-66%.

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

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

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

2014-02-14

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

Method for making a dynamic pressure sensor and a pressure sensor made according to the method

NASA Technical Reports Server (NTRS)

Zuckerwar, Allan J. (Inventor); Robbins, William E. (Inventor); Robins, Glenn M. (Inventor)

1994-01-01

A method for providing a perfectly flat top with a sharp edge on a dynamic pressure sensor using a cup-shaped stretched membrane as a sensing element is described. First, metal is deposited on the membrane and surrounding areas. Next, the side wall of the pressure sensor with the deposited metal is machined to a predetermined size. Finally, deposited metal is removed from the top of the membrane in small steps, by machining or lapping while the pressure sensor is mounted in a jig or the wall of a test object, until the true top surface of the membrane appears. A thin indicator layer having a color contrasting with the color of the membrane may be applied to the top of the membrane before metal is deposited to facilitate the determination of when to stop metal removal from the top surface of the membrane.

Optimally combining dynamical decoupling and quantum error correction.

PubMed

Paz-Silva, Gerardo A; Lidar, D A

2013-01-01

Quantum control and fault-tolerant quantum computing (FTQC) are two of the cornerstones on which the hope of realizing a large-scale quantum computer is pinned, yet only preliminary steps have been taken towards formalizing the interplay between them. Here we explore this interplay using the powerful strategy of dynamical decoupling (DD), and show how it can be seamlessly and optimally integrated with FTQC. To this end we show how to find the optimal decoupling generator set (DGS) for various subspaces relevant to FTQC, and how to simultaneously decouple them. We focus on stabilizer codes, which represent the largest contribution to the size of the DGS, showing that the intuitive choice comprising the stabilizers and logical operators of the code is in fact optimal, i.e., minimizes a natural cost function associated with the length of DD sequences. Our work brings hybrid DD-FTQC schemes, and their potentially considerable advantages, closer to realization.

Optimally combining dynamical decoupling and quantum error correction

PubMed Central

Paz-Silva, Gerardo A.; Lidar, D. A.

2013-01-01

Quantum control and fault-tolerant quantum computing (FTQC) are two of the cornerstones on which the hope of realizing a large-scale quantum computer is pinned, yet only preliminary steps have been taken towards formalizing the interplay between them. Here we explore this interplay using the powerful strategy of dynamical decoupling (DD), and show how it can be seamlessly and optimally integrated with FTQC. To this end we show how to find the optimal decoupling generator set (DGS) for various subspaces relevant to FTQC, and how to simultaneously decouple them. We focus on stabilizer codes, which represent the largest contribution to the size of the DGS, showing that the intuitive choice comprising the stabilizers and logical operators of the code is in fact optimal, i.e., minimizes a natural cost function associated with the length of DD sequences. Our work brings hybrid DD-FTQC schemes, and their potentially considerable advantages, closer to realization. PMID:23559088

Observation of Spectral Signatures of 1/f Dynamics in Avalanches on Granular Piles

NASA Astrophysics Data System (ADS)

Kim, Yong W.; Nishino, Thomas K.

1997-03-01

Granular piles of monodisperse glass spheres, 0.46+0.03 mm in diameter, have been studied. The base diameter of the pile has been varied from 3/8" to 2" in 1/8" increments. A single-grain dispenser with greater than 95consisting of a stepping motor-actuated reciprocating arm with a single-grain scoop. Each grain is dropped on the apex of the pile with lowest possible landing velocity at intervals at least 30longer than the duration of largest avalanches for each given pile. Each grain being added and being lost in avalanches from the pile is optically detected and recorded. The power spectrum of the net addition of grains to the pile as a function of time is found to be robustly 1/f for all base sizes. A wide variety of dynamical properties of 1/f systems, as obtained from the high precision data, will be presented.

Atomistic simulation of Al-graphene thin film growth on polycrystalline Al substrate

NASA Astrophysics Data System (ADS)

Zhang, Lan; Zhu, Yongchao; Li, Na; Rong, Yan; Xia, Huimin; Ma, Huizhong

2018-03-01

The growth of Al-Graphene composite coatings on polycrystalline Al substrate was investigated by using classical molecular dynamics (MD) simulations. Unlike the diffusion behaviors on single crystal surface, most of adatoms were easily bound by the steps on polycrystalline Al surface, owing to the local accelerated energy. Both Ehrlich-Schwoebel (ES) barriers and the steering effect backed up the volmer-weber growth mode, which was consistent with the dynamic growth process observed in the deposit. The morphology of composite coatings was significantly affected by graphene flakes. Enrichment of graphene flakes gave rise to an increase of the local thickness, and graphene flakes only existed in Al grain boundaries. The size of Al grains in the composite coating visibly decreased when compared with that in the pure Al coating. This grain refinement and the mechanical property can be reinforced by the increase of graphene flakes.

Low leakage Ru-strontium titanate-Ru metal-insulator-metal capacitors for sub-20 nm technology node in dynamic random access memory

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

Popovici, M., E-mail: Mihaela.Ioana.Popovici@imec.be; Swerts, J.; Redolfi, A.

2014-02-24

Improved metal-insulator-metal capacitor (MIMCAP) stacks with strontium titanate (STO) as dielectric sandwiched between Ru as top and bottom electrode are shown. The Ru/STO/Ru stack demonstrates clearly its potential to reach sub-20 nm technology nodes for dynamic random access memory. Downscaling of the equivalent oxide thickness, leakage current density (J{sub g}) of the MIMCAPs, and physical thickness of the STO have been realized by control of the Sr/Ti ratio and grain size using a heterogeneous TiO{sub 2}/STO based nanolaminate stack deposition and a two-step crystallization anneal. Replacement of TiN with Ru as both top and bottom electrodes reduces the amount of electricallymore » active defects and is essential to achieve a low leakage current in the MIM capacitor.« less

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

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

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

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

PubMed Central

Nasica-Labouze, Jessica; Meli, Massimiliano; Derreumaux, Philippe; Colombo, Giorgio; Mousseau, Normand

2011-01-01

The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided. PMID:21625573

Silica Encapsulation of Ferrimagnetic Zinc Ferrite Nanocubes Enabled by Layer-by-layer Polyelectrolyte Deposition

PubMed Central

Park, Jooneon; Porter, Marc D.; Granger, Michael C.

2016-01-01

Stable suspensions of magnetic nanoparticles (MNPs) with large magnetic moment, m, per particle have tremendous utility in a wide range of biological applications. However, due to the strong magnetic coupling interactions often present in these systems, it is challenging to stabilize individual, high moment, ferro- and ferrimagnetic nanoparticles. A novel approach to encapsulate large, i.e., >100 nm, ferrimagnetic zinc ferrite nanocubes (ZFNCs) with silica after an intermediary layer-by-layer polyelectrolyte deposition step is described in this paper. The seed ZFNCs are uniform in shape and size and have high saturation mass magnetic moment (σs ~100 emu/g, m~4×10−13 emu/particle at 150 Oe). For the MNP system described within, successful silica encapsulation and creation of discrete ZFNCs were realized only after depositing polyelectrolyte multilayers composed of alternating polyallylamine and polystyrene sulfonate. Without the intermediary polyelectrolyte layers, magnetic dipole-dipole interactions led to the formation of linearly chained ZFNCs embedded in a silica matrix. Characterization of particle samples was performed by electron microscopy, energy-dispersive X-ray spectroscopy, infrared spectroscopy, powder X-ray diffraction, dynamic light scattering (hydrodynamic size and ζ-potential), and vibrating sample magnetometry. The results of these characterizations, which were performed after each of the synthetic steps, and synthetic details are presented. PMID:25756216

The role of intramolecular nonbonded interaction and angle sampling in single-step free energy perturbation

NASA Astrophysics Data System (ADS)

Chiang, Ying-Chih; Pang, Yui Tik; Wang, Yi

2016-12-01

Single-step free energy perturbation (sFEP) has often been proposed as an efficient tool for a quick free energy scan due to its straightforward protocol and the ability to recycle an existing molecular dynamics trajectory for free energy calculations. Although sFEP is expected to fail when the sampling of a system is inefficient, it is often expected to hold for an alchemical transformation between ligands with a moderate difference in their sizes, e.g., transforming a benzene into an ethylbenzene. Yet, exceptions were observed in calculations for anisole and methylaniline, which have similar physical sizes as ethylbenzene. In this study, we show that such exceptions arise from the sampling inefficiency on an unexpected rigid degree of freedom, namely, the bond angle θ. The distributions of θ differ dramatically between two end states of a sFEP calculation, i.e., the conformation of the ligand changes significantly during the alchemical transformation process. Our investigation also reveals the interrelation between the ligand conformation and the intramolecular nonbonded interactions. This knowledge suggests a best combination of the ghost ligand potential and the dual topology setting, which improves the accuracy in a single reference sFEP calculation by bringing down its error from around 5kBT to kBT.

Optimized method of dispersion of titanium dioxide nanoparticles for evaluation of safety aspects in cosmetics

NASA Astrophysics Data System (ADS)

Carvalho, Karina Penedo; Martins, Nathalia Balthazar; Ribeiro, Ana Rosa Lopes Pereira; Lopes, Taliria Silva; de Sena, Rodrigo Caciano; Sommer, Pascal; Granjeiro, José Mauro

2016-08-01

Nanoparticles agglomerate when in contact with biological solutions, depending on the solutions' nature. The agglomeration state will directly influence cellular response, since free nanoparticles are prone to interact with cells and get absorbed into them. In sunscreens, titanium dioxide nanoparticles (TiO2-NPs) form mainly aggregates between 30 and 150 nm. Until now, no toxicological study with skin cells has reached this range of size distribution. Therefore, in order to reliably evaluate their safety, it is essential to prepare suspensions with reproducibility, irrespective of the biological solution used, representing the above particle size distribution range of NPs (30-150 nm) found on sunscreens. Thus, the aim of this study was to develop a unique protocol of TiO2 dispersion, combining these features after dilution in different skin cell culture media, for in vitro tests. This new protocol was based on physicochemical characteristics of TiO2, which led to the choice of the optimal pH condition for ultrasonication. The next step consisted of stabilization of protein capping with acidified bovine serum albumin, followed by an adjustment of pH to 7.0. At each step, the solutions were analyzed by dynamic light scattering and transmission electron microscopy. The final concentration of NPs was determined by inductively coupled plasma-optical emission spectroscopy. Finally, when diluted in dulbecco's modified eagle medium, melanocytes growth medium, or keratinocytes growth medium, TiO2-NPs displayed a highly reproducible size distribution, within the desired size range and without significant differences among the media. Together, these results demonstrate the consistency achieved by this new methodology and its suitability for in vitro tests involving skin cell cultures.

Thermal-Acoustic Analysis of a Metallic Integrated Thermal Protection System Structure

NASA Technical Reports Server (NTRS)

Behnke, Marlana N.; Sharma, Anurag; Przekop, Adam; Rizzi, Stephen A.

2010-01-01

A study is undertaken to investigate the response of a representative integrated thermal protection system structure under combined thermal, aerodynamic pressure, and acoustic loadings. A two-step procedure is offered and consists of a heat transfer analysis followed by a nonlinear dynamic analysis under a combined loading environment. Both analyses are carried out in physical degrees-of-freedom using implicit and explicit solution techniques available in the Abaqus commercial finite-element code. The initial study is conducted on a reduced-size structure to keep the computational effort contained while validating the procedure and exploring the effects of individual loadings. An analysis of a full size integrated thermal protection system structure, which is of ultimate interest, is subsequently presented. The procedure is demonstrated to be a viable approach for analysis of spacecraft and hypersonic vehicle structures under a typical mission cycle with combined loadings characterized by largely different time-scales.

Experimental mixture design as a tool for the synthesis of antimicrobial selective molecularly imprinted monodisperse microbeads.

PubMed

Benito-Peña, Elena; Navarro-Villoslada, Fernando; Carrasco, Sergio; Jockusch, Steffen; Ottaviani, M Francesca; Moreno-Bondi, Maria C

2015-05-27

The effect of the cross-linker on the shape and size of molecular imprinted polymer (MIP) beads prepared by precipitation polymerization has been evaluated using a chemometric approach. Molecularly imprinted microspheres for the selective recognition of fluoroquinolone antimicrobials were prepared in a one-step precipitation polymerization procedure using enrofloxacin (ENR) as the template molecule, methacrylic acid as functional monomer, 2-hydroxyethyl methacrylate as hydrophilic comonomer, and acetonitrile as the porogen. The type and amount of cross-linker, namely ethylene glycol dimethacrylate, divinylbenzene or trimethylolpropane trimethacrylate, to obtain monodispersed MIP spherical beads in the micrometer range was optimized using a simplex lattice design. Particle size and morphology were assessed by scanning electron microscopy, dynamic light scattering, and nitrogen adsorption measurements. Electron paramagnetic resonance spectroscopy in conjunction with a nitroxide as spin probe revealed information about the microviscosity and polarity of the binding sites in imprinted and nonimprinted polymer beads.

Hetero-diffusion of Au epitaxy on stepped Ag(110) surface: Study of the jump rate and diffusion coefficient

NASA Astrophysics Data System (ADS)

Benlattar, M.; El koraychy, E.; Kotri, A.; Mazroui, M.

2017-12-01

We have used molecular dynamics simulations combined with an interatomic potential derived from the embedded atom method, to investigate the hetero-diffusion of Au adatom near a stepped Ag(110) surface with the height of one monoatomic layer. The activation energies for different diffusion processes, which occur on the terrace and near the step edge, are calculated both by molecular statics and molecular dynamics simulations. Static energies are found by the drag method, whereas the dynamic barriers are computed at high temperature from the Arrhenius plots. Our numerical results reveal that the jump process requires very high activation energy compared to the exchange process either on the terrace or near the step edge. In this work, other processes, such as upward and downward diffusion at step edges, have also been discussed.

Relative dosimetrical verification in high dose rate brachytherapy using two-dimensional detector array IMatriXX

PubMed Central

Manikandan, A.; Biplab, Sarkar; David, Perianayagam A.; Holla, R.; Vivek, T. R.; Sujatha, N.

2011-01-01

For high dose rate (HDR) brachytherapy, independent treatment verification is needed to ensure that the treatment is performed as per prescription. This study demonstrates dosimetric quality assurance of the HDR brachytherapy using a commercially available two-dimensional ion chamber array called IMatriXX, which has a detector separation of 0.7619 cm. The reference isodose length, step size, and source dwell positional accuracy were verified. A total of 24 dwell positions, which were verified for positional accuracy gave a total error (systematic and random) of –0.45 mm, with a standard deviation of 1.01 mm and maximum error of 1.8 mm. Using a step size of 5 mm, reference isodose length (the length of 100% isodose line) was verified for single and multiple catheters of same and different source loadings. An error ≤1 mm was measured in 57% of tests analyzed. Step size verification for 2, 3, 4, and 5 cm was performed and 70% of the step size errors were below 1 mm, with maximum of 1.2 mm. The step size ≤1 cm could not be verified by the IMatriXX as it could not resolve the peaks in dose profile. PMID:21897562

Combining gas-phase electrophoretic mobility molecular analysis (GEMMA), light scattering, field flow fractionation and cryo electron microscopy in a multidimensional approach to characterize liposomal carrier vesicles.

PubMed

Urey, Carlos; Weiss, Victor U; Gondikas, Andreas; von der Kammer, Frank; Hofmann, Thilo; Marchetti-Deschmann, Martina; Allmaier, Günter; Marko-Varga, György; Andersson, Roland

2016-11-20

For drug delivery, characterization of liposomes regarding size, particle number concentrations, occurrence of low-sized liposome artefacts and drug encapsulation are of importance to understand their pharmacodynamic properties. In our study, we aimed to demonstrate the applicability of nano Electrospray Gas-Phase Electrophoretic Mobility Molecular Analyser (nES GEMMA) as a suitable technique for analyzing these parameters. We measured number-based particle concentrations, identified differences in size between nominally identical liposomal samples, and detected the presence of low-diameter material which yielded bimodal particle size distributions. Subsequently, we compared these findings to dynamic light scattering (DLS) data and results from light scattering experiments coupled to Asymmetric Flow-Field Flow Fractionation (AF4), the latter improving the detectability of smaller particles in polydisperse samples due to a size separation step prior detection. However, the bimodal size distribution could not be detected due to method inherent limitations. In contrast, cryo transmission electron microscopy corroborated nES GEMMA results. Hence, gas-phase electrophoresis proved to be a versatile tool for liposome characterization as it could analyze both vesicle size and size distribution. Finally, a correlation of nES GEMMA results with cell viability experiments was carried out to demonstrate the importance of liposome batch-to-batch control as low-sized sample components possibly impact cell viability. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Switchable Chiral Selection of Aspartic Acids by Dynamic States of Brushite

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

Jiang, Wenge; Pan, Haihua; Zhang, Zhisen

Here, we show the chiral recognition and separation of aspartic acid (Asp) enantiomers by achiral brushite due to the asymmetries of their dynamical steps in its nonequilibrium states. Growing brushite has a higher adsorption affinity to d-Asp, while l-Asp is predominant on the dissolving brushite surface. Microstructural characterization reveals that chiral selection is mainly attributed to brushite [101] steps, which exhibit two different configurations during crystal growth and dissolution, respectively, with each preferring a distinct enantiomer due to this asymmetry. Because these transition step configurations have different stabilities, they subsequently result in asymmetric adsorption. Furthermore, by varying free energy barriersmore » through solution thermodynamic driving force (i.e., supersaturation), the dominant nonequilibrium intermediate states can be switched and chiral selection regulated. This finding highlights that the dynamic steps can be vital for chiral selection, which may provide a potential pathway for chirality generation through the dynamic nature.« less

Switchable Chiral Selection of Aspartic Acids by Dynamic States of Brushite

DOE PAGES

Jiang, Wenge; Pan, Haihua; Zhang, Zhisen; ...

2017-06-15

Here, we show the chiral recognition and separation of aspartic acid (Asp) enantiomers by achiral brushite due to the asymmetries of their dynamical steps in its nonequilibrium states. Growing brushite has a higher adsorption affinity to d-Asp, while l-Asp is predominant on the dissolving brushite surface. Microstructural characterization reveals that chiral selection is mainly attributed to brushite [101] steps, which exhibit two different configurations during crystal growth and dissolution, respectively, with each preferring a distinct enantiomer due to this asymmetry. Because these transition step configurations have different stabilities, they subsequently result in asymmetric adsorption. Furthermore, by varying free energy barriersmore » through solution thermodynamic driving force (i.e., supersaturation), the dominant nonequilibrium intermediate states can be switched and chiral selection regulated. This finding highlights that the dynamic steps can be vital for chiral selection, which may provide a potential pathway for chirality generation through the dynamic nature.« less

The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs.

PubMed

Thompson, Jennifer A; Fielding, Katherine; Hargreaves, James; Copas, Andrew

2017-12-01

Background/Aims We sought to optimise the design of stepped wedge trials with an equal allocation of clusters to sequences and explored sample size comparisons with alternative trial designs. Methods We developed a new expression for the design effect for a stepped wedge trial, assuming that observations are equally correlated within clusters and an equal number of observations in each period between sequences switching to the intervention. We minimised the design effect with respect to (1) the fraction of observations before the first and after the final sequence switches (the periods with all clusters in the control or intervention condition, respectively) and (2) the number of sequences. We compared the design effect of this optimised stepped wedge trial to the design effects of a parallel cluster-randomised trial, a cluster-randomised trial with baseline observations, and a hybrid trial design (a mixture of cluster-randomised trial and stepped wedge trial) with the same total cluster size for all designs. Results We found that a stepped wedge trial with an equal allocation to sequences is optimised by obtaining all observations after the first sequence switches and before the final sequence switches to the intervention; this means that the first sequence remains in the control condition and the last sequence remains in the intervention condition for the duration of the trial. With this design, the optimal number of sequences is [Formula: see text], where [Formula: see text] is the cluster-mean correlation, [Formula: see text] is the intracluster correlation coefficient, and m is the total cluster size. The optimal number of sequences is small when the intracluster correlation coefficient and cluster size are small and large when the intracluster correlation coefficient or cluster size is large. A cluster-randomised trial remains more efficient than the optimised stepped wedge trial when the intracluster correlation coefficient or cluster size is small. A cluster-randomised trial with baseline observations always requires a larger sample size than the optimised stepped wedge trial. The hybrid design can always give an equally or more efficient design, but will be at most 5% more efficient. We provide a strategy for selecting a design if the optimal number of sequences is unfeasible. For a non-optimal number of sequences, the sample size may be reduced by allowing a proportion of observations before the first or after the final sequence has switched. Conclusion The standard stepped wedge trial is inefficient. To reduce sample sizes when a hybrid design is unfeasible, stepped wedge trial designs should have no observations before the first sequence switches or after the final sequence switches.

A random rule model of surface growth

NASA Astrophysics Data System (ADS)

Mello, Bernardo A.

2015-02-01

Stochastic models of surface growth are usually based on randomly choosing a substrate site to perform iterative steps, as in the etching model, Mello et al. (2001) [5]. In this paper I modify the etching model to perform sequential, instead of random, substrate scan. The randomicity is introduced not in the site selection but in the choice of the rule to be followed in each site. The change positively affects the study of dynamic and asymptotic properties, by reducing the finite size effect and the short-time anomaly and by increasing the saturation time. It also has computational benefits: better use of the cache memory and the possibility of parallel implementation.

Scanning Shack-Hartmann wavefront sensor

NASA Astrophysics Data System (ADS)

Molebny, Vasyl V.

2004-09-01

Criss-crossing of focal images is the cause of a narrow dynamic range in Shack-Hartmann sensors. Practically, aberration range wider than +/-3 diopters can not be measured. A method has been proposed for ophthalmologic applications using a rarefied lenslet array through which a wave front is projected with the successive step-by-step changing of the global tilt. The data acquired in each step are accumulated and processed. In experimental setup, a doubled dynamic range was achieved with four steps of wave front tilting.

Computational plasticity algorithm for particle dynamics simulations

NASA Astrophysics Data System (ADS)

Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.

2018-01-01

The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.

Linear micromechanical stepping drive for pinhole array positioning

NASA Astrophysics Data System (ADS)

Endrödy, Csaba; Mehner, Hannes; Grewe, Adrian; Hoffmann, Martin

2015-05-01

A compact linear micromechanical stepping drive for positioning a 7 × 5.5 mm2 optical pinhole array is presented. The system features a step size of 13.2 µm and a full displacement range of 200 µm. The electrostatic inch-worm stepping mechanism shows a compact design capable of positioning a payload 50% of its own weight. The stepping drive movement, step sizes and position accuracy are characterized. The actuated pinhole array is integrated in a confocal chromatic hyperspectral imaging system, where coverage of the object plane, and therefore the useful picture data, can be multiplied by 14 in contrast to a non-actuated array.

Does footwear type impact the number of steps required to reach gait steady state?: an innovative look at the impact of foot orthoses on gait initiation.

PubMed

Najafi, Bijan; Miller, Daniel; Jarrett, Beth D; Wrobel, James S

2010-05-01

Many studies have attempted to better elucidate the effect of foot orthoses on gait dynamics. To our knowledge, most previous studies exclude the first few steps of gait and begin analysis at steady state walking. These unanalyzed steps of gait may contain important information about the dynamic and complex processes required to achieve equilibrium for a given gait velocity. The purpose of this study was to quantify gait initiation and determine how many steps were required to reach steady state walking under three footwear conditions: barefoot, habitual shoes, and habitual shoes with a prefabricated foot orthoses. Fifteen healthy subjects walked 50m at habitual speed in each condition. Wearing habitual shoes with the prefabricated orthoses enabled subjects to reach steady state walking in fewer steps (3.5 steps+/-2.0) compared to the barefoot condition (5.2 steps+/-3.0; p=0.02) as well as compared to the habitual shoes condition (4.7 steps+/-1.6; p=0.05). Interestingly, the subjects' dynamic medial-lateral balance was significantly improved (22%, p<0.05) by using foot orthoses compared to other footwear conditions. These findings suggest that foot orthoses may help individuals reach steady state more quickly and with a better dynamic balance in the medial-lateral direction, independent of foot type. The findings of this pilot study may open new avenues for objectively assessing the impact of prescription footwear on dynamic balance and spatio-temporal parameters of gait. Further work to better assess the impact of foot orthoses on gait initiation in patients suffering from gait and instability pathologies may be warranted. Copyright 2010 Elsevier B.V. All rights reserved.

Foam Optics and Mechanics

NASA Technical Reports Server (NTRS)

Durian, Douglas J.; Zimmerli, Gregory A.

2002-01-01

The Foam Optics and Mechanics (FOAM) project will exploit the microgravity environment to more accurately measure the rheological and optical characteristics of wet aqueous foams. Using both rheology and laser light scattering diagnostics, the goal is to quantify the unusual elastic character of foams in terms of their underlying microscopic structure and dynamics. Of particular interest is determining how the elastic character vanishes, i.e., how the foam 'melts' into a simple viscous liquid, as a function of both increasing liquid content and increasing shear strain rate. The unusual elastic character of foams will be quantified macroscopically by measurement of the shear stress as a function of shear strain rate and of time following a step strain. Such data will be analyzed in terms of a yield stress, shear moduli, and dynamical time scales. Microscopic information about bubble packing and rearrangement dynamics, from which the macroscopic non-Newtonian properties ultimately arise, will be obtained non-invasively by multiple-light scattering: diffuse transmission spectroscopy (DTS) and diffusing wave spectroscopy (DWS). Quantitative trends with materials parameters, most importantly average bubble size and liquid content, will be sought in order to elucidate the fundamental connection between the microscopic structure and dynamics and the macroscopic rheology.

Development of 1D Liner Compression Code for IDL

NASA Astrophysics Data System (ADS)

Shimazu, Akihisa; Slough, John; Pancotti, Anthony

2015-11-01

A 1D liner compression code is developed to model liner implosion dynamics in the Inductively Driven Liner Experiment (IDL) where FRC plasmoid is compressed via inductively-driven metal liners. The driver circuit, magnetic field, joule heating, and liner dynamics calculations are performed at each time step in sequence to couple these effects in the code. To obtain more realistic magnetic field results for a given drive coil geometry, 2D and 3D effects are incorporated into the 1D field calculation through use of correction factor table lookup approach. Commercial low-frequency electromagnetic fields solver, ANSYS Maxwell 3D, is used to solve the magnetic field profile for static liner condition at various liner radius in order to derive correction factors for the 1D field calculation in the code. The liner dynamics results from the code is verified to be in good agreement with the results from commercial explicit dynamics solver, ANSYS Explicit Dynamics, and previous liner experiment. The developed code is used to optimize the capacitor bank and driver coil design for better energy transfer and coupling. FRC gain calculations are also performed using the liner compression data from the code for the conceptual design of the reactor sized system for fusion energy gains.

Liposome retention in size exclusion chromatography

PubMed Central

Ruysschaert, Tristan; Marque, Audrey; Duteyrat, Jean-Luc; Lesieur, Sylviane; Winterhalter, Mathias; Fournier, Didier

2005-01-01

Background Size exclusion chromatography is the method of choice for separating free from liposome-encapsulated molecules. However, if the column is not presaturated with lipids this type of chromatography causes a significant loss of lipid material. To date, the mechanism of lipid retention is poorly understood. It has been speculated that lipid binds to the column material or the entire liposome is entrapped inside the void. Results Here we show that intact liposomes and their contents are retained in the exclusion gel. Retention depends on the pore size, the smaller the pores, the higher the retention. Retained liposomes are not tightly fixed to the beads and are slowly released from the gels upon direct or inverted eluent flow, long washing steps or column repacking. Further addition of free liposomes leads to the elution of part of the gel-trapped liposomes, showing that the retention is transitory. Trapping reversibility should be related to a mechanism of partitioning of the liposomes between the stationary phase, water-swelled polymeric gel, and the mobile aqueous phase. Conclusion Retention of liposomes by size exclusion gels is a dynamic and reversible process, which should be accounted for to control lipid loss and sample contamination during chromatography. PMID:15885140

One-step analysis of DNA/chitosan complexes by field-flow fractionation reveals particle size and free chitosan content.

PubMed

Ma, Pei Lian; Buschmann, Michael D; Winnik, Françoise M

2010-03-08

The composition of samples obtained upon complexation of DNA with chitosan was analyzed by asymmetrical flow field flow fractionation (AF4) with online UV-visible, multiangle light scattering (MALS), and dynamic light scattering (DLS) detectors. A chitosan labeled with rhodamine B to facilitate UV-vis detection of the polycation was complexed with DNA under conditions commonly used for transfection (chitosan glucosamine to DNA phosphate molar ratio of 5). AF4 analysis revealed that 73% of the chitosan-rhodamine remained free in the dispersion and that the DNA/chitosan complexes had a broad size distribution ranging from 20 to 160 nm in hydrodynamic radius. The accuracy of the data was assessed by comparison with data from batch-mode DLS and scanning electron microscopy. The AF4 combined with DLS allowed the characterization of small particles that were not detected by conventional batch-mode DLS. The AF4 analysis will prove to be an important tool in the field of gene therapy because it readily provides, in a single measurement, three important physicochemical parameters of the complexes: the amount of unbound polycation, the hydrodynamic size of the complexes, and their size distribution.

Multiple-time-stepping generalized hybrid Monte Carlo methods

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

Escribano, Bruno, E-mail: bescribano@bcamath.org; Akhmatskaya, Elena; IKERBASQUE, Basque Foundation for Science, E-48013 Bilbao

2015-01-01

Performance of the generalized shadow hybrid Monte Carlo (GSHMC) method [1], which proved to be superior in sampling efficiency over its predecessors [2–4], molecular dynamics and hybrid Monte Carlo, can be further improved by combining it with multi-time-stepping (MTS) and mollification of slow forces. We demonstrate that the comparatively simple modifications of the method not only lead to better performance of GSHMC itself but also allow for beating the best performed methods, which use the similar force splitting schemes. In addition we show that the same ideas can be successfully applied to the conventional generalized hybrid Monte Carlo method (GHMC).more » The resulting methods, MTS-GHMC and MTS-GSHMC, provide accurate reproduction of thermodynamic and dynamical properties, exact temperature control during simulation and computational robustness and efficiency. MTS-GHMC uses a generalized momentum update to achieve weak stochastic stabilization to the molecular dynamics (MD) integrator. MTS-GSHMC adds the use of a shadow (modified) Hamiltonian to filter the MD trajectories in the HMC scheme. We introduce a new shadow Hamiltonian formulation adapted to force-splitting methods. The use of such Hamiltonians improves the acceptance rate of trajectories and has a strong impact on the sampling efficiency of the method. Both methods were implemented in the open-source MD package ProtoMol and were tested on a water and a protein systems. Results were compared to those obtained using a Langevin Molly (LM) method [5] on the same systems. The test results demonstrate the superiority of the new methods over LM in terms of stability, accuracy and sampling efficiency. This suggests that putting the MTS approach in the framework of hybrid Monte Carlo and using the natural stochasticity offered by the generalized hybrid Monte Carlo lead to improving stability of MTS and allow for achieving larger step sizes in the simulation of complex systems.« less

Rapid measurement of sub-micrometer aerosol size distribution using a fast integrated mobility spectrometer

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

Wang, Yang; Pinterich, Tamara; Wang, Jian

We present rapid measurement of submicron particle size distributions enables the characterization of aerosols with fast changing properties, and is often necessary for measurements onboard mobile platforms (e.g., research aircraft). Aerosol mobility size distribution is commonly measured by a scanning mobility particle sizer (SMPS), which relies on voltage scanning or stepping to classify particles of different sizes, and may take up to several minutes to obtain a complete size spectrum of aerosol particles. The recently developed fast integrated mobility spectrometer (FIMS) with enhanced dynamic size range classifies and detects particles from 10 to ~600 nm simultaneously, allowing submicron aerosol mobilitymore » size distributions to be captured at a time resolution of 1 second. In this study, we present a detailed data inversion routine for deriving aerosol size distribution from FIMS measurements. The inversion routine takes into consideration the FIMS transfer function, particle penetration efficiency in the FIMS, and multiple charging of aerosols. The accuracy of the FIMS measurement is demonstrated by comparing parallel FIMS and SMPS measurements of stable aerosols with a wide range of size spectrum shapes, including ambient aerosols and aerosols classified by a differential mobility analyzer (DMA). The FIMS and SMPS-derived size distributions show excellent agreements for all aerosols tested. In addition, total number concentrations of ambient aerosols were integrated from 1 Hz FIMS size distributions, and compared with those directly measured by a condensation particle counter (CPC) operated in parallel. Finally, the integrated and measured total particle concentrations agree well within 5%.« less

Rapid measurement of sub-micrometer aerosol size distribution using a fast integrated mobility spectrometer

DOE PAGES

Wang, Yang; Pinterich, Tamara; Wang, Jian

2018-03-30

We present rapid measurement of submicron particle size distributions enables the characterization of aerosols with fast changing properties, and is often necessary for measurements onboard mobile platforms (e.g., research aircraft). Aerosol mobility size distribution is commonly measured by a scanning mobility particle sizer (SMPS), which relies on voltage scanning or stepping to classify particles of different sizes, and may take up to several minutes to obtain a complete size spectrum of aerosol particles. The recently developed fast integrated mobility spectrometer (FIMS) with enhanced dynamic size range classifies and detects particles from 10 to ~600 nm simultaneously, allowing submicron aerosol mobilitymore » size distributions to be captured at a time resolution of 1 second. In this study, we present a detailed data inversion routine for deriving aerosol size distribution from FIMS measurements. The inversion routine takes into consideration the FIMS transfer function, particle penetration efficiency in the FIMS, and multiple charging of aerosols. The accuracy of the FIMS measurement is demonstrated by comparing parallel FIMS and SMPS measurements of stable aerosols with a wide range of size spectrum shapes, including ambient aerosols and aerosols classified by a differential mobility analyzer (DMA). The FIMS and SMPS-derived size distributions show excellent agreements for all aerosols tested. In addition, total number concentrations of ambient aerosols were integrated from 1 Hz FIMS size distributions, and compared with those directly measured by a condensation particle counter (CPC) operated in parallel. Finally, the integrated and measured total particle concentrations agree well within 5%.« less

Varying behavior of different window sizes on the classification of static and dynamic physical activities from a single accelerometer.

PubMed

Fida, Benish; Bernabucci, Ivan; Bibbo, Daniele; Conforto, Silvia; Schmid, Maurizio

2015-07-01

Accuracy of systems able to recognize in real time daily living activities heavily depends on the processing step for signal segmentation. So far, windowing approaches are used to segment data and the window size is usually chosen based on previous studies. However, literature is vague on the investigation of its effect on the obtained activity recognition accuracy, if both short and long duration activities are considered. In this work, we present the impact of window size on the recognition of daily living activities, where transitions between different activities are also taken into account. The study was conducted on nine participants who wore a tri-axial accelerometer on their waist and performed some short (sitting, standing, and transitions between activities) and long (walking, stair descending and stair ascending) duration activities. Five different classifiers were tested, and among the different window sizes, it was found that 1.5 s window size represents the best trade-off in recognition among activities, with an obtained accuracy well above 90%. Differences in recognition accuracy for each activity highlight the utility of developing adaptive segmentation criteria, based on the duration of the activities. Copyright © 2015 IPEM. Published by Elsevier Ltd. All rights reserved.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-01

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory.

PubMed

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-13

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Quantifying sediment dynamics on alluvial fans, Iglesia basin, south Central Argentine Andes

NASA Astrophysics Data System (ADS)

Harries, Rebekah; Kirstein, Linda; Whittaker, Alex; Attal, Mikael; Peralta, Silvio

2017-04-01

Qualitative interpretations of environmental change drawn from alluvial fan stratigraphy typically tie the deposition of greater volumes of coarser sediment to wetter climatic periods. For example, step changes in sediment flux and discharge associated with glacial-interglacial cycles are often linked to the progradation and back stepping of a fan's toe (Harvey et al, 2002). Indeed, more recent quantitative stratigraphic models demonstrate changes in the volume and calibre of sediment fluxed from an uplifted catchment can produce predictable shifts in the rate at which fluvial deposits fine downstream (Duller et al. 2010, Armitage et al. 2011). These interpretations, however, make three important assumptions: 1) the volume and calibre of the sediment transferred from an eroding mountain belt to a depositional basin is directly related to climate through some value of time-averaged discharge or catchment wetness; 2) lateral sources of sediment, such as tributaries, do not significantly influence the pattern of deposition in a basin and, similarly, 3) the reworking of older fan surfaces is minimal and does not impact the depositional pattern of younger deposits. Here we demonstrate each of these assumptions underestimates the importance of variance in transportable grain sizes in influencing the local and basin-wide deposited grain size trends. Using the Iglesia basin in the Argentine south Central Andes as a natural laboratory, we compare three large, adjacent, alluvial fan systems whose catchments experience the same background tectonic and climatic forcing. We find regional climate forcing is not expressed uniformly in the downstream grain size fining rates of their modern systems. Furthermore, we observe the variance in transportable grain sizes supplied from each primary catchment and the variance of material introduced by tributaries and fan surfaces downstream can act as first order controls on the rate of downstream fining. We also raise the importance of considering factors such as climate storminess and degree of glacial cover in having a dominant control on the variance of sediment released. These findings have significant implications for our ability to invert the fluvial stratigraphy for climatically driven changes in discharge and highlight a need to quantify the impact of sediment dynamics on modern systems so that we may better understand the limitations in applying quantitative models to ancient stratigraphy.

Dependence of Hurricane intensity and structures on vertical resolution and time-step size

NASA Astrophysics Data System (ADS)

Zhang, Da-Lin; Wang, Xiaoxue

2003-09-01

In view of the growing interests in the explicit modeling of clouds and precipitation, the effects of varying vertical resolution and time-step sizes on the 72-h explicit simulation of Hurricane Andrew (1992) are studied using the Pennsylvania State University/National Center for Atmospheric Research (PSU/NCAR) mesoscale model (i.e., MM5) with the finest grid size of 6 km. It is shown that changing vertical resolution and time-step size has significant effects on hurricane intensity and inner-core cloud/precipitation, but little impact on the hurricane track. In general, increasing vertical resolution tends to produce a deeper storm with lower central pressure and stronger three-dimensional winds, and more precipitation. Similar effects, but to a less extent, occur when the time-step size is reduced. It is found that increasing the low-level vertical resolution is more efficient in intensifying a hurricane, whereas changing the upper-level vertical resolution has little impact on the hurricane intensity. Moreover, the use of a thicker surface layer tends to produce higher maximum surface winds. It is concluded that the use of higher vertical resolution, a thin surface layer, and smaller time-step sizes, along with higher horizontal resolution, is desirable to model more realistically the intensity and inner-core structures and evolution of tropical storms as well as the other convectively driven weather systems.

Event- and Time-Driven Techniques Using Parallel CPU-GPU Co-processing for Spiking Neural Networks

PubMed Central

Naveros, Francisco; Garrido, Jesus A.; Carrillo, Richard R.; Ros, Eduardo; Luque, Niceto R.

2017-01-01

Modeling and simulating the neural structures which make up our central neural system is instrumental for deciphering the computational neural cues beneath. Higher levels of biological plausibility usually impose higher levels of complexity in mathematical modeling, from neural to behavioral levels. This paper focuses on overcoming the simulation problems (accuracy and performance) derived from using higher levels of mathematical complexity at a neural level. This study proposes different techniques for simulating neural models that hold incremental levels of mathematical complexity: leaky integrate-and-fire (LIF), adaptive exponential integrate-and-fire (AdEx), and Hodgkin-Huxley (HH) neural models (ranged from low to high neural complexity). The studied techniques are classified into two main families depending on how the neural-model dynamic evaluation is computed: the event-driven or the time-driven families. Whilst event-driven techniques pre-compile and store the neural dynamics within look-up tables, time-driven techniques compute the neural dynamics iteratively during the simulation time. We propose two modifications for the event-driven family: a look-up table recombination to better cope with the incremental neural complexity together with a better handling of the synchronous input activity. Regarding the time-driven family, we propose a modification in computing the neural dynamics: the bi-fixed-step integration method. This method automatically adjusts the simulation step size to better cope with the stiffness of the neural model dynamics running in CPU platforms. One version of this method is also implemented for hybrid CPU-GPU platforms. Finally, we analyze how the performance and accuracy of these modifications evolve with increasing levels of neural complexity. We also demonstrate how the proposed modifications which constitute the main contribution of this study systematically outperform the traditional event- and time-driven techniques under increasing levels of neural complexity. PMID:28223930

Evaluation of rheological behavior of 10W40 lubricant containing hybrid nano-material by measuring dynamic viscosity

NASA Astrophysics Data System (ADS)

Ahmadi Nadooshan, Afshin; Hemmat Esfe, Mohammad; Afrand, Masoud

2017-08-01

In the present paper, the dynamic viscosity of 10W40 lubricant containing hybrid nano-materials has been examined. Hybrid nano-materials were composed of 90% of silica (SiO2) with 20-30 nm mean particle size and 10% of multi-walled carbon nanotubes (MWCNTs) with inner diameter of 2-6 nm and outer diameter of 5-20 nm. Nano-lubricant samples were prepared by two-step method with solid volume fractions of 0.05%, 0.1%, 0.25%, 0.5%, 0.75% and 1%. Dynamic viscosity of the samples was measured at temperatures between 5 and 55 °C and at shear rates of 666.5 s-1 up to 11,997 s-1. Experimental results indicated that the nano-lubricant had non-Newtonian behavior at all temperatures, while 10w40 oil was non-Newtonian only at high temperatures. With the use of the curve fitting technique of experimental data, power law and consistency indexes were obtained; furthermore, these coefficients were assessed by shear stress and viscosity diagram.

Frequency-dependent hydrodynamic interaction between two solid spheres

NASA Astrophysics Data System (ADS)

Jung, Gerhard; Schmid, Friederike

2017-12-01

Hydrodynamic interactions play an important role in many areas of soft matter science. In simulations with implicit solvent, various techniques such as Brownian or Stokesian dynamics explicitly include hydrodynamic interactions a posteriori by using hydrodynamic diffusion tensors derived from the Stokes equation. However, this equation assumes the interaction to be instantaneous which is an idealized approximation and only valid on long time scales. In the present paper, we go one step further and analyze the time-dependence of hydrodynamic interactions between finite-sized particles in a compressible fluid on the basis of the linearized Navier-Stokes equation. The theoretical results show that at high frequencies, the compressibility of the fluid has a significant impact on the frequency-dependent pair interactions. The predictions of hydrodynamic theory are compared to molecular dynamics simulations of two nanocolloids in a Lennard-Jones fluid. For this system, we reconstruct memory functions by extending the inverse Volterra technique. The simulation data agree very well with the theory, therefore, the theory can be used to implement dynamically consistent hydrodynamic interactions in the increasingly popular field of non-Markovian modeling.

Development of high-productivity, strong cation-exchange adsorbers for protein capture by graft polymerization from membranes with different pore sizes

PubMed Central

Chenette, Heather C.S.; Robinson, Julie R.; Hobley, Eboni; Husson, Scott M.

2012-01-01

This paper describes the surface modification of macroporous membranes using ATRP (atom transfer radical polymerization) to create cation-exchange adsorbers with high protein binding capacity at high product throughput. The work is motivated by the need for a more economical and rapid capture step in downstream processing of protein therapeutics. Membranes with three reported nominal pore sizes (0.2, 0.45, 1.0 μm) were modified with poly(3-sulfopropyl methacrylate, potassium salt) tentacles, to create a high density of protein binding sites. A special formulation was used in which the monomer was protected by a crown ether to enable surface-initiated ATRP of this cationic polyelectrolyte. Success with modification was supported by chemical analysis using Fourier-transform infrared spectroscopy and indirectly by measurement of pure water flux as a function of polymerization time. Uniformity of modification within the membranes was visualized with confocal laser scanning microscopy. Static and dynamic binding capacities were measured using lysozyme protein to allow comparisons with reported performance data for commercial cation-exchange materials. Dynamic binding capacities were measured for flow rates ranging from 13 to 109 column volumes (CV)/min. Results show that this unique ATRP formulation can be used to fabricate cation-exchange membrane adsorbers with dynamic binding capacities as high as 70 mg/mL at a throughput of 100 CV/min and unprecedented productivity of 300 mg/mL/min. PMID:23175597

Scalable and balanced dynamic hybrid data assimilation

NASA Astrophysics Data System (ADS)

Kauranne, Tuomo; Amour, Idrissa; Gunia, Martin; Kallio, Kari; Lepistö, Ahti; Koponen, Sampsa

2017-04-01

Scalability of complex weather forecasting suites is dependent on the technical tools available for implementing highly parallel computational kernels, but to an equally large extent also on the dependence patterns between various components of the suite, such as observation processing, data assimilation and the forecast model. Scalability is a particular challenge for 4D variational assimilation methods that necessarily couple the forecast model into the assimilation process and subject this combination to an inherently serial quasi-Newton minimization process. Ensemble based assimilation methods are naturally more parallel, but large models force ensemble sizes to be small and that results in poor assimilation accuracy, somewhat akin to shooting with a shotgun in a million-dimensional space. The Variational Ensemble Kalman Filter (VEnKF) is an ensemble method that can attain the accuracy of 4D variational data assimilation with a small ensemble size. It achieves this by processing a Gaussian approximation of the current error covariance distribution, instead of a set of ensemble members, analogously to the Extended Kalman Filter EKF. Ensemble members are re-sampled every time a new set of observations is processed from a new approximation of that Gaussian distribution which makes VEnKF a dynamic assimilation method. After this a smoothing step is applied that turns VEnKF into a dynamic Variational Ensemble Kalman Smoother VEnKS. In this smoothing step, the same process is iterated with frequent re-sampling of the ensemble but now using past iterations as surrogate observations until the end result is a smooth and balanced model trajectory. In principle, VEnKF could suffer from similar scalability issues as 4D-Var. However, this can be avoided by isolating the forecast model completely from the minimization process by implementing the latter as a wrapper code whose only link to the model is calling for many parallel and totally independent model runs, all of them implemented as parallel model runs themselves. The only bottleneck in the process is the gathering and scattering of initial and final model state snapshots before and after the parallel runs which requires a very efficient and low-latency communication network. However, the volume of data communicated is small and the intervening minimization steps are only 3D-Var, which means their computational load is negligible compared with the fully parallel model runs. We present example results of scalable VEnKF with the 4D lake and shallow sea model COHERENS, assimilating simultaneously continuous in situ measurements in a single point and infrequent satellite images that cover a whole lake, with the fully scalable VEnKF.

Flight test of a synthetic aperture radar antenna using STEP

NASA Technical Reports Server (NTRS)

Zimcik, D. G.; Vigeron, F. R.; Ahmed, S.

1984-01-01

To establish confidence in its overall performance, credible information on the synthetic aperture radar antenna's mechanical properties in orbit must be obtained. However, the antenna's size, design, and operating environment make it difficult to simulate operating conditions under 1-g Earth conditions. The Space Technology Experiments Platform (STEP) offers a timely opportunity to mechanically qualify and characterize the antenna design in a representative environment. The proposed experimental configuration would employ a half-system of the full-scale RADARSAT antenna which would be mounted on the STEP platform in the orbiter cargo bay such that it could be deployed and retracted in orbit (as shown in this figure). The antenna would be subjected to typical environmental exposures while an array of targets and sensors on the antenna support structure and reflecting surface are observed and monitored. In particular, the typical environments would include deployment and retraction, dynamic response to vehicle thruster or base exciter inputs, and thermal soak and transient effects upon entering or exiting Earth eclipse. The proposed experiment would also provide generic information on the properties of large space structures in space and on techniques to obtain the desired information.

Flow resistance dynamics in step‐pool stream channels: 1. Large woody debris and controls on total resistance

USGS Publications Warehouse

Wilcox, Andrew C.; Wohl, Ellen E.

2006-01-01

Flow resistance dynamics in step‐pool channels were investigated through physical modeling using a laboratory flume. Variables contributing to flow resistance in step‐pool channels were manipulated in order to measure the effects of various large woody debris (LWD) configurations, steps, grains, discharge, and slope on total flow resistance. This entailed nearly 400 flume runs, organized into a series of factorial experiments. Factorial analyses of variance indicated significant two‐way and three‐way interaction effects between steps, grains, and LWD, illustrating the complexity of flow resistance in these channels. Interactions between steps and LWD resulted in substantially greater flow resistance for steps with LWD than for steps lacking LWD. LWD position contributed to these interactions, whereby LWD pieces located near the lip of steps, analogous to step‐forming debris in natural channels, increased the effective height of steps and created substantially higher flow resistance than pieces located farther upstream on step treads. Step geometry and LWD density and orientation also had highly significant effects on flow resistance. Flow resistance dynamics and the resistance effect of bed roughness configurations were strongly discharge‐dependent; discharge had both highly significant main effects on resistance and highly significant interactions with all other variables.

Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

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

White, Alexander J.; Center for Nonlinear Studies; Gorshkov, Vyacheslav N.

2014-11-14

Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantummore » mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement.« less

Criticality in conserved dynamical systems: experimental observation vs. exact properties.

PubMed

Marković, Dimitrije; Gros, Claudius; Schuelein, André

2013-03-01

Conserved dynamical systems are generally considered to be critical. We study a class of critical routing models, equivalent to random maps, which can be solved rigorously in the thermodynamic limit. The information flow is conserved for these routing models and governed by cyclic attractors. We consider two classes of information flow, Markovian routing without memory and vertex routing involving a one-step routing memory. Investigating the respective cycle length distributions for complete graphs, we find log corrections to power-law scaling for the mean cycle length, as a function of the number of vertices, and a sub-polynomial growth for the overall number of cycles. When observing experimentally a real-world dynamical system one normally samples stochastically its phase space. The number and the length of the attractors are then weighted by the size of their respective basins of attraction. This situation is equivalent, for theory studies, to "on the fly" generation of the dynamical transition probabilities. For the case of vertex routing models, we find in this case power law scaling for the weighted average length of attractors, for both conserved routing models. These results show that the critical dynamical systems are generically not scale-invariant but may show power-law scaling when sampled stochastically. It is hence important to distinguish between intrinsic properties of a critical dynamical system and its behavior that one would observe when randomly probing its phase space.

Regulation of DNA conformations and dynamics in flows with hybrid field microfluidics.

PubMed

Ren, Fangfang; Zu, Yingbo; Kumar Rajagopalan, Kartik; Wang, Shengnian

2012-01-01

Visualizing single DNA dynamics in flow provides a wealth of physical insights in biophysics and complex flow study. However, large signal fluctuations, generated from diversified conformations, deformation history dependent dynamics and flow induced stochastic tumbling, often frustrate its wide adoption in single molecule and polymer flow study. We use a hybrid field microfluidic (HFM) approach, in which an electric field is imposed at desired locations and appropriate moments to balance the flow stress on charged molecules, to effectively regulate the initial conformations and the deformation dynamics of macromolecules in flow. With λ-DNA and a steady laminar shear flow as the model system, we herein studied the performance of HFM on regulating DNA trapping, relaxation, coil-stretch transition, and accumulation. DNA molecules were found to get captured in the focused planes when motions caused by flow, and the electric field were balanced. The trapped macromolecules relaxed in two different routes while eventually became more uniform in size and globule conformations. When removing the electric field, the sudden stretching dynamics of DNA molecules exhibited a more pronounced extension overshoot in their transient response under a true step function of flow stress while similar behaviors to what other pioneering work in steady shear flow. Such regulation strategies could be useful to control the conformations of other important macromolecules (e.g., proteins) and help better reveal their molecular dynamics.

Comparison of two integration methods for dynamic causal modeling of electrophysiological data.

PubMed

Lemaréchal, Jean-Didier; George, Nathalie; David, Olivier

2018-06-01

Dynamic causal modeling (DCM) is a methodological approach to study effective connectivity among brain regions. Based on a set of observations and a biophysical model of brain interactions, DCM uses a Bayesian framework to estimate the posterior distribution of the free parameters of the model (e.g. modulation of connectivity) and infer architectural properties of the most plausible model (i.e. model selection). When modeling electrophysiological event-related responses, the estimation of the model relies on the integration of the system of delay differential equations (DDEs) that describe the dynamics of the system. In this technical note, we compared two numerical schemes for the integration of DDEs. The first, and standard, scheme approximates the DDEs (more precisely, the state of the system, with respect to conduction delays among brain regions) using ordinary differential equations (ODEs) and solves it with a fixed step size. The second scheme uses a dedicated DDEs solver with adaptive step sizes to control error, making it theoretically more accurate. To highlight the effects of the approximation used by the first integration scheme in regard to parameter estimation and Bayesian model selection, we performed simulations of local field potentials using first, a simple model comprising 2 regions and second, a more complex model comprising 6 regions. In these simulations, the second integration scheme served as the standard to which the first one was compared. Then, the performances of the two integration schemes were directly compared by fitting a public mismatch negativity EEG dataset with different models. The simulations revealed that the use of the standard DCM integration scheme was acceptable for Bayesian model selection but underestimated the connectivity parameters and did not allow an accurate estimation of conduction delays. Fitting to empirical data showed that the models systematically obtained an increased accuracy when using the second integration scheme. We conclude that inference on connectivity strength and delay based on DCM for EEG/MEG requires an accurate integration scheme. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

The Relaxation of Vicinal (001) with ZigZag [110] Steps

NASA Astrophysics Data System (ADS)

Hawkins, Micah; Hamouda, Ajmi Bh; González-Cabrera, Diego Luis; Einstein, Theodore L.

2012-02-01

This talk presents a kinetic Monte Carlo study of the relaxation dynamics of [110] steps on a vicinal (001) simple cubic surface. This system is interesting because [110] steps have different elementary excitation energetics and favor step diffusion more than close-packed [100] steps. In this talk we show how this leads to relaxation dynamics showing greater fluctuations on a shorter time scale for [110] steps as well as 2-bond breaking processes being rate determining in contrast to 3-bond breaking processes for [100] steps. The existence of a steady state is shown via the convergence of terrace width distributions at times much longer than the relaxation time. In this time regime excellent fits to the modified generalized Wigner distribution (as well as to the Berry-Robnik model when steps can overlap) were obtained. Also, step-position correlation function data show diffusion-limited increase for small distances along the step as well as greater average step displacement for zigzag steps compared to straight steps for somewhat longer distances along the step. Work supported by NSF-MRSEC Grant DMR 05-20471 as well as a DOE-CMCSN Grant.

Temporal variability and memory in sediment transport in an experimental step-pool channel

NASA Astrophysics Data System (ADS)

Saletti, Matteo; Molnar, Peter; Zimmermann, André; Hassan, Marwan A.; Church, Michael

2015-11-01

Temporal dynamics of sediment transport in steep channels using two experiments performed in a steep flume (8%) with natural sediment composed of 12 grain sizes are studied. High-resolution (1 s) time series of sediment transport were measured for individual grain-size classes at the outlet of the flume for different combinations of sediment input rates and flow discharges. Our aim in this paper is to quantify (a) the relation of discharge and sediment transport and (b) the nature and strength of memory in grain-size-dependent transport. None of the simple statistical descriptors of sediment transport (mean, extreme values, and quantiles) display a clear relation with water discharge, in fact a large variability between discharge and sediment transport is observed. Instantaneous transport rates have probability density functions with heavy tails. Bed load bursts have a coarser grain-size distribution than that of the entire experiment. We quantify the strength and nature of memory in sediment transport rates by estimating the Hurst exponent and the autocorrelation coefficient of the time series for different grain sizes. Our results show the presence of the Hurst phenomenon in transport rates, indicating long-term memory which is grain-size dependent. The short-term memory in coarse grain transport increases with temporal aggregation and this reveals the importance of the sampling duration of bed load transport rates in natural streams, especially for large fractions.

A new theory for multistep discretizations of stiff ordinary differential equations: Stability with large step sizes

NASA Technical Reports Server (NTRS)

Majda, G.

1985-01-01

A large set of variable coefficient linear systems of ordinary differential equations which possess two different time scales, a slow one and a fast one is considered. A small parameter epsilon characterizes the stiffness of these systems. A system of o.d.e.s. in this set is approximated by a general class of multistep discretizations which includes both one-leg and linear multistep methods. Sufficient conditions are determined under which each solution of a multistep method is uniformly bounded, with a bound which is independent of the stiffness of the system of o.d.e.s., when the step size resolves the slow time scale, but not the fast one. This property is called stability with large step sizes. The theory presented lets one compare properties of one-leg methods and linear multistep methods when they approximate variable coefficient systems of stiff o.d.e.s. In particular, it is shown that one-leg methods have better stability properties with large step sizes than their linear multistep counter parts. The theory also allows one to relate the concept of D-stability to the usual notions of stability and stability domains and to the propagation of errors for multistep methods which use large step sizes.

Dust-Particle Transport in Tokamak Edge Plasmas

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

Pigarov, A Y; Krasheninnikov, S I; Soboleva, T K

2005-09-12

Dust particulates in the size range of 10nm-100{micro}m are found in all fusion devices. Such dust can be generated during tokamak operation due to strong plasma/material-surface interactions. Some recent experiments and theoretical estimates indicate that dust particles can provide an important source of impurities in the tokamak plasma. Moreover, dust can be a serious threat to the safety of next-step fusion devices. In this paper, recent experimental observations on dust in fusion devices are reviewed. A physical model for dust transport simulation, and a newly developed code DUSTT, are discussed. The DUSTT code incorporates both dust dynamics due to comprehensivemore » dust-plasma interactions as well as the effects of dust heating, charging, and evaporation. The code tracks test dust particles in realistic plasma backgrounds as provided by edge-plasma transport codes. Results are presented for dust transport in current and next-step tokamaks. The effect of dust on divertor plasma profiles and core plasma contamination is examined.« less

Towards Cluster-Assembled Materials of True Monodispersity in Size and Chemical Environment: Synthesis, Dynamics and Activity

DTIC Science & Technology

2016-10-27

AFRL-AFOSR-UK-TR-2016-0037 Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and...Towards cluster-assembled materials of true monodispersity in size and chemical environment: synthesis, dynamics and activity 5a.  CONTRACT NUMBER 5b...report Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and Activity Ulrich Heiz

Conformational Dynamics Guides Coherent Exciton Migration in Conjugated Polymer Materials: First-Principles Quantum Dynamical Study

NASA Astrophysics Data System (ADS)

Binder, Robert; Lauvergnat, David; Burghardt, Irene

2018-06-01

We report on high-dimensional quantum dynamical simulations of photoinduced exciton migration in a single-chain oligothiophene segment, in view of elucidating the controversial nature of the elementary exciton transport steps in semiconducting polymers. A novel first-principles parametrized Frenkel J aggregate Hamiltonian is employed that goes significantly beyond the standard Frenkel-Holstein Hamiltonian. Departing from a nonequilibrium state created by photoexcitation, these simulations provide evidence of an ultrafast two-timescale process at low temperatures, involving exciton-polaron formation within tens of femtoseconds (fs), followed by torsional relaxation on an ˜400 fs timescale. The second step is the driving force for exciton migration, as initial conjugation breaks are removed by dynamical planarization. The quantum coherent nature of the elementary exciton migration step is consistent with experimental observations highlighting the correlated and vibrationally coherent nature of the dynamics on ultrafast timescales.

Conformational Dynamics Guides Coherent Exciton Migration in Conjugated Polymer Materials: First-Principles Quantum Dynamical Study.

PubMed

Binder, Robert; Lauvergnat, David; Burghardt, Irene

2018-06-01

We report on high-dimensional quantum dynamical simulations of photoinduced exciton migration in a single-chain oligothiophene segment, in view of elucidating the controversial nature of the elementary exciton transport steps in semiconducting polymers. A novel first-principles parametrized Frenkel J aggregate Hamiltonian is employed that goes significantly beyond the standard Frenkel-Holstein Hamiltonian. Departing from a nonequilibrium state created by photoexcitation, these simulations provide evidence of an ultrafast two-timescale process at low temperatures, involving exciton-polaron formation within tens of femtoseconds (fs), followed by torsional relaxation on an ∼400  fs timescale. The second step is the driving force for exciton migration, as initial conjugation breaks are removed by dynamical planarization. The quantum coherent nature of the elementary exciton migration step is consistent with experimental observations highlighting the correlated and vibrationally coherent nature of the dynamics on ultrafast timescales.

Thermal lattice BGK models for fluid dynamics

NASA Astrophysics Data System (ADS)

Huang, Jian

1998-11-01

As an alternative in modeling fluid dynamics, the Lattice Boltzmann method has attracted considerable attention. In this thesis, we shall present a general form of thermal Lattice BGK. This form can handle large differences in density, temperature, and high Mach number. This generalized method can easily model gases with different adiabatic index values. The numerical transport coefficients of this model are estimated both theoretically and numerically. Their dependency on the sizes of integration steps in time and space, and on the flow velocity and temperature, are studied and compared with other established CFD methods. This study shows that the numerical viscosity of the Lattice Boltzmann method depends linearly on the space interval, and on the flow velocity as well for supersonic flow. This indicates this method's limitation in modeling high Reynolds number compressible thermal flow. On the other hand, the Lattice Boltzmann method shows promise in modeling micro-flows, i.e., gas flows in micron-sized devices. A two-dimensional code has been developed based on the conventional thermal lattice BGK model, with some modifications and extensions for micro- flows and wall-fluid interactions. Pressure-driven micro- channel flow has been simulated. Results are compared with experiments and simulations using other methods, such as a spectral element code using slip boundary condition with Navier-Stokes equations and a Direct Simulation Monte Carlo (DSMC) method.

A Life-Cycle Model of Human Social Groups Produces a U-Shaped Distribution in Group Size.

PubMed

Salali, Gul Deniz; Whitehouse, Harvey; Hochberg, Michael E

2015-01-01

One of the central puzzles in the study of sociocultural evolution is how and why transitions from small-scale human groups to large-scale, hierarchically more complex ones occurred. Here we develop a spatially explicit agent-based model as a first step towards understanding the ecological dynamics of small and large-scale human groups. By analogy with the interactions between single-celled and multicellular organisms, we build a theory of group lifecycles as an emergent property of single cell demographic and expansion behaviours. We find that once the transition from small-scale to large-scale groups occurs, a few large-scale groups continue expanding while small-scale groups gradually become scarcer, and large-scale groups become larger in size and fewer in number over time. Demographic and expansion behaviours of groups are largely influenced by the distribution and availability of resources. Our results conform to a pattern of human political change in which religions and nation states come to be represented by a few large units and many smaller ones. Future enhancements of the model should include decision-making rules and probabilities of fragmentation for large-scale societies. We suggest that the synthesis of population ecology and social evolution will generate increasingly plausible models of human group dynamics.

A Life-Cycle Model of Human Social Groups Produces a U-Shaped Distribution in Group Size

PubMed Central

Salali, Gul Deniz; Whitehouse, Harvey; Hochberg, Michael E.

2015-01-01

One of the central puzzles in the study of sociocultural evolution is how and why transitions from small-scale human groups to large-scale, hierarchically more complex ones occurred. Here we develop a spatially explicit agent-based model as a first step towards understanding the ecological dynamics of small and large-scale human groups. By analogy with the interactions between single-celled and multicellular organisms, we build a theory of group lifecycles as an emergent property of single cell demographic and expansion behaviours. We find that once the transition from small-scale to large-scale groups occurs, a few large-scale groups continue expanding while small-scale groups gradually become scarcer, and large-scale groups become larger in size and fewer in number over time. Demographic and expansion behaviours of groups are largely influenced by the distribution and availability of resources. Our results conform to a pattern of human political change in which religions and nation states come to be represented by a few large units and many smaller ones. Future enhancements of the model should include decision-making rules and probabilities of fragmentation for large-scale societies. We suggest that the synthesis of population ecology and social evolution will generate increasingly plausible models of human group dynamics. PMID:26381745

Asymmetric phospholipid: lipopolysaccharide bilayers; a Gram-negative bacterial outer membrane mimic

PubMed Central

Clifton, Luke A.; Skoda, Maximilian W. A.; Daulton, Emma L.; Hughes, Arwel V.; Le Brun, Anton P.; Lakey, Jeremy H.; Holt, Stephen A.

2013-01-01

The Gram-negative bacterial outer membrane (OM) is a complex and highly asymmetric biological barrier but the small size of bacteria has hindered advances in in vivo examination of membrane dynamics. Thus, model OMs, amenable to physical study, are important sources of data. Here, we present data from asymmetric bilayers which emulate the OM and are formed by a simple two-step approach. The bilayers were deposited on an SiO2 surface by Langmuir–Blodgett deposition of phosphatidylcholine as the inner leaflet and, via Langmuir–Schaefer deposition, an outer leaflet of either Lipid A or Escherichia coli rough lipopolysaccharides (LPS). The membranes were examined using neutron reflectometry (NR) to examine the coverage and mixing of lipids between the bilayer leaflets. NR data showed that in all cases, the initial deposition asymmetry was mostly maintained for more than 16 h. This stability enabled the sizes of the headgroups and bilayer roughness of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and Lipid A, Rc-LPS and Ra-LPS to be clearly resolved. The results show that rough LPS can be manipulated like phospholipids and used to fabricate advanced asymmetric bacterial membrane models using well-known bilayer deposition techniques. Such models will enable OM dynamics and interactions to be studied under in vivo-like conditions. PMID:24132206

Analyzing multistep homogeneous nucleation in vapor-to-solid transitions using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tanaka, Kyoko K.; Diemand, Jürg; Tanaka, Hidekazu; Angélil, Raymond

2017-08-01

In this paper, we present multistep homogeneous nucleations in vapor-to-solid transitions as revealed by molecular dynamics simulations on Lennard-Jones molecules, where liquidlike clusters are created and crystallized. During a long, direct N V E (constant volume, energy, and number of molecules) involving the integration of (1.9 -15 )× 106 molecules in up to 200 million steps (=4.3 μ s ), crystallization in many large, supercooled nanoclusters is observed once the liquid clusters grow to a certain size (˜800 molecules for the case of T ≃0.5 ɛ /k ). In the simulations, we discovered an interesting process associated with crystallization: the solid clusters lost 2-5 % of their mass during crystallization at low temperatures below their melting temperatures. Although the crystallized clusters were heated by latent heat, they were stabilized by cooling due to evaporation. The clusters crystallized quickly and completely except at surface layers. However, they did not have stable crystal structures, rather they had metastable structures such as icosahedral, decahedral, face-centered-cubic-rich (fcc-rich), and hexagonal-close-packed-rich (hcp-rich). Several kinds of cluster structures coexisted in the same size range of ˜1000 -5000 molecules. Our results imply that multistep nucleation is a common first stage of condensation from vapor to solid.

Analysis of stability for stochastic delay integro-differential equations.

PubMed

Zhang, Yu; Li, Longsuo

2018-01-01

In this paper, we concern stability of numerical methods applied to stochastic delay integro-differential equations. For linear stochastic delay integro-differential equations, it is shown that the mean-square stability is derived by the split-step backward Euler method without any restriction on step-size, while the Euler-Maruyama method could reproduce the mean-square stability under a step-size constraint. We also confirm the mean-square stability of the split-step backward Euler method for nonlinear stochastic delay integro-differential equations. The numerical experiments further verify the theoretical results.

Pocket-Size Interferometric Systems

NASA Astrophysics Data System (ADS)

Waters, James P.; Fernald, Mark R.

1990-04-01

Optical sensors have the intrinsic advantages over electronic sensors of complete safety in hazardous areas and absolute immunity from both transmitting or picking up electromagnetic radiation. However, adoption of optical sensors in real-world applications requires a sensor design which has a sensitivity, resolution, and dynamic range comparable to an equivalent electronic sensor and at the same time must fulfill the practical considerations of small size and low cost. While sensitivity, resolution and dynamic range can be easily achieved with optical heterodyne sensors, the practical considerations make their near-term adoption unlikely. Significant improvements to optical heterodyne vibration and velocity sensors (flexibility, reliability and environmental immunity) have been realized with the use of semiconductor lasers, optical fibers and fiber-optic components. In fact, all of the discrete optical components in a heterodyne interferometer have been replaced with much smaller and more rugged devices except for the optical frequency shifter, acousto-optic modulator (AOM). The AOM and associated power supply, however, account for a substantial portion of both the size and cost. Previous work has shown that an integrated-optic, serrodyne phase modulator with an inexpensive drive circuit can be used for single sideband heterodyne detection. This paper describes the next step, design and implementation of a heterodyne interferometer using integrated-Optic technology to provide the polarization maintaining couplers and phase modulator. The couplers were made using a proton exchange process which produced devices with an extinction ratio of better than 40 dB. The serrodyne phase modulator had the advantage over an AOM of being considerably smaller and having a drive power of less than a milliwatt. The results of this work show that this technology is an effective way of reducing the size of the system and the cost of multiple units without sacarifying performance.

Surface effects on dynamic stability and loading during outdoor running using wireless trunk accelerometry.

PubMed

Schütte, Kurt H; Aeles, Jeroen; De Beéck, Tim Op; van der Zwaard, Babette C; Venter, Rachel; Vanwanseele, Benedicte

2016-07-01

Despite frequently declared benefits of using wireless accelerometers to assess running gait in real-world settings, available research is limited. The purpose of this study was to investigate outdoor surface effects on dynamic stability and dynamic loading during running using tri-axial trunk accelerometry. Twenty eight runners (11 highly-trained, 17 recreational) performed outdoor running on three outdoor training surfaces (concrete road, synthetic track and woodchip trail) at self-selected comfortable running speeds. Dynamic postural stability (tri-axial acceleration root mean square (RMS) ratio, step and stride regularity, sample entropy), dynamic loading (impact and breaking peak amplitudes and median frequencies), as well as spatio-temporal running gait measures (step frequency, stance time) were derived from trunk accelerations sampled at 1024Hz. Results from generalized estimating equations (GEE) analysis showed that compared to concrete road, woodchip trail had several significant effects on dynamic stability (higher AP ratio of acceleration RMS, lower ML inter-step and inter-stride regularity), on dynamic loading (downward shift in vertical and AP median frequency), and reduced step frequency (p<0.05). Surface effects were unaffected when both running level and running speed were added as potential confounders. Results suggest that woodchip trails disrupt aspects of dynamic stability and loading that are detectable using a single trunk accelerometer. These results provide further insight into how runners adapt their locomotor biomechanics on outdoor surfaces in situ. Copyright © 2016 Elsevier B.V. All rights reserved.

One-step formation of multiple Pickering emulsions stabilized by self-assembled poly(dodecyl acrylate-co-acrylic acid) nanoparticles.

PubMed

Zhu, Ye; Sun, Jianhua; Yi, Chenglin; Wei, Wei; Liu, Xiaoya

2016-09-13

In this study, a one-step generation of stable multiple Pickering emulsions using pH-responsive polymeric nanoparticles as the only emulsifier was reported. The polymeric nanoparticles were self-assembled from an amphiphilic random copolymer poly(dodecyl acrylate-co-acrylic acid) (PDAA), and the effect of the copolymer content on the size and morphology of PDAA nanoparticles was determined by dynamic light scattering (DLS) and transmission electron microscopy (TEM). The emulsification study of PDAA nanoparticles revealed that multiple Pickering emulsions could be generated through a one-step phase inversion process by using PDAA nanoparticles as the stabilizer. Moreover, the emulsification performance of PDAA nanoparticles at different pH values demonstrated that multiple emulsions with long-time stability could only be stabilized by PDAA nanoparticles at pH 5.5, indicating that the surface wettability of PDAA nanoparticles plays a crucial role in determining the type and stability of the prepared Pickering emulsions. Additionally, the polarity of oil does not affect the emulsification performance of PDAA nanoparticles, and a wide range of oils could be used as the oil phase to prepare multiple emulsions. These results demonstrated that multiple Pickering emulsions could be generated via the one-step emulsification process using self-assembled polymeric nanoparticles as the stabilizer, and the prepared multiple emulsions have promising potential to be applied in the cosmetic, medical, and food industries.

Operative air temperature data for different measures applied on a building envelope in warm climate.

PubMed

Baglivo, Cristina; Congedo, Paolo Maria

2018-04-01

Several technical combinations have been evaluated in order to design high energy performance buildings for the warm climate. The analysis has been developed in several steps, avoiding the use of HVAC systems. The methodological approach of this study is based on a sequential search technique and it is shown on the paper entitled "Envelope Design Optimization by Thermal Modeling of a Building in a Warm Climate" [1]. The Operative Air Temperature trends (TOP), for each combination, have been plotted through a dynamic simulation performed using the software TRNSYS 17 (a transient system simulation program, University of Wisconsin, Solar Energy Laboratory, USA, 2010). Starting from the simplest building configuration consisting of 9 rooms (equal-sized modules of 5 × 5 m 2 ), the different building components are sequentially evaluated until the envelope design is optimized. The aim of this study is to perform a step-by-step simulation, simplifying as much as possible the model without making additional variables that can modify their performances. Walls, slab-on-ground floor, roof, shading and windows are among the simulated building components. The results are shown for each combination and evaluated for Brindisi, a city in southern Italy having 1083 degrees day, belonging to the national climatic zone C. The data show the trends of the TOP for each measure applied in the case study for a total of 17 combinations divided into eight steps.

Constrained motion model of mobile robots and its applications.

PubMed

Zhang, Fei; Xi, Yugeng; Lin, Zongli; Chen, Weidong

2009-06-01

Target detecting and dynamic coverage are fundamental tasks in mobile robotics and represent two important features of mobile robots: mobility and perceptivity. This paper establishes the constrained motion model and sensor model of a mobile robot to represent these two features and defines the k -step reachable region to describe the states that the robot may reach. We show that the calculation of the k-step reachable region can be reduced from that of 2(k) reachable regions with the fixed motion styles to k + 1 such regions and provide an algorithm for its calculation. Based on the constrained motion model and the k -step reachable region, the problems associated with target detecting and dynamic coverage are formulated and solved. For target detecting, the k-step detectable region is used to describe the area that the robot may detect, and an algorithm for detecting a target and planning the optimal path is proposed. For dynamic coverage, the k-step detected region is used to represent the area that the robot has detected during its motion, and the dynamic-coverage strategy and algorithm are proposed. Simulation results demonstrate the efficiency of the coverage algorithm in both convex and concave environments.

Structures to Resist the Effects of Accidental Explosions. Volume 3. Principles of Dynamic Analysis

DTIC Science & Technology

1984-06-01

multi-degree-of-freedom systems) is presented. A step-by-step numerical integration of an element’s motion under dynamic loads using the...structural arrangements; providing closures, and preventing damage to interior portions of structures due to structual motion , shock, and fragment...an element’s motion under dynamic loads utilizing the Acceleration-Impulse- Extrapolation Method or the Average Acceleration Method and design charts

Modeling bed load transport and step-pool morphology with a reduced-complexity approach

NASA Astrophysics Data System (ADS)

Saletti, Matteo; Molnar, Peter; Hassan, Marwan A.; Burlando, Paolo

2016-04-01

Steep mountain channels are complex fluvial systems, where classical methods developed for lowland streams fail to capture the dynamics of sediment transport and bed morphology. Estimations of sediment transport based on average conditions have more than one order of magnitude of uncertainty because of the wide grain-size distribution of the bed material, the small relative submergence of coarse grains, the episodic character of sediment supply, and the complex boundary conditions. Most notably, bed load transport is modulated by the structure of the bed, where grains are imbricated in steps and similar bedforms and, therefore, they are much more stable then predicted. In this work we propose a new model based on a reduced-complexity (RC) approach focused on the reproduction of the step-pool morphology. In our 2-D cellular-automaton model entrainment, transport and deposition of particles are considered via intuitive rules based on physical principles. A parsimonious set of parameters allows the control of the behavior of the system, and the basic processes can be considered in a deterministic or stochastic way. The probability of entrainment of grains (and, as a consequence, particle travel distances and resting times) is a function of flow conditions and bed topography. Sediment input is fed at the upper boundary of the channel at a constant or variable rate. Our model yields realistic results in terms of longitudinal bed profiles and sediment transport trends. Phases of aggradation and degradation can be observed in the channel even under a constant input and the memory of the morphology can be quantified with long-range persistence indicators. Sediment yield at the channel outlet shows intermittency as observed in natural streams. Steps are self-formed in the channel and their stability is tested against the model parameters. Our results show the potential of RC models as complementary tools to more sophisticated models. They provide a realistic description of complex morphological systems and help to better identify the key physical principles that rule their dynamics.

Predator-prey-subsidy population dynamics on stepping-stone domains.

PubMed

Shen, Lulan; Van Gorder, Robert A

2017-05-07

Predator-prey-subsidy dynamics on stepping-stone domains are examined using a variety of network configurations. Our problem is motivated by the interactions between arctic foxes (predator) and lemmings (prey) in the presence of seal carrion (subsidy) provided by polar bears. We use the n-Patch Model, which considers space explicitly as a "Stepping Stone" system. We consider the role that the carrying capacity, predator migration rate, input subsidy rate, predator mortality rate, and proportion of predators surviving migration play in the predator-prey-subsidy population dynamics. We find that for certain types of networks, added mobility will help predator populations, allowing them to survive or coexist when they would otherwise go extinct if confined to one location, while in other situations (such as when sparsely distributed nodes in the network have few resources available) the added mobility will hurt the predator population. We also find that a combination of favourable conditions for the prey and subsidy can lead to the formation of limit cycles (boom and bust dynamic) from stable equilibrium states. These modifications to the dynamics vary depending on the specific network structure employed, highlighting the fact that network structure can strongly influence the predator-prey-subsidy dynamics in stepping-stone domains. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Wang, Shaobu; Lu, Shuai; Zhou, Ning

In interconnected power systems, dynamic model reduction can be applied on generators outside the area of interest to mitigate the computational cost with transient stability studies. This paper presents an approach of deriving the reduced dynamic model of the external area based on dynamic response measurements, which comprises of three steps, dynamic-feature extraction, attribution and reconstruction (DEAR). In the DEAR approach, a feature extraction technique, such as singular value decomposition (SVD), is applied to the measured generator dynamics after a disturbance. Characteristic generators are then identified in the feature attribution step for matching the extracted dynamic features with the highestmore » similarity, forming a suboptimal ‘basis’ of system dynamics. In the reconstruction step, generator state variables such as rotor angles and voltage magnitudes are approximated with a linear combination of the characteristic generators, resulting in a quasi-nonlinear reduced model of the original external system. Network model is un-changed in the DEAR method. Tests on several IEEE standard systems show that the proposed method gets better reduction ratio and response errors than the traditional coherency aggregation methods.« less

Modifications to WRF's dynamical core to improve the treatment of moisture for large-eddy simulations: WRF DY-CORE MOISTURE TREATMENT

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

Xiao, Heng; Endo, Satoshi; Wong, May

Yamaguchi and Feingold (2012) note that the cloud fields in their Weather Research and Forecasting (WRF) large-eddy simulations (LESs) of marine stratocumulus exhibit a strong sensitivity to time stepping choices. In this study, we reproduce and analyze this sensitivity issue using two stratocumulus cases, one marine and one continental. Results show that (1) the sensitivity is associated with spurious motions near the moisture jump between the boundary layer and the free atmosphere, and (2) these spurious motions appear to arise from neglecting small variations in water vapor mixing ratio (qv) in the pressure gradient calculation in the acoustic sub­stepping portionmore » of the integration procedure. We show that this issue is remedied in the WRF dynamical core by replacing the prognostic equation for the potential temperature θ with one for the moist potential temperature θm=θ(1+1.61qv), which allows consistent treatment of moisture in the calculation of pressure during the acoustic sub­steps. With this modification, the spurious motions and the sensitivity to the time stepping settings (i.e., the dynamic time step length and number of acoustic sub­steps) are eliminated in both of the example stratocumulus cases. This modification improves the applicability of WRF for LES applications, and possibly other models using similar dynamical core formulations, and also permits the use of longer time steps than in the original code.« less

Modifications to WRFs dynamical core to improve the treatment of moisture for large-eddy simulations

DOE PAGES

Xiao, Heng; Endo, Satoshi; Wong, May; ...

2015-10-29

Yamaguchi and Feingold (2012) note that the cloud fields in their large-eddy simulations (LESs) of marine stratocumulus using the Weather Research and Forecasting (WRF) model exhibit a strong sensitivity to time stepping choices. In this study, we reproduce and analyze this sensitivity issue using two stratocumulus cases, one marine and one continental. Results show that (1) the sensitivity is associated with spurious motions near the moisture jump between the boundary layer and the free atmosphere, and (2) these spurious motions appear to arise from neglecting small variations in water vapor mixing ratio (qv) in the pressure gradient calculation in themore » acoustic sub-stepping portion of the integration procedure. We show that this issue is remedied in the WRF dynamical core by replacing the prognostic equation for the potential temperature θ with one for the moist potential temperature θm=θ(1+1.61qv), which allows consistent treatment of moisture in the calculation of pressure during the acoustic sub-steps. With this modification, the spurious motions and the sensitivity to the time stepping settings (i.e., the dynamic time step length and number of acoustic sub-steps) are eliminated in both of the example stratocumulus cases. In conclusion, this modification improves the applicability of WRF for LES applications, and possibly other models using similar dynamical core formulations, and also permits the use of longer time steps than in the original code.« less

Process for preparation of large-particle-size monodisperse latexes

NASA Technical Reports Server (NTRS)

Vanderhoff, J. W.; Micale, F. J.; El-Aasser, M. S.; Kornfeld, D. M. (Inventor)

1981-01-01

Monodisperse latexes having a particle size in the range of 2 to 40 microns are prepared by seeded emulsion polymerization in microgravity. A reaction mixture containing smaller monodisperse latex seed particles, predetermined amounts of monomer, emulsifier, initiator, inhibitor and water is placed in a microgravity environment, and polymerization is initiated by heating. The reaction is allowed to continue until the seed particles grow to a predetermined size, and the resulting enlarged particles are then recovered. A plurality of particle-growing steps can be used to reach larger sizes within the stated range, with enlarge particles from the previous steps being used as seed particles for the succeeding steps. Microgravity enables preparation of particles in the stated size range by avoiding gravity related problems of creaming and settling, and flocculation induced by mechanical shear that have precluded their preparation in a normal gravity environment.

Constraints on Fluctuations in Sparsely Characterized Biological Systems.

PubMed

Hilfinger, Andreas; Norman, Thomas M; Vinnicombe, Glenn; Paulsson, Johan

2016-02-05

Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such "noise" is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.

Constraints on Fluctuations in Sparsely Characterized Biological Systems

NASA Astrophysics Data System (ADS)

Hilfinger, Andreas; Norman, Thomas M.; Vinnicombe, Glenn; Paulsson, Johan

2016-02-01

Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such "noise" is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.

High efficient perovskite solar cell material CH3NH3PbI3: Synthesis of films and their characterization

NASA Astrophysics Data System (ADS)

Bera, Amrita Mandal; Wargulski, Dan Ralf; Unold, Thomas

2018-04-01

Hybrid organometal perovskites have been emerged as promising solar cell material and have exhibited solar cell efficiency more than 20%. Thin films of Methylammonium lead iodide CH3NH3PbI3 perovskite materials have been synthesized by two different (one step and two steps) methods and their morphological properties have been studied by scanning electron microscopy and optical microscope imaging. The morphology of the perovskite layer is one of the most important parameters which affect solar cell efficiency. The morphology of the films revealed that two steps method provides better surface coverage than the one step method. However, the grain sizes were smaller in case of two steps method. The films prepared by two steps methods on different substrates revealed that the grain size also depend on the substrate where an increase of the grain size was found from glass substrate to FTO with TiO2 blocking layer to FTO without any change in the surface coverage area. Present study reveals that an improved quality of films can be obtained by two steps method by an optimization of synthesis processes.

Natural Gas Evolution in a Gas Hydrate Melt: Effect of Thermodynamic Hydrate Inhibitors.

PubMed

Sujith, K S; Ramachandran, C N

2017-01-12

Natural gas extraction from gas hydrate sediments by injection of hydrate inhibitors involves the decomposition of hydrates. The evolution of dissolved gas from the hydrate melt is an important step in the extraction process. Using classical molecular dynamics simulations, we study the evolution of dissolved methane from its hydrate melt in the presence of two thermodynamic hydrate inhibitors, NaCl and CH 3 OH. An increase in the concentration of hydrate inhibitors is found to promote the nucleation of methane nanobubbles in the hydrate melt. Whereas NaCl promotes bubble formation by enhancing the hydrophobic interaction between aqueous CH 4 molecules, CH 3 OH molecules assist bubble formation by stabilizing CH 4 bubble nuclei formed in the solution. The CH 3 OH molecules accumulate around the nuclei leading to a decrease in the surface tension at their interface with water. The nanobubbles formed are found to be highly dynamic with frequent exchange of CH 4 molecules between the bubble and the surrounding liquid. A quantitative analysis of the dynamic behavior of the bubble is performed by introducing a unit step function whose value depends on the location of CH 4 molecules with respect to the bubble. It is observed that an increase in the concentration of thermodynamic hydrate inhibitors reduces the exchange process, making the bubble less dynamic. It is also found that for a given concentration of the inhibitor, larger bubbles are less dynamic compared to smaller ones. The dependence of the dynamic nature of nanobubbles on bubble size and inhibitor concentration is correlated with the solubility of CH 4 and the Laplace pressure within the bubble. The effect of CO 2 on the formation of nanobubble in the CH 4 -CO 2 mixed gas hydrate melt in the presence of inhibitors is also examined. The simulations show that the presence of CO 2 molecules significantly reduces the induction time for methane nanobubble nucleation. The role of CO 2 in the early nucleation of bubble is explained based on the interaction between the bubble and the dissolved CO 2 molecules.

Global error estimation based on the tolerance proportionality for some adaptive Runge-Kutta codes

NASA Astrophysics Data System (ADS)

Calvo, M.; González-Pinto, S.; Montijano, J. I.

2008-09-01

Modern codes for the numerical solution of Initial Value Problems (IVPs) in ODEs are based in adaptive methods that, for a user supplied tolerance [delta], attempt to advance the integration selecting the size of each step so that some measure of the local error is [similar, equals][delta]. Although this policy does not ensure that the global errors are under the prescribed tolerance, after the early studies of Stetter [Considerations concerning a theory for ODE-solvers, in: R. Burlisch, R.D. Grigorieff, J. Schröder (Eds.), Numerical Treatment of Differential Equations, Proceedings of Oberwolfach, 1976, Lecture Notes in Mathematics, vol. 631, Springer, Berlin, 1978, pp. 188-200; Tolerance proportionality in ODE codes, in: R. März (Ed.), Proceedings of the Second Conference on Numerical Treatment of Ordinary Differential Equations, Humbold University, Berlin, 1980, pp. 109-123] and the extensions of Higham [Global error versus tolerance for explicit Runge-Kutta methods, IMA J. Numer. Anal. 11 (1991) 457-480; The tolerance proportionality of adaptive ODE solvers, J. Comput. Appl. Math. 45 (1993) 227-236; The reliability of standard local error control algorithms for initial value ordinary differential equations, in: Proceedings: The Quality of Numerical Software: Assessment and Enhancement, IFIP Series, Springer, Berlin, 1997], it has been proved that in many existing explicit Runge-Kutta codes the global errors behave asymptotically as some rational power of [delta]. This step-size policy, for a given IVP, determines at each grid point tn a new step-size hn+1=h(tn;[delta]) so that h(t;[delta]) is a continuous function of t. In this paper a study of the tolerance proportionality property under a discontinuous step-size policy that does not allow to change the size of the step if the step-size ratio between two consecutive steps is close to unity is carried out. This theory is applied to obtain global error estimations in a few problems that have been solved with the code Gauss2 [S. Gonzalez-Pinto, R. Rojas-Bello, Gauss2, a Fortran 90 code for second order initial value problems, ], based on an adaptive two stage Runge-Kutta-Gauss method with this discontinuous step-size policy.

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

PubMed Central

Luk, Louis Y. P.; Javier Ruiz-Pernía, J.; Dawson, William M.; Roca, Maite; Loveridge, E. Joel; Glowacki, David R.; Harvey, Jeremy N.; Mulholland, Adrian J.; Tuñón, Iñaki; Moliner, Vicent; Allemann, Rudolf K.

2013-01-01

Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy (15N, 13C, 2H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for “promoting motions” in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate. PMID:24065822

Mean-field theory of a plastic network of integrate-and-fire neurons.

PubMed

Chen, Chun-Chung; Jasnow, David

2010-01-01

We consider a noise-driven network of integrate-and-fire neurons. The network evolves as result of the activities of the neurons following spike-timing-dependent plasticity rules. We apply a self-consistent mean-field theory to the system to obtain the mean activity level for the system as a function of the mean synaptic weight, which predicts a first-order transition and hysteresis between a noise-dominated regime and a regime of persistent neural activity. Assuming Poisson firing statistics for the neurons, the plasticity dynamics of a synapse under the influence of the mean-field environment can be mapped to the dynamics of an asymmetric random walk in synaptic-weight space. Using a master equation for small steps, we predict a narrow distribution of synaptic weights that scales with the square root of the plasticity rate for the stationary state of the system given plausible physiological parameter values describing neural transmission and plasticity. The dependence of the distribution on the synaptic weight of the mean-field environment allows us to determine the mean synaptic weight self-consistently. The effect of fluctuations in the total synaptic conductance and plasticity step sizes are also considered. Such fluctuations result in a smoothing of the first-order transition for low number of afferent synapses per neuron and a broadening of the synaptic-weight distribution, respectively.

New cellular automaton designed to simulate geometration in gel electrophoresis

NASA Astrophysics Data System (ADS)

Krawczyk, M. J.; Kułakowski, K.; Maksymowicz, A. Z.

2002-08-01

We propose a new kind of cellular automaton to simulate transportation of molecules of DNA through agarose gel. Two processes are taken into account: reptation at strong electric field E, described in the particle model, and geometration, i.e. subsequent hookings and releases of long molecules at and from gel fibres. The automaton rules are deterministic and they are designed to describe both processes within one unified approach. Thermal fluctuations are not taken into account. The number of simultaneous hookings is limited by the molecule length. The features of the automaton are: (i) the size of the cell neighbourhood for the automaton rule varies dynamically, from nearest neighbors to the entire molecule; (ii) the length of the time step is determined at each step according to dynamic rules. Calculations are made up to N=244 reptons in a molecule. Two subsequent stages of the motion are found. Firstly, an initial set of random configurations of molecules is transformed into a more ordered phase, where most molecules are elongated along the applied field direction. After some transient time, the mobility μ reaches a constant value. Then, it varies with N as 1/ N for long molecules. The band dispersion varies with time t approximately as Nt1/2. Our results indicate that the well-known plateau of the mobility μ vs. N does not hold at large electric fields.

Evolution of Particle Size Distributions in Fragmentation Over Time

NASA Astrophysics Data System (ADS)

Charalambous, C. A.; Pike, W. T.

2013-12-01

We present a new model of fragmentation based on a probabilistic calculation of the repeated fracture of a particle population. The resulting continuous solution, which is in closed form, gives the evolution of fragmentation products from an initial block, through a scale-invariant power-law relationship to a final comminuted powder. Models for the fragmentation of particles have been developed separately in mainly two different disciplines: the continuous integro-differential equations of batch mineral grinding (Reid, 1965) and the fractal analysis of geophysics (Turcotte, 1986) based on a discrete model with a single probability of fracture. The first gives a time-dependent development of the particle-size distribution, but has resisted a closed-form solution, while the latter leads to the scale-invariant power laws, but with no time dependence. Bird (2009) recently introduced a bridge between these two approaches with a step-wise iterative calculation of the fragmentation products. The development of the particle-size distribution occurs with discrete steps: during each fragmentation event, the particles will repeatedly fracture probabilistically, cascading down the length scales to a final size distribution reached after all particles have failed to further fragment. We have identified this process as the equivalent to a sequence of trials for each particle with a fixed probability of fragmentation. Although the resulting distribution is discrete, it can be reformulated as a continuous distribution in maturity over time and particle size. In our model, Turcotte's power-law distribution emerges at a unique maturation index that defines a regime boundary. Up to this index, the fragmentation is in an erosional regime with the initial particle size setting the scaling. Fragmentation beyond this index is in a regime of comminution with rebreakage of the particles down to the size limit of fracture. The maturation index can increment continuously, for example under grinding conditions, or as discrete steps, such as with impact events. In both cases our model gives the energy associated with the fragmentation in terms of the developing surface area of the population. We show the agreement of our model to the evolution of particle size distributions associated with episodic and continuous fragmentation and how the evolution of some popular fractals may be represented using this approach. C. A. Charalambous and W. T. Pike (2013). Multi-Scale Particle Size Distributions of Mars, Moon and Itokawa based on a time-maturation dependent fragmentation model. Abstract Submitted to the AGU 46th Fall Meeting. Bird, N. R. A., Watts, C. W., Tarquis, A. M., & Whitmore, A. P. (2009). Modeling dynamic fragmentation of soil. Vadose Zone Journal, 8(1), 197-201. Reid, K. J. (1965). A solution to the batch grinding equation. Chemical Engineering Science, 20(11), 953-963. Turcotte, D. L. (1986). Fractals and fragmentation. Journal of Geophysical Research: Solid Earth 91(B2), 1921-1926.

[Influence on microstructure of dental zirconia ceramics prepared by two-step sintering].

PubMed

Jian, Chao; Li, Ning; Wu, Zhikai; Teng, Jing; Yan, Jiazhen

2013-10-01

To investigate the microstructure of dental zirconia ceramics prepared by two-step sintering. Nanostructured zirconia powder was dry compacted, cold isostatic pressed, and pre-sintered. The pre-sintered discs were cut processed into samples. Conventional sintering, single-step sintering, and two-step sintering were carried out, and density and grain size of the samples were measured. Afterward, T1 and/or T2 of two-step sintering ranges were measured. Effects on microstructure of different routes, which consisted of two-step sintering and conventional sintering were discussed. The influence of T1 and/or T2 on density and grain size were analyzed as well. The range of T1 was between 1450 degrees C and 1550 degrees C, and the range of T2 was between 1250 degrees C and 1350 degrees C. Compared with conventional sintering, finer microstructure of higher density and smaller grain could be obtained by two-step sintering. Grain growth was dependent on T1, whereas density was not much related with T1. However, density was dependent on T2, and grain size was minimally influenced. Two-step sintering could ensure a sintering body with high density and small grain, which is good for optimizing the microstructure of dental zirconia ceramics.

Surfactant-controlled polymerization of semiconductor clusters to quantum dots through competing step-growth and living chain-growth mechanisms.

PubMed

Evans, Christopher M; Love, Alyssa M; Weiss, Emily A

2012-10-17

This article reports control of the competition between step-growth and living chain-growth polymerization mechanisms in the formation of cadmium chalcogenide colloidal quantum dots (QDs) from CdSe(S) clusters by varying the concentration of anionic surfactant in the synthetic reaction mixture. The growth of the particles proceeds by step-addition from initially nucleated clusters in the absence of excess phosphinic or carboxylic acids, which adsorb as their anionic conjugate bases, and proceeds indirectly by dissolution of clusters, and subsequent chain-addition of monomers to stable clusters (Ostwald ripening) in the presence of excess phosphinic or carboxylic acid. Fusion of clusters by step-growth polymerization is an explanation for the consistent observation of so-called "magic-sized" clusters in QD growth reactions. Living chain-addition (chain addition with no explicit termination step) produces QDs over a larger range of sizes with better size dispersity than step-addition. Tuning the molar ratio of surfactant to Se(2-)(S(2-)), the limiting ionic reagent, within the living chain-addition polymerization allows for stoichiometric control of QD radius without relying on reaction time.

An Ecological Approach to Learning Dynamics

ERIC Educational Resources Information Center

Normak, Peeter; Pata, Kai; Kaipainen, Mauri

2012-01-01

New approaches to emergent learner-directed learning design can be strengthened with a theoretical framework that considers learning as a dynamic process. We propose an approach that models a learning process using a set of spatial concepts: learning space, position of a learner, niche, perspective, step, path, direction of a step and step…

SIVA/DIVA- INITIAL VALUE ORDINARY DIFFERENTIAL EQUATION SOLUTION VIA A VARIABLE ORDER ADAMS METHOD

NASA Technical Reports Server (NTRS)

Krogh, F. T.

1994-01-01

The SIVA/DIVA package is a collection of subroutines for the solution of ordinary differential equations. There are versions for single precision and double precision arithmetic. These solutions are applicable to stiff or nonstiff differential equations of first or second order. SIVA/DIVA requires fewer evaluations of derivatives than other variable order Adams predictor-corrector methods. There is an option for the direct integration of second order equations which can make integration of trajectory problems significantly more efficient. Other capabilities of SIVA/DIVA include: monitoring a user supplied function which can be separate from the derivative; dynamically controlling the step size; displaying or not displaying output at initial, final, and step size change points; saving the estimated local error; and reverse communication where subroutines return to the user for output or computation of derivatives instead of automatically performing calculations. The user must supply SIVA/DIVA with: 1) the number of equations; 2) initial values for the dependent and independent variables, integration stepsize, error tolerance, etc.; and 3) the driver program and operational parameters necessary for subroutine execution. SIVA/DIVA contains an extensive diagnostic message library should errors occur during execution. SIVA/DIVA is written in FORTRAN 77 for batch execution and is machine independent. It has a central memory requirement of approximately 120K of 8 bit bytes. This program was developed in 1983 and last updated in 1987.

Capturing Pressure Oscillations in Numerical Simulations of Internal Combustion Engines

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

Gubba, Sreenivasa Rao; Jupudi, Ravichandra S.; Pasunurthi, Shyam Sundar

In an earlier publication, the authors compared numerical predictions of the mean cylinder pressure of diesel and dual-fuel combustion, to that of measured pressure data from a medium-speed, large-bore engine. In these earlier comparisons, measured data from a flush-mounted in-cylinder pressure transducer showed notable and repeatable pressure oscillations which were not evident in the mean cylinder pressure predictions from computational fluid dynamics (CFD). In this paper, the authors present a methodology for predicting and reporting the local cylinder pressure consistent with that of a measurement location. Such predictions for large-bore, medium-speed engine operation demonstrate pressure oscillations in accordance with thosemore » measured. The temporal occurrences of notable pressure oscillations were during the start of combustion and around the time of maximum cylinder pressure. With appropriate resolutions in time steps and mesh sizes, the local cell static pressure predicted for the transducer location showed oscillations in both diesel and dual-fuel combustion modes which agreed with those observed in the experimental data. Fast Fourier transform (FFT) analysis on both experimental and calculated pressure traces revealed that the CFD predictions successfully captured both the amplitude and frequency range of the oscillations. Furthermore, resolving propagating pressure waves with the smaller time steps and grid sizes necessary to achieve these results required a significant increase in computer resources.« less

Computation of Sensitivity Derivatives of Navier-Stokes Equations using Complex Variables

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.

2004-01-01

Accurate computation of sensitivity derivatives is becoming an important item in Computational Fluid Dynamics (CFD) because of recent emphasis on using nonlinear CFD methods in aerodynamic design, optimization, stability and control related problems. Several techniques are available to compute gradients or sensitivity derivatives of desired flow quantities or cost functions with respect to selected independent (design) variables. Perhaps the most common and oldest method is to use straightforward finite-differences for the evaluation of sensitivity derivatives. Although very simple, this method is prone to errors associated with choice of step sizes and can be cumbersome for geometric variables. The cost per design variable for computing sensitivity derivatives with central differencing is at least equal to the cost of three full analyses, but is usually much larger in practice due to difficulty in choosing step sizes. Another approach gaining popularity is the use of Automatic Differentiation software (such as ADIFOR) to process the source code, which in turn can be used to evaluate the sensitivity derivatives of preselected functions with respect to chosen design variables. In principle, this approach is also very straightforward and quite promising. The main drawback is the large memory requirement because memory use increases linearly with the number of design variables. ADIFOR software can also be cumber-some for large CFD codes and has not yet reached a full maturity level for production codes, especially in parallel computing environments.

Capturing Pressure Oscillations in Numerical Simulations of Internal Combustion Engines

DOE PAGES

Gubba, Sreenivasa Rao; Jupudi, Ravichandra S.; Pasunurthi, Shyam Sundar; ...

2018-04-09

In an earlier publication, the authors compared numerical predictions of the mean cylinder pressure of diesel and dual-fuel combustion, to that of measured pressure data from a medium-speed, large-bore engine. In these earlier comparisons, measured data from a flush-mounted in-cylinder pressure transducer showed notable and repeatable pressure oscillations which were not evident in the mean cylinder pressure predictions from computational fluid dynamics (CFD). In this paper, the authors present a methodology for predicting and reporting the local cylinder pressure consistent with that of a measurement location. Such predictions for large-bore, medium-speed engine operation demonstrate pressure oscillations in accordance with thosemore » measured. The temporal occurrences of notable pressure oscillations were during the start of combustion and around the time of maximum cylinder pressure. With appropriate resolutions in time steps and mesh sizes, the local cell static pressure predicted for the transducer location showed oscillations in both diesel and dual-fuel combustion modes which agreed with those observed in the experimental data. Fast Fourier transform (FFT) analysis on both experimental and calculated pressure traces revealed that the CFD predictions successfully captured both the amplitude and frequency range of the oscillations. Furthermore, resolving propagating pressure waves with the smaller time steps and grid sizes necessary to achieve these results required a significant increase in computer resources.« less

Data analysis-based autonomic bandwidth adjustment in software defined multi-vendor optical transport networks.

PubMed

Li, Yajie; Zhao, Yongli; Zhang, Jie; Yu, Xiaosong; Jing, Ruiquan

2017-11-27

Network operators generally provide dedicated lightpaths for customers to meet the demand for high-quality transmission. Considering the variation of traffic load, customers usually rent peak bandwidth that exceeds the practical average traffic requirement. In this case, bandwidth provisioning is unmetered and customers have to pay according to peak bandwidth. Supposing that network operators could keep track of traffic load and allocate bandwidth dynamically, bandwidth can be provided as a metered service and customers would pay for the bandwidth that they actually use. To achieve cost-effective bandwidth provisioning, this paper proposes an autonomic bandwidth adjustment scheme based on data analysis of traffic load. The scheme is implemented in a software defined networking (SDN) controller and is demonstrated in the field trial of multi-vendor optical transport networks. The field trial shows that the proposed scheme can track traffic load and realize autonomic bandwidth adjustment. In addition, a simulation experiment is conducted to evaluate the performance of the proposed scheme. We also investigate the impact of different parameters on autonomic bandwidth adjustment. Simulation results show that the step size and adjustment period have significant influences on bandwidth savings and packet loss. A small value of step size and adjustment period can bring more benefits by tracking traffic variation with high accuracy. For network operators, the scheme can serve as technical support of realizing bandwidth as metered service in the future.

Changes in the limb kinematics and walking-distance estimation after shank elongation: evidence for a locomotor body schema?

PubMed

Dominici, Nadia; Daprati, Elena; Nico, Daniele; Cappellini, Germana; Ivanenko, Yuri P; Lacquaniti, Francesco

2009-03-01

When walking, step length provides critical information on traveled distance along the ongoing path [corrected] Little is known on the role that knowledge about body dimensions plays within this process. Here we directly addressed this question by evaluating whether changes in body proportions interfere with computation of traveled distance for targets located outside the reaching space. We studied locomotion and distance estimation in an achondroplastic child (ACH, 11 yr) before and after surgical elongation of the shank segments of both lower limbs and in healthy adults walking on stilts, designed to mimic shank-segment elongation. Kinematic analysis of gait revealed that dynamic coupling of the thigh, shank, and foot segments changed substantially as a result of elongation. Step length remained unvaried, in spite of the significant increase in total limb length ( approximately 1.5-fold). These relatively shorter strides resulted from smaller oscillations of the shank segment, as would be predicted by proportional increments in limb size and not by asymmetrical segmental increment as in the present case (length of thighs was not modified). Distance estimation was measured by walking with eyes closed toward a memorized target. Before surgery, the behavior of ACH was comparable to that of typically developing participants. In contrast, following shank elongation, the ACH walked significantly shorter distances when aiming at the same targets. Comparable changes in limb kinematics, stride length, and estimation of traveled distance were found in adults wearing on stilts, suggesting that path integration errors in both cases were related to alterations in the intersegmental coordination of the walking limbs. The results are consistent with a dynamic locomotor body schema used for controlling step length and path estimation, based on inherent relationships between gait parameters and body proportions.

Step Detection Robust against the Dynamics of Smartphones

PubMed Central

Lee, Hwan-hee; Choi, Suji; Lee, Myeong-jin

2015-01-01

A novel algorithm is proposed for robust step detection irrespective of step mode and device pose in smartphone usage environments. The dynamics of smartphones are decoupled into a peak-valley relationship with adaptive magnitude and temporal thresholds. For extracted peaks and valleys in the magnitude of acceleration, a step is defined as consisting of a peak and its adjacent valley. Adaptive magnitude thresholds consisting of step average and step deviation are applied to suppress pseudo peaks or valleys that mostly occur during the transition among step modes or device poses. Adaptive temporal thresholds are applied to time intervals between peaks or valleys to consider the time-varying pace of human walking or running for the correct selection of peaks or valleys. From the experimental results, it can be seen that the proposed step detection algorithm shows more than 98.6% average accuracy for any combination of step mode and device pose and outperforms state-of-the-art algorithms. PMID:26516857

Design of a universal logic block for fault-tolerant realization of any logic operation in trapped-ion quantum circuits

NASA Astrophysics Data System (ADS)

Goudarzi, H.; Dousti, M. J.; Shafaei, A.; Pedram, M.

2014-05-01

This paper presents a physical mapping tool for quantum circuits, which generates the optimal universal logic block (ULB) that can, on average, perform any logical fault-tolerant (FT) quantum operations with the minimum latency. The operation scheduling, placement, and qubit routing problems tackled by the quantum physical mapper are highly dependent on one another. More precisely, the scheduling solution affects the quality of the achievable placement solution due to resource pressures that may be created as a result of operation scheduling, whereas the operation placement and qubit routing solutions influence the scheduling solution due to resulting distances between predecessor and current operations, which in turn determines routing latencies. The proposed flow for the quantum physical mapper captures these dependencies by applying (1) a loose scheduling step, which transforms an initial quantum data flow graph into one that explicitly captures the no-cloning theorem of the quantum computing and then performs instruction scheduling based on a modified force-directed scheduling approach to minimize the resource contention and quantum circuit latency, (2) a placement step, which uses timing-driven instruction placement to minimize the approximate routing latencies while making iterative calls to the aforesaid force-directed scheduler to correct scheduling levels of quantum operations as needed, and (3) a routing step that finds dynamic values of routing latencies for the qubits. In addition to the quantum physical mapper, an approach is presented to determine the single best ULB size for a target quantum circuit by examining the latency of different FT quantum operations mapped onto different ULB sizes and using information about the occurrence frequency of operations on critical paths of the target quantum algorithm to weigh these latencies. Experimental results show an average latency reduction of about 40 % compared to previous work.

Simulations of solid-fluid coupling with application to crystal entrainment in vigorous convection

NASA Astrophysics Data System (ADS)

Suckale, J.; Elkins-Tanton, L. T.; Sethian, J.; Yu, J.

2009-12-01

Many problems in computational geophysics require the accurate coupling of a solid body to viscous flow. Examples range from understanding the role of highly crystalline magma for the dynamic of volcanic eruptions to crystal entrainment in magmatic flow and the emplacement of xenoliths. In this paper, we present and validate a numerical method for solid-fluid coupling. The algorithm relies on a two-step projection scheme: In the first step, we solve the multiple-phase Navier-Stokes or Stokes equation in both domains. In the second step, we project the velocity field in the solid domain onto a rigid-body motion by enforcing that the deformation tensor in the respective domain is zero. This procedure is also used to enforce the no-slip boundary condition on the solid-fluid interface. We perform several benchmark computations to validate our computations. More precisely, we investigate the formation of a wake behind both fixed and mobile cylinders and cuboids with and without imposed velocity fields in the fluid. These preliminary tests indicate that our code is able to simulate solid-fluid coupling for Reynolds numbers of up to 1000. Finally, we apply our method to the problem of crystal entrainment in vigorous convection. The interplay between sedimentation and re-entrainment of crystals in convective flow is of fundamental importance for understanding the compositional evolution of magmatic reservoirs of various sizes from small lava ponds to magma oceans at the planetary scale. Previous studies of this problem have focused primarily on laboratory experiments, often with conflicting conclusions. Our work is complementary to these prior studies as we model the competing processes of gravitational sedimentation and entrainment of crystals at the length scale of the size of the crystals.

Lower pitch is larger, yet falling pitches shrink.

PubMed

Eitan, Zohar; Schupak, Asi; Gotler, Alex; Marks, Lawrence E

2014-01-01

Experiments using diverse paradigms, including speeded discrimination, indicate that pitch and visually-perceived size interact perceptually, and that higher pitch is congruent with smaller size. While nearly all of these studies used static stimuli, here we examine the interaction of dynamic pitch and dynamic size, using Garner's speeded discrimination paradigm. Experiment 1 examined the interaction of continuous rise/fall in pitch and increase/decrease in object size. Experiment 2 examined the interaction of static pitch and size (steady high/low pitches and large/small visual objects), using an identical procedure. Results indicate that static and dynamic auditory and visual stimuli interact in opposite ways. While for static stimuli (Experiment 2), higher pitch is congruent with smaller size (as suggested by earlier work), for dynamic stimuli (Experiment 1), ascending pitch is congruent with growing size, and descending pitch with shrinking size. In addition, while static stimuli (Experiment 2) exhibit both congruence and Garner effects, dynamic stimuli (Experiment 1) present congruence effects without Garner interference, a pattern that is not consistent with prevalent interpretations of Garner's paradigm. Our interpretation of these results focuses on effects of within-trial changes on processing in dynamic tasks and on the association of changes in apparent size with implied changes in distance. Results suggest that static and dynamic stimuli can differ substantially in their cross-modal mappings, and may rely on different processing mechanisms.

Optimal setups for forced-choice staircases with fixed step sizes.

PubMed

García-Pérez, M A

2000-01-01

Forced-choice staircases with fixed step sizes are used in a variety of formats whose relative merits have never been studied. This paper presents a comparative study aimed at determining their optimal format. Factors included in the study were the up/down rule, the length (number of reversals), and the size of the steps. The study also addressed the issue of whether a protocol involving three staircases running for N reversals each (with a subsequent average of the estimates provided by each individual staircase) has better statistical properties than an alternative protocol involving a single staircase running for 3N reversals. In all cases the size of a step up was different from that of a step down, in the appropriate ratio determined by García-Pérez (Vision Research, 1998, 38, 1861 - 1881). The results of a simulation study indicate that a) there are no conditions in which the 1-down/1-up rule is advisable; b) different combinations of up/down rule and number of reversals appear equivalent in terms of precision and cost: c) using a single long staircase with 3N reversals is more efficient than running three staircases with N reversals each: d) to avoid bias and attain sufficient accuracy, threshold estimates should be based on at least 30 reversals: and e) to avoid excessive cost and imprecision, the size of the step up should be between 2/3 and 3/3 the (known or presumed) spread of the psychometric function. An empirical study with human subjects confirmed the major characteristics revealed by the simulations.

Double emulsion formation through hierarchical flow-focusing microchannel

NASA Astrophysics Data System (ADS)

Azarmanesh, Milad; Farhadi, Mousa; Azizian, Pooya

2016-03-01

A microfluidic device is presented for creating double emulsions, controlling their sizes and also manipulating encapsulation processes. As a result of three immiscible liquids' interaction using dripping instability, double emulsions can be produced elegantly. Effects of dimensionless numbers are investigated which are Weber number of the inner phase (Wein), Capillary number of the inner droplet (Cain), and Capillary number of the outer droplet (Caout). They affect the formation process, inner and outer droplet size, and separation frequency. Direct numerical simulation of governing equations was done using volume of fluid method and adaptive mesh refinement technique. Two kinds of double emulsion formation, the two-step and the one-step, were simulated in which the thickness of the sheath of double emulsions can be adjusted. Altering each dimensionless number will change detachment location, outer droplet size and droplet formation period. Moreover, the decussate regime of the double-emulsion/empty-droplet is observed in low Wein. This phenomenon can be obtained by adjusting the Wein in which the maximum size of the sheath is discovered. Also, the results show that Cain has significant influence on the outer droplet size in the two-step process, while Caout affects the sheath in the one-step formation considerably.

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

PubMed

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

Falls-risk post-stroke: Examining contributions from paretic versus non paretic limbs to unexpected forward gait slips.

PubMed

Kajrolkar, Tejal; Bhatt, Tanvi

2016-09-06

Community-dwelling stroke survivors show a high incidence of falls with unexpected external perturbations during dynamic activities like walking. Previous evidence has demonstrated the importance of compensatory stepping to restore dynamic stability in response to perturbations in hemiparetic stroke survivors. However, these studies were limited to either stance perturbations or perturbation induced under the unaffected limb. This study aimed to compare the differences, if any, between the non-paretic and paretic sides in dynamic stability and protective stepping strategies when exposed to unexpected external perturbation during walking. Twenty hemiparetic subjects experienced an unexpected forward slip during walking on the laboratory walkway either on the paretic (n=10) or the nonparetic limb (n=10). Both groups demonstrated a backward loss of balance with a compensatory stepping response, with the nonparetic-side slip group resorting mainly to an aborted step response (60%) and the paretic-side slip group mainly exhibiting a recovery step response (90%). Although both groups showed an equal incidence of falls, the nonparetic-side slip group demonstrated a higher stability at recovery step touchdown, resulting from lower perturbation magnitudes (slip displacement and velocity) compared to the paretic-side slip group. The results indicate that the paretic side had difficulty initiating and executing a successful stepping response (nonparetic-side slip) and also in reactive limb control while in stance (paretic-side slip). Based on these results it is suggested that intervention strategies for fall-prevention in chronic stroke survivors should focus on paretic limb training for both reactive stepping and weight bearing for improving balance control for recovery from unpredictable perturbations during dynamic activities such as walking. Copyright © 2016. Published by Elsevier Ltd.

Emergence of the self-similar property in gene expression dynamics

NASA Astrophysics Data System (ADS)

Ochiai, T.; Nacher, J. C.; Akutsu, T.

2007-08-01

Many theoretical models have recently been proposed to understand the structure of cellular systems composed of various types of elements (e.g., proteins, metabolites and genes) and their interactions. However, the cell is a highly dynamic system with thousands of functional elements fluctuating across temporal states. Therefore, structural analysis alone is not sufficient to reproduce the cell's observed behavior. In this article, we analyze the gene expression dynamics (i.e., how the amount of mRNA molecules in cell fluctuate in time) by using a new constructive approach, which reveals a symmetry embedded in gene expression fluctuations and characterizes the dynamical equation of gene expression (i.e., a specific stochastic differential equation). First, by using experimental data of human and yeast gene expression time series, we found a symmetry in short-time transition probability from time t to time t+1. We call it self-similarity symmetry (i.e., the gene expression short-time fluctuations contain a repeating pattern of smaller and smaller parts that are like the whole, but different in size). Secondly, we reconstruct the global behavior of the observed distribution of gene expression (i.e., scaling-law) and the local behavior of the power-law tail of this distribution. This approach may represent a step forward toward an integrated image of the basic elements of the whole cell.

Bragg Coherent Diffractive Imaging of Zinc Oxide Acoustic Phonons at Picosecond Timescales

DOE PAGES

Ulvestad, A.; Cherukara, M. J.; Harder, R.; ...

2017-08-29

Mesoscale thermal transport is of fundamental interest and practical importance in materials such as thermoelectrics. Coherent lattice vibrations (acoustic phonons) govern thermal transport in crystalline solids and are affected by the shape, size, and defect density in nanoscale materials. The advent of hard x-ray free electron lasers (XFELs) capable of producing ultrafast x-ray pulses has significantly impacted the understanding of acoustic phonons by enabling their direct study with x-rays. However, previous studies have reported ensemble-averaged results that cannot distinguish the impact of mesoscale heterogeneity on the phonon dynamics. Here we use Bragg coherent diffractive imaging (BCDI) to resolve the 4Dmore » evolution of the acoustic phonons in a single zinc oxide rod with a spatial resolution of 50 nm and a temporal resolution of 25 picoseconds. We observe homogeneous (lattice breathing/rotation) and inhomogeneous (shear) acoustic phonon modes, which are compared to finite element simulations. We investigate the possibility of changing phonon dynamics by altering the crystal through acid etching. Lastly, we find that the acid heterogeneously dissolves the crystal volume, which will significantly impact the phonon dynamics. In general, our results represent the first step towards understanding the effect of structural properties at the individual crystal level on phonon dynamics.« less

6 DOF articulated-arm robot and mobile platform: Dynamic modelling as Multibody System and its validation via Experimental Modal Analysis.

NASA Astrophysics Data System (ADS)

Toledo Fuentes, A.; Kipfmueller, M.; José Prieto, M. A.

2017-10-01

Mobile manipulators are becoming a key instrument to increase the flexibility in industrial processes. Some of their requirements include handling of objects with different weights and sizes and their “fast” transportation, without jeopardizing production workers and machines. The compensation of forces affecting the system dynamic is therefore needed to avoid unwanted oscillations and tilting by sudden accelerations and decelerations. One general solution may be the implementation of external positioning elements to active stabilize the system. To accomplish the approach, the dynamic behavior of a robotic arm and a mobile platform was investigated to develop the stabilization mechanism using multibody simulations. The methodology used was divided into two phases for each subsystem: their natural frequencies and modal shapes were obtained using experimental modal analyses. Then, based on these experimental results, multibody simulation models (MBS) were set up and its dynamical parameters adjusted. Their modal shapes together with their obtained natural frequencies allowed a quantitative and qualitative analysis. In summary, the MBS models were successfully validated with the real subsystems, with a maximal percentage error of 15%. These models will serve as the basis for future steps in the design of the external actuators and its control strategy using a co-simulation tool.

Bragg Coherent Diffractive Imaging of Zinc Oxide Acoustic Phonons at Picosecond Timescales

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

Ulvestad, A.; Cherukara, M. J.; Harder, R.

Mesoscale thermal transport is of fundamental interest and practical importance in materials such as thermoelectrics. Coherent lattice vibrations (acoustic phonons) govern thermal transport in crystalline solids and are affected by the shape, size, and defect density in nanoscale materials. The advent of hard x-ray free electron lasers (XFELs) capable of producing ultrafast x-ray pulses has significantly impacted the understanding of acoustic phonons by enabling their direct study with x-rays. However, previous studies have reported ensemble-averaged results that cannot distinguish the impact of mesoscale heterogeneity on the phonon dynamics. Here we use Bragg coherent diffractive imaging (BCDI) to resolve the 4Dmore » evolution of the acoustic phonons in a single zinc oxide rod with a spatial resolution of 50 nm and a temporal resolution of 25 picoseconds. We observe homogeneous (lattice breathing/rotation) and inhomogeneous (shear) acoustic phonon modes, which are compared to finite element simulations. We investigate the possibility of changing phonon dynamics by altering the crystal through acid etching. Lastly, we find that the acid heterogeneously dissolves the crystal volume, which will significantly impact the phonon dynamics. In general, our results represent the first step towards understanding the effect of structural properties at the individual crystal level on phonon dynamics.« less

On the integral use of foundational concepts in verifying validity during skull-photo superimposition.

PubMed

Jayaprakash, Paul T

2017-09-01

Often cited reliability test on video superimposition method integrated scaling face-images in relation to skull-images, tragus-auditory meatus relationship in addition to exocanthion-Whitnall's tubercle relationship when orientating the skull-image and wipe mode imaging in addition to mix mode imaging when obtaining skull-face image overlay and evaluating the goodness of match. However, a report that found higher false positive matches in computer assisted superimposition method transited from the above foundational concepts and relied on images of unspecified sizes that are lesser than 'life-size', frontal plane landmarks in the skull- and face- images alone for orientating the skull-image and mix images alone for evaluating the goodness of match. Recently, arguing the use of 'life-size' images as 'archaic', the authors who tested the reliability in the computer assisted superimposition method have denied any method transition. This article describes that the use of images of unspecified sizes at lesser than 'life-size' eliminates the only possibility to quantify parameters during superimposition which alone enables dynamic skull orientation when overlaying a skull-image with a face-image in an anatomically acceptable orientation. The dynamic skull orientation process mandatorily requires aligning the tragus in the 2D face-image with the auditory meatus in the 3D skull-image for anatomically orientating the skull-image in relation to the posture in the face-image, a step not mentioned by the authors describing the computer assisted superimposition method. Furthermore, mere reliance on mix type images during image overlay eliminates the possibility to assess the relationship between the leading edges of the skull- and face-image outlines as also specific area match among the corresponding craniofacial organs during superimposition. Indicating the possibility of increased false positive matches as a consequence of the above method transitions, the need for testing the reliability in the superimposition method adopting concepts that are considered safe is stressed. Copyright © 2017 Elsevier B.V. All rights reserved.

Advanced in Visualization of 3D Time-Dependent CFD Solutions

NASA Technical Reports Server (NTRS)

Lane, David A.; Lasinski, T. A. (Technical Monitor)

1995-01-01

Numerical simulations of complex 3D time-dependent (unsteady) flows are becoming increasingly feasible because of the progress in computing systems. Unfortunately, many existing flow visualization systems were developed for time-independent (steady) solutions and do not adequately depict solutions from unsteady flow simulations. Furthermore, most systems only handle one time step of the solutions individually and do not consider the time-dependent nature of the solutions. For example, instantaneous streamlines are computed by tracking the particles using one time step of the solution. However, for streaklines and timelines, particles need to be tracked through all time steps. Streaklines can reveal quite different information about the flow than those revealed by instantaneous streamlines. Comparisons of instantaneous streamlines with dynamic streaklines are shown. For a complex 3D flow simulation, it is common to generate a grid system with several millions of grid points and to have tens of thousands of time steps. The disk requirement for storing the flow data can easily be tens of gigabytes. Visualizing solutions of this magnitude is a challenging problem with today's computer hardware technology. Even interactive visualization of one time step of the flow data can be a problem for some existing flow visualization systems because of the size of the grid. Current approaches for visualizing complex 3D time-dependent CFD solutions are described. The flow visualization system developed at NASA Ames Research Center to compute time-dependent particle traces from unsteady CFD solutions is described. The system computes particle traces (streaklines) by integrating through the time steps. This system has been used by several NASA scientists to visualize their CFD time-dependent solutions. The flow visualization capabilities of this system are described, and visualization results are shown.

Automated measurement of diatom size

USGS Publications Warehouse

Spaulding, Sarah A.; Jewson, David H.; Bixby, Rebecca J.; Nelson, Harry; McKnight, Diane M.

2012-01-01

Size analysis of diatom populations has not been widely considered, but it is a potentially powerful tool for understanding diatom life histories, population dynamics, and phylogenetic relationships. However, measuring cell dimensions on a light microscope is a time-consuming process. An alternative technique has been developed using digital flow cytometry on a FlowCAM® (Fluid Imaging Technologies) to capture hundreds, or even thousands, of images of a chosen taxon from a single sample in a matter of minutes. Up to 30 morphological measures may be quantified through post-processing of the high resolution images. We evaluated FlowCAM size measurements, comparing them against measurements from a light microscope. We found good agreement between measurement of apical cell length in species with elongated, straight valves, including small Achnanthidium minutissimum (11-21 µm) and largeDidymosphenia geminata (87–137 µm) forms. However, a taxon with curved cells, Hannaea baicalensis (37–96 µm), showed differences of ~ 4 µm between the two methods. Discrepancies appear to be influenced by the choice of feret or geodesic measurement for asymmetric cells. We describe the operating conditions necessary for analysis of size distributions and present suggestions for optimal instrument conditions for size analysis of diatom samples using the FlowCAM. The increased speed of data acquisition through use of imaging flow cytometers like the FlowCAM is an essential step for advancing studies of diatom populations.

A TAPS Interactive Multimedia Package to Solve Engineering Dynamics Problem

ERIC Educational Resources Information Center

Sidhu, S. Manjit; Selvanathan, N.

2005-01-01

Purpose: To expose engineering students to using modern technologies, such as multimedia packages, to learn, visualize and solve engineering problems, such as in mechanics dynamics. Design/methodology/approach: A multimedia problem-solving prototype package is developed to help students solve an engineering problem in a step-by-step approach. A…

Rotordynamics on the PC: Transient Analysis With ARDS

NASA Technical Reports Server (NTRS)

Fleming, David P.

1997-01-01

Personal computers can now do many jobs that formerly required a large mainframe computer. An example is NASA Lewis Research Center's program Analysis of RotorDynamic Systems (ARDS), which uses the component mode synthesis method to analyze the dynamic motion of up to five rotating shafts. As originally written in the early 1980's, this program was considered large for the mainframe computers of the time. ARDS, which was written in Fortran 77, has been successfully ported to a 486 personal computer. Plots appear on the computer monitor via calls programmed for the original CALCOMP plotter; plots can also be output on a standard laser printer. The executable code, which uses the full array sizes of the mainframe version, easily fits on a high-density floppy disk. The program runs under DOS with an extended memory manager. In addition to transient analysis of blade loss, step turns, and base acceleration, with simulation of squeeze-film dampers and rubs, ARDS calculates natural frequencies and unbalance response.

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

PubMed

Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

2017-09-30

GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Model reduction of multiscale chemical langevin equations: a numerical case study.

PubMed

Sotiropoulos, Vassilios; Contou-Carrere, Marie-Nathalie; Daoutidis, Prodromos; Kaznessis, Yiannis N

2009-01-01

Two very important characteristics of biological reaction networks need to be considered carefully when modeling these systems. First, models must account for the inherent probabilistic nature of systems far from the thermodynamic limit. Often, biological systems cannot be modeled with traditional continuous-deterministic models. Second, models must take into consideration the disparate spectrum of time scales observed in biological phenomena, such as slow transcription events and fast dimerization reactions. In the last decade, significant efforts have been expended on the development of stochastic chemical kinetics models to capture the dynamics of biomolecular systems, and on the development of robust multiscale algorithms, able to handle stiffness. In this paper, the focus is on the dynamics of reaction sets governed by stiff chemical Langevin equations, i.e., stiff stochastic differential equations. These are particularly challenging systems to model, requiring prohibitively small integration step sizes. We describe and illustrate the application of a semianalytical reduction framework for chemical Langevin equations that results in significant gains in computational cost.

The evolution of syntactic communication

NASA Astrophysics Data System (ADS)

Nowak, Martin A.; Plotkin, Joshua B.; Jansen, Vincent A. A.

2000-03-01

Animal communication is typically non-syntactic, which means that signals refer to whole situations. Human language is syntactic, and signals consist of discrete components that have their own meaning. Syntax is a prerequisite for taking advantage of combinatorics, that is, ``making infinite use of finite means''. The vast expressive power of human language would be impossible without syntax, and the transition from non-syntactic to syntactic communication was an essential step in the evolution of human language. We aim to understand the evolutionary dynamics of this transition and to analyse how natural selection can guide it. Here we present a model for the population dynamics of language evolution, define the basic reproductive ratio of words and calculate the maximum size of a lexicon. Syntax allows larger repertoires and the possibility to formulate messages that have not been learned beforehand. Nevertheless, according to our model natural selection can only favour the emergence of syntax if the number of required signals exceeds a threshold value. This result might explain why only humans evolved syntactic communication and hence complex language.

An adaptive time-stepping strategy for solving the phase field crystal model

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

Zhang, Zhengru, E-mail: zrzhang@bnu.edu.cn; Ma, Yuan, E-mail: yuner1022@gmail.com; Qiao, Zhonghua, E-mail: zqiao@polyu.edu.hk

2013-09-15

In this work, we will propose an adaptive time step method for simulating the dynamics of the phase field crystal (PFC) model. The numerical simulation of the PFC model needs long time to reach steady state, and then large time-stepping method is necessary. Unconditionally energy stable schemes are used to solve the PFC model. The time steps are adaptively determined based on the time derivative of the corresponding energy. It is found that the use of the proposed time step adaptivity cannot only resolve the steady state solution, but also the dynamical development of the solution efficiently and accurately. Themore » numerical experiments demonstrate that the CPU time is significantly saved for long time simulations.« less

Understanding the barriers to crystal growth: dynamical simulation of the dissolution and growth of urea from aqueous solution.

PubMed

Piana, Stefano; Gale, Julian D

2005-02-16

Both the dissolution and growth of a molecular crystalline material, urea, has been studied using dynamical atomistic simulation. The kinetic steps of dissolution and growth are clearly identified, and the activation energies for each possible step are calculated. Our molecular dynamics simulations indicate that crystal growth on the [001] face is characterized by a nucleation and growth mechanism. Nucleation on the [001] urea crystal face is predicted to occur at a very high rate, followed by rapid propagation of the steps. The rate-limiting step for crystallization is actually found to be the removal of surface defects, rather than the initial formation of the next surface layer. Through kinetic Monte Carlo modeling of the surface growth, it is found that this crystal face evolves via a rough surface topography, rather than a clean layer-by-layer mechanism.

The effects of landscape modifications on the long-term persistence of animal populations.

PubMed

Nabe-Nielsen, Jacob; Sibly, Richard M; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

2010-01-28

The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

[On the relation between encounter rate and population density: Are classical models of population dynamics justified?].

PubMed

Nedorezov, L V

2015-01-01

A stochastic model of migrations on a lattice and with discrete time is considered. It is assumed that space is homogenous with respect to its properties and during one time step every individual (independently of local population numbers) can migrate to nearest nodes of lattice with equal probabilities. It is also assumed that population size remains constant during certain time interval of computer experiments. The following variants of estimation of encounter rate between individuals are considered: when for the fixed time moments every individual in every node of lattice interacts with all other individuals in the node; when individuals can stay in nodes independently, or can be involved in groups in two, three or four individuals. For each variant of interactions between individuals, average value (with respect to space and time) is computed for various values of population size. The samples obtained were compared with respective functions of classic models of isolated population dynamics: Verhulst model, Gompertz model, Svirezhev model, and theta-logistic model. Parameters of functions were calculated with least square method. Analyses of deviations were performed using Kolmogorov-Smirnov test, Lilliefors test, Shapiro-Wilk test, and other statistical tests. It is shown that from traditional point of view there are no correspondence between the encounter rate and functions describing effects of self-regulatory mechanisms on population dynamics. Best fitting of samples was obtained with Verhulst and theta-logistic models when using the dataset resulted from the situation when every individual in the node interacts with all other individuals.

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions.

PubMed

Saha, Tanumoy; Rathmann, Isabel; Galic, Milos

2017-07-11

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

Influence of viscoelastic nature on the intermittent peel-front dynamics of adhesive tape

NASA Astrophysics Data System (ADS)

Kumar, Jagadish; Ananthakrishna, G.

2010-07-01

We investigate the influence of viscoelastic nature of the adhesive on the intermittent peel front dynamics by extending a recently introduced model for peeling of an adhesive tape. As time and rate-dependent deformation of the adhesives are measured in stationary conditions, a crucial step in incorporating the viscoelastic effects applicable to unstable intermittent peel dynamics is the introduction of a dynamization scheme that eliminates the explicit time dependence in terms of dynamical variables. We find contrasting influences of viscoelastic contribution in different regions of tape mass, roller inertia, and pull velocity. As the model acoustic energy dissipated depends on the nature of the peel front and its dynamical evolution, the combined effect of the roller inertia and pull velocity makes the acoustic energy noisier for small tape mass and low-pull velocity while it is burstlike for low-tape mass, intermediate values of the roller inertia and high-pull velocity. The changes are quantified by calculating the largest Lyapunov exponent and analyzing the statistical distributions of the amplitudes and durations of the model acoustic energy signals. Both single and two stage power-law distributions are observed. Scaling relations between the exponents are derived which show that the exponents corresponding to large values of event sizes and durations are completely determined by those for small values. The scaling relations are found to be satisfied in all cases studied. Interestingly, we find only five types of model acoustic emission signals among multitude of possibilities of the peel front configurations.

A model for oscillations and pattern formation in protoplasmic droplets of Physarum polycephalum

NASA Astrophysics Data System (ADS)

Radszuweit, M.; Engel, H.; Bär, M.

2010-12-01

A mechano-chemical model for the spatiotemporal dynamics of free calcium and the thickness in protoplasmic droplets of the true slime mold Physarum polycephalum is derived starting from a physiologically detailed description of intracellular calcium oscillations proposed by Smith and Saldana (Biopys. J. 61, 368 (1992)). First, we have modified the Smith-Saldana model for the temporal calcium dynamics in order to reproduce the experimentally observed phase relation between calcium and mechanical tension oscillations. Then, we formulate a model for spatiotemporal dynamics by adding spatial coupling in the form of calcium diffusion and advection due to calcium-dependent mechanical contraction. In another step, the resulting reaction-diffusion model with mechanical coupling is simplified to a reaction-diffusion model with global coupling that approximates the mechanical part. We perform a bifurcation analysis of the local dynamics and observe a Hopf bifurcation upon increase of a biochemical activity parameter. The corresponding reaction-diffusion model with global coupling shows regular and chaotic spatiotemporal behaviour for parameters with oscillatory dynamics. In addition, we show that the global coupling leads to a long-wavelength instability even for parameters where the local dynamics possesses a stable spatially homogeneous steady state. This instability causes standing waves with a wavelength of twice the system size in one dimension. Simulations of the model in two dimensions are found to exhibit defect-mediated turbulence as well as various types of spiral wave patterns in qualitative agreement with earlier experimental observation by Takagi and Ueda (Physica D, 237, 420 (2008)).

What is the alternative to the Alexander-Orbach relation?

NASA Astrophysics Data System (ADS)

Sokolov, Igor M.

2016-03-01

The Alexander-Orbach (AO) relation d w = 2d f /d s connecting the fractal dimension of a random walk’s (RW) trajectory d w or the exponent of anomalous diffusion α = 2/d w on a fractal structure with the fractal and spectral dimension of the structure itself plays a key role in discussion of dynamical properties of complex systems including living cells and single biomolecules. This relation however does not hold universally and breaks down for some structures like diffusion limited aggregates and Eden trees. We show that the alternative to the AO relation is the explicit dependence of the coefficient of the anomalous diffusion on the system’s size, i.e. the absence of its thermodynamical limit. The prerequisite for its breakdown is the dependence of the local structure of possible steps of the RW on the system’s size. The discussion is illustrated by the examples of diffusion on a Koch curve (AO-conform) and on a Cantor dust (violating AO relation).

Intrinsic frame transport for a model of nematic liquid crystal

NASA Astrophysics Data System (ADS)

Cozzini, S.; Rull, L. F.; Ciccotti, G.; Paolini, G. V.

1997-02-01

We present a computer simulation study of the dynamical properties of a nematic liquid crystal model. The diffusional motion of the nematic director is taken into account in our calculations in order to give a proper estimate of the transport coefficients. Differently from other groups we do not attempt to stabilize the director through rigid constraints or applied external fields. We instead define an intrinsic frame which moves along with the director at each step of the simulation. The transport coefficients computed in the intrinsic frame are then compared against the ones calculated in the fixed laboratory frame, to show the inadequacy of the latter for systems with less than 500 molecules. Using this general scheme on the Gay-Berne liquid crystal model, we evidence the natural motion of the director and attempt to quantify its intrinsic time scale and size dependence. Through extended simulations of systems of different size we calculate the diffusion and viscosity coefficients of this model and compare our results with values previously obtained with fixed director.

STEP Experiment Requirements

NASA Technical Reports Server (NTRS)

Brumfield, M. L. (Compiler)

1984-01-01

A plan to develop a space technology experiments platform (STEP) was examined. NASA Langley Research Center held a STEP Experiment Requirements Workshop on June 29 and 30 and July 1, 1983, at which experiment proposers were invited to present more detailed information on their experiment concept and requirements. A feasibility and preliminary definition study was conducted and the preliminary definition of STEP capabilities and experiment concepts and expected requirements for support services are presented. The preliminary definition of STEP capabilities based on detailed review of potential experiment requirements is investigated. Topics discussed include: Shuttle on-orbit dynamics; effects of the space environment on damping materials; erectable beam experiment; technology for development of very large solar array deployers; thermal energy management process experiment; photovoltaic concentrater pointing dynamics and plasma interactions; vibration isolation technology; flight tests of a synthetic aperture radar antenna with use of STEP.

Analysis Techniques for Microwave Dosimetric Data.

DTIC Science & Technology

1985-10-01

the number of steps in the frequency list . 0062 C ----------------------------------------------------------------------- 0063 CALL FILE2() 0064...starting frequency, 0061 C the step size, and the number of steps in the frequency list . 0062 C

Molecular dynamics studies of transport properties and equation of state of supercritical fluids

NASA Astrophysics Data System (ADS)

Nwobi, Obika C.

Many chemical propulsion systems operate with one or more of the reactants above the critical point in order to enhance their performance. Most of the computational fluid dynamics (CFD) methods used to predict these flows require accurate information on the transport properties and equation of state at these supercritical conditions. This work involves the determination of transport coefficients and equation of state of supercritical fluids by equilibrium molecular dynamics (MD) simulations on parallel computers using the Green-Kubo formulae and the virial equation of state, respectively. MD involves the solution of equations of motion of a system of molecules that interact with each other through an intermolecular potential. Provided that an accurate potential can be found for the system of interest, MD can be used regardless of the phase and thermodynamic conditions of the substances involved. The MD program uses the effective Lennard-Jones potential, with system sizes of 1000-1200 molecules and, simulations of 2,000,000 time-steps for computing transport coefficients and 200,000 time-steps for pressures. The computer code also uses linked cell lists for efficient sorting of molecules, periodic boundary conditions, and a modified velocity Verlet algorithm for particle displacement. Particle decomposition is used for distributing the molecules to different processors of a parallel computer. Simulations have been carried out on pure argon, nitrogen, oxygen and ethylene at various supercritical conditions, with self-diffusion coefficients, shear viscosity coefficients, thermal conductivity coefficients and pressures computed for most of the conditions. Results compare well with experimental and the National Institute of Standards and Technology (NIST) values. The results show that the number of molecules and the potential cut-off radius have no significant effect on the computed coefficients, while long-time integration is necessary for accurate determination of the coefficients.

Testing electroexplosive devices by programmed pulsing techniques

NASA Technical Reports Server (NTRS)

Rosenthal, L. A.; Menichelli, V. J.

1976-01-01

A novel method for testing electroexplosive devices is proposed wherein capacitor discharge pulses, with increasing energy in a step-wise fashion, are delivered to the device under test. The size of the energy increment can be programmed so that firing takes place after many, or after only a few, steps. The testing cycle is automatically terminated upon firing. An energy-firing contour relating the energy required to the programmed step size describes the single-pulse firing energy and the possible sensitization or desensitization of the explosive device.

Influence of Age, Maturity, and Body Size on the Spatiotemporal Determinants of Maximal Sprint Speed in Boys.

PubMed

Meyers, Robert W; Oliver, Jon L; Hughes, Michael G; Lloyd, Rhodri S; Cronin, John B

2017-04-01

Meyers, RW, Oliver, JL, Hughes, MG, Lloyd, RS, and Cronin, JB. Influence of age, maturity, and body size on the spatiotemporal determinants of maximal sprint speed in boys. J Strength Cond Res 31(4): 1009-1016, 2017-The aim of this study was to investigate the influence of age, maturity, and body size on the spatiotemporal determinants of maximal sprint speed in boys. Three-hundred and seventy-five boys (age: 13.0 ± 1.3 years) completed a 30-m sprint test, during which maximal speed, step length, step frequency, contact time, and flight time were recorded using an optical measurement system. Body mass, height, leg length, and a maturity offset represented somatic variables. Step frequency accounted for the highest proportion of variance in speed (∼58%) in the pre-peak height velocity (pre-PHV) group, whereas step length explained the majority of the variance in speed (∼54%) in the post-PHV group. In the pre-PHV group, mass was negatively related to speed, step length, step frequency, and contact time; however, measures of stature had a positive influence on speed and step length yet a negative influence on step frequency. Speed and step length were also negatively influence by mass in the post-PHV group, whereas leg length continued to positively influence step length. The results highlighted that pre-PHV boys may be deemed step frequency reliant, whereas those post-PHV boys may be marginally step length reliant. Furthermore, the negative influence of body mass, both pre-PHV and post-PHV, suggests that training to optimize sprint performance in youth should include methods such as plyometric and strength training, where a high neuromuscular focus and the development force production relative to body weight are key foci.

Sparse dynamics for partial differential equations

PubMed Central

Schaeffer, Hayden; Caflisch, Russel; Hauck, Cory D.; Osher, Stanley

2013-01-01

We investigate the approximate dynamics of several differential equations when the solutions are restricted to a sparse subset of a given basis. The restriction is enforced at every time step by simply applying soft thresholding to the coefficients of the basis approximation. By reducing or compressing the information needed to represent the solution at every step, only the essential dynamics are represented. In many cases, there are natural bases derived from the differential equations, which promote sparsity. We find that our method successfully reduces the dynamics of convection equations, diffusion equations, weak shocks, and vorticity equations with high-frequency source terms. PMID:23533273

Sparse dynamics for partial differential equations.

PubMed

Schaeffer, Hayden; Caflisch, Russel; Hauck, Cory D; Osher, Stanley

2013-04-23

We investigate the approximate dynamics of several differential equations when the solutions are restricted to a sparse subset of a given basis. The restriction is enforced at every time step by simply applying soft thresholding to the coefficients of the basis approximation. By reducing or compressing the information needed to represent the solution at every step, only the essential dynamics are represented. In many cases, there are natural bases derived from the differential equations, which promote sparsity. We find that our method successfully reduces the dynamics of convection equations, diffusion equations, weak shocks, and vorticity equations with high-frequency source terms.

Scanning tunneling microscope with a rotary piezoelectric stepping motor

NASA Astrophysics Data System (ADS)

Yakimov, V. N.

1996-02-01

A compact scanning tunneling microscope (STM) with a novel rotary piezoelectric stepping motor for coarse positioning has been developed. An inertial method for rotating of the rotor by the pair of piezoplates has been used in the piezomotor. Minimal angular step size was about several arcsec with the spindle working torque up to 1 N×cm. Design of the STM was noticeably simplified by utilization of the piezomotor with such small step size. A shaft eccentrically attached to the piezomotor spindle made it possible to push and pull back the cylindrical bush with the tubular piezoscanner. A linear step of coarse positioning was about 50 nm. STM resolution in vertical direction was better than 0.1 nm without an external vibration isolation.

Neuronal differentiation of human mesenchymal stem cells in response to the domain size of graphene substrates.

PubMed

Lee, Yoo-Jung; Seo, Tae Hoon; Lee, Seula; Jang, Wonhee; Kim, Myung Jong; Sung, Jung-Suk

2018-01-01

Graphene is a noncytotoxic monolayer platform with unique physical, chemical, and biological properties. It has been demonstrated that graphene substrate may provide a promising biocompatible scaffold for stem cell therapy. Because chemical vapor deposited graphene has a two dimensional polycrystalline structure, it is important to control the individual domain size to obtain desirable properties for nano-material. However, the biological effects mediated by differences in domain size of graphene have not yet been reported. On the basis of the control of graphene domain achieved by one-step growth (1step-G, small domain) and two-step growth (2step-G, large domain) process, we found that the neuronal differentiation of bone marrow-derived human mesenchymal stem cells (hMSCs) highly depended on the graphene domain size. The defects at the domain boundaries in 1step-G graphene was higher (×8.5) and had a relatively low (13% lower) contact angle of water droplet than 2step-G graphene, leading to enhanced cell-substrate adhesion and upregulated neuronal differentiation of hMSCs. We confirmed that the strong interactions between cells and defects at the domain boundaries in 1step-G graphene can be obtained due to their relatively high surface energy, which is stronger than interactions between cells and graphene surfaces. Our results may provide valuable information on the development of graphene-based scaffold by understanding which properties of graphene domain influence cell adhesion efficacy and stem cell differentiation. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 43-51, 2018. © 2017 Wiley Periodicals, Inc.

Tailoring plasmonic properties of metal nanoparticle-embedded dielectric thin films: the sandwich method of preparation

NASA Astrophysics Data System (ADS)

Laha, Ranjit; Malar, P.; Osipowicz, Thomas; Kasiviswanathan, S.

2017-09-01

Tailoring of plasmonic properties of metal nanoparticle-embedded dielectric thin films are very crucial for many thin film-based applications. We, herein, investigate the various ways of tuning the plasmonic positions of gold nanoparticles (AuNPs)-embedded indium oxide thin films (Au:IO) through a sequence-specific sandwich method. The sandwich method is a four-step process involving deposition of In2O3 film by magnetron sputtering in first and fourth steps, thermal evaporation of Au on to In2O3 film in second and annealing of Au/In2O3 film in the third step. The Au:IO films were characterized by x-ray diffraction, spectrophotometry and transmission electron microscopy. The size and shape of the embedded nanoparticles were found from Rutherford back-scattering spectrometry. Based on dynamic Maxwell Garnett theory, the observed plasmon resonance position was ascribed to the oblate shape of AuNPs formed in sandwich method. Finally, through experimental data, it was shown that the plasmon resonance position of Au:IO thin films can be tuned by 125 nm. The method shown here can be used to tune the plasmon resonance position over the entire range of visible region for the thin films made from other combinations of metal-dielectric pair.

End-of-life flows of multiple cycle consumer products.

PubMed

Tsiliyannis, C A

2011-11-01

Explicit expressions for the end-of-life flows (EOL) of single and multiple cycle products (MCPs) are presented, including deterministic and stochastic EOL exit. The expressions are given in terms of the physical parameters (maximum lifetime, T, annual cycling frequency, f, number of cycles, N, and early discard or usage loss). EOL flows are also obtained for hi-tech products, which are rapidly renewed and thus may not attain steady state (e.g., electronic products, passenger cars). A ten-step recursive procedure for obtaining the dynamic EOL flow evolution is proposed. Applications of the EOL expressions and the ten-step procedure are given for electric household appliances, industrial machinery, tyres, vehicles and buildings, both for deterministic and stochastic EOL exit, (normal, Weibull and uniform exit distributions). The effect of the physical parameters and the stochastic characteristics on the EOL flow is investigated in the examples: it is shown that the EOL flow profile is determined primarily by the early discard dynamics; it also depends strongly on longevity and cycling frequency: higher lifetime or early discard/loss imply lower dynamic and steady state EOL flows. The stochastic exit shapes the overall EOL dynamic profile: Under symmetric EOL exit distribution, as the variance of the distribution increases (uniform to normal to deterministic) the initial EOL flow rise becomes steeper but the steady state or maximum EOL flow level is lower. The steepest EOL flow profile, featuring the highest steady state or maximum level, as well, corresponds to skew, earlier shifted EOL exit (e.g., Weibull). Since the EOL flow of returned products consists the sink of the reuse/remanufacturing cycle (sink to recycle) the results may be used in closed loop product lifecycle management operations for scheduling and sizing reverse manufacturing and for planning recycle logistics. Decoupling and quantification of both the full age EOL and of the early discard flows is useful, the latter being the target of enacted legislation aiming at increasing reuse. Copyright © 2011 Elsevier Ltd. All rights reserved.

Influence of Air Discontinuity and Wall Effects on the Measurements of Hydraulic Parameters Under Dynamic Conditions

NASA Astrophysics Data System (ADS)

Looms, M. C.; Jensen, K. H.; Wildenschild, D.; Christensen, B. S.; Gudbjerg, J.

2003-12-01

Both dynamic (one-step) and semi-static (syringe pump) outflow experiments were carried out in the lab to test whether the resulting retention characteristics differed according to experiment type. Three sands of varying uniformity and coarseness were packed in a cylindrical sample holder. Compressed air was used to control the air phase pressure, while water was allowed to drain at atmospheric pressure from the outlet at the bottom of the sample. During the outflow experiments the capillary pressure was measured within the sample holder using a tensiometer connected to a pressure transducer. A medical CT-scanner was used to visualize and quantify the outflow patterns within the sand matrix during selected outflow experiments. Positive vertical shifts in capillary pressure during dynamic experiments were found in all three sand types at saturations close to porosity. The size and shape of the shifts corresponded with the dynamic effects found in previous work on the topic. Furthermore, the shifts were slightly greater in the coarsest and most uniform sand type. Numerical simulations of the one-step experiments using HYDRUS1D and T2VOC showed, however, that one of the basic assumptions when calculating the capillary pressure was most likely violated. The air phase could not be considered to be continuous at all times, and assuming this to be the case would result in positive shifts of the retention curves when running T2VOC. The results of using the CT-scanner showed the importance of achieving a homogeneous packing, since the investigated sand packing turned out to have an area at the edge of the sample holder with a higher porosity. This caused the edge to control the initial drainage. Therefore, the data collected at high saturations could not be expected to adequately describe the hydraulic properties of the inner sand. We also found that the time at which the inner sand commenced drainage coincided with a jump in capillary pressure for the resulting measured retention curve.

Charge and spin control of ultrafast electron and hole dynamics in single CdSe/ZnSe quantum dots

NASA Astrophysics Data System (ADS)

Hinz, C.; Gumbsheimer, P.; Traum, C.; Holtkemper, M.; Bauer, B.; Haase, J.; Mahapatra, S.; Frey, A.; Brunner, K.; Reiter, D. E.; Kuhn, T.; Seletskiy, D. V.; Leitenstorfer, A.

2018-01-01

We study the dynamics of photoexcited electrons and holes in single negatively charged CdSe/ZnSe quantum dots with two-color femtosecond pump-probe spectroscopy. An initial characterization of the energy level structure is performed at low temperatures and magnetic fields of up to 5 T. Emission and absorption resonances are assigned to specific transitions between few-fermion states by a theoretical model based on a configuration interaction approach. To analyze the dynamics of individual charge carriers, we initialize the quantum system into excited trion states with defined energy and spin. Subsequently, the time-dependent occupation of the trion ground state is monitored by spectrally resolved differential transmission measurements. We observe subpicosecond dynamics for a hole excited to the D shell. The energy dependence of this D -to-S shell intraband transition is investigated in quantum dots of varying size. Excitation of an electron-hole pair in the respective p shells leads to the formation of singlet and triplet spin configurations. Relaxation of the p -shell singlet is observed to occur on a time scale of a few picoseconds. Pumping of p -shell triplet transitions opens up two pathways with distinctly different scattering times. These processes are shown to be governed by the mixing of singlet and triplet states due to exchange interactions enabling simultaneous electron and hole spin flips. To isolate the relaxation channels, we align the spin of the residual electron by a magnetic field and employ laser pulses of defined helicity. This step provides ultrafast preparation of a fully inverted trion ground state of the quantum dot with near unity probability, enabling deterministic addition of a single photon to the probe pulse. Therefore our experiments represent a significant step towards using single quantum emitters with well-controled inversion to manipulate the photon statistics of ultrafast light pulses.

Static and dynamic postural control in low-vision and normal-vision adults.

PubMed

Tomomitsu, Mônica S V; Alonso, Angelica Castilho; Morimoto, Eurica; Bobbio, Tatiana G; Greve, Julia M D

2013-04-01

This study aimed to evaluate the influence of reduced visual information on postural control by comparing low-vision and normal-vision adults in static and dynamic conditions. Twenty-five low-vision subjects and twenty-five normal sighted adults were evaluated for static and dynamic balance using four protocols: 1) the Modified Clinical Test of Sensory Interaction on Balance on firm and foam surfaces with eyes opened and closed; 2) Unilateral Stance with eyes opened and closed; 3) Tandem Walk; and 4) Step Up/Over. The results showed that the low-vision group presented greater body sway compared with the normal vision during balance on a foam surface (p≤0.001), the Unilateral Stance test for both limbs (p≤0.001), and the Tandem Walk test. The low-vision group showed greater step width (p≤0.001) and slower gait speed (p≤0.004). In the Step Up/Over task, low-vision participants were more cautious in stepping up (right p≤0.005 and left p≤0.009) and in executing the movement (p≤0.001). These findings suggest that visual feedback is crucial for determining balance, especially for dynamic tasks and on foam surfaces. Low-vision individuals had worse postural stability than normal-vision adults in terms of dynamic tests and balance on foam surfaces.

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

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

Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.

Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

DOE PAGES

Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.; ...

2015-04-21

Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

Effects of Turbulence Model and Numerical Time Steps on Von Karman Flow Behavior and Drag Accuracy of Circular Cylinder

NASA Astrophysics Data System (ADS)

Amalia, E.; Moelyadi, M. A.; Ihsan, M.

2018-04-01

The flow of air passing around a circular cylinder on the Reynolds number of 250,000 is to show Von Karman Vortex Street Phenomenon. This phenomenon was captured well by using a right turbulence model. In this study, some turbulence models available in software ANSYS Fluent 16.0 was tested to simulate Von Karman vortex street phenomenon, namely k- epsilon, SST k-omega and Reynolds Stress, Detached Eddy Simulation (DES), and Large Eddy Simulation (LES). In addition, it was examined the effect of time step size on the accuracy of CFD simulation. The simulations are carried out by using two-dimensional and three- dimensional models and then compared with experimental data. For two-dimensional model, Von Karman Vortex Street phenomenon was captured successfully by using the SST k-omega turbulence model. As for the three-dimensional model, Von Karman Vortex Street phenomenon was captured by using Reynolds Stress Turbulence Model. The time step size value affects the smoothness quality of curves of drag coefficient over time, as well as affecting the running time of the simulation. The smaller time step size, the better inherent drag coefficient curves produced. Smaller time step size also gives faster computation time.

Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes.

PubMed

Hernandez-Perez, Ruth; García-Cordero, José L; Escobar, Juan V

2017-12-01

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depending on whether evaporation is limited by the diffusion of vapor molecules or by the transfer rate across the liquid-vapor interface. For the diffusion-limited regime, we find that a mass-loss rate equal to 3/7 of that of a free-standing evaporating droplet brings a good balance between simplicity and physical correctness. We also find a scaling law for the evaporation of multicomponent solutions. The scaling laws found are validated against experiments of the evaporation of droplets of (1) water, (2) blood plasma, and (3) a mixture of water and polyethylene glycol, pinned on acrylic pillars of different diameters. These results shed light on the macroscopic dynamics of evaporation on pillars as a first step towards the understanding of other complex phenomena that may be taking place during the evaporation process, such as particle transport and chemical reactions.

Depressive Symptoms Among Older Chinese Americans: Examining the Role of Acculturation and Family Dynamics.

PubMed

Sun, Fei; Gao, Xiang; Gao, Shuo; Li, Qilun; Hodge, David R

2018-06-14

This study identified the prevalence of depression and tested the influence of acculturation and family dynamics on depressive symptoms, among a community sample of older Chinese Americans. Data came from a survey of 385 Chinese Americans aged 55 and older (Mage = 72.4 years, SD = 8.7) living in a large metropolitan area in the American Southwest. The survey was administered in 2013 through face-to-face interviews. Depressive symptoms were assessed with the 12-item Center for Epidemiological Studies Depression scale. Approximately 19.5% of the sample reported mild depressive symptoms and an additional 8.5% reported moderate depressive symptoms. Three-step hierarchical regression analyses indicated that smaller family support network size and more family conflict were risk factors for depressive symptoms. The effect of acculturation was not significantly associated with depressive symptoms after controlling for family dynamics. Family support and conflict play a prominent role in explaining depressive symptoms among Chinese American older adults. The effect of acculturation is minimal when older adults have supportive families and good health. Interventions or services aimed at promoting family harmony for members of this population should be considered.

De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic.

PubMed

Murphy, Grant S; Greisman, Jack B; Hecht, Michael H

2016-01-29

Designing and producing novel proteins that fold into stable structures and provide essential biological functions are key goals in synthetic biology. In initial steps toward achieving these goals, we constructed a combinatorial library of de novo proteins designed to fold into 4-helix bundles. As described previously, screening this library for sequences that function in vivo to rescue conditionally lethal mutants of Escherichia coli (auxotrophs) yielded several de novo sequences, termed SynRescue proteins, which rescued four different E. coli auxotrophs. In an effort to understand the structural requirements necessary for auxotroph rescue, we investigated the biophysical properties of the SynRescue proteins, using both computational and experimental approaches. Results from circular dichroism, size-exclusion chromatography, and NMR demonstrate that the SynRescue proteins are α-helical and relatively stable. Surprisingly, however, they do not form well-ordered structures. Instead, they form dynamic structures that fluctuate between monomeric and dimeric states. These findings show that a well-ordered structure is not a prerequisite for life-sustaining functions, and suggests that dynamic structures may have been important in the early evolution of protein function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes

NASA Astrophysics Data System (ADS)

Hernandez-Perez, Ruth; García-Cordero, José L.; Escobar, Juan V.

2017-12-01

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depending on whether evaporation is limited by the diffusion of vapor molecules or by the transfer rate across the liquid-vapor interface. For the diffusion-limited regime, we find that a mass-loss rate equal to 3/7 of that of a free-standing evaporating droplet brings a good balance between simplicity and physical correctness. We also find a scaling law for the evaporation of multicomponent solutions. The scaling laws found are validated against experiments of the evaporation of droplets of (1) water, (2) blood plasma, and (3) a mixture of water and polyethylene glycol, pinned on acrylic pillars of different diameters. These results shed light on the macroscopic dynamics of evaporation on pillars as a first step towards the understanding of other complex phenomena that may be taking place during the evaporation process, such as particle transport and chemical reactions.

Acoustic investigation of the aperture dynamics of an elastic membrane closing an overpressurized cylindrical cavity

NASA Astrophysics Data System (ADS)

Sánchez, Claudia; Vidal, Valérie; Melo, Francisco

2015-08-01

We report an experimental study of the acoustic signal produced by the rupture of an elastic membrane that initially closes a cylindrical overpressurized cavity. This configuration has been recently used as an experimental model system for the investigation of the acoustic emission from the bursting of elongated gas bubbles rising in a conduit. Here, we investigate the effect of the membrane rupture dynamics on the acoustic signal produced by the pressure release by changing the initial tension of the membrane. The initial overpressure in the cavity is fixed at a value such that the system remains in the linear acoustic regime. For large initial membrane deformation, the rupture time τ rup is small compared to the wave propagation time in the cavity and the pressure wave inside the conduit can be fully captured by the linear theory. For low membrane tension, a hole is pierced in the membrane but its rupture does not occur. For intermediate deformation, finally, the rupture progresses in two steps: first the membrane opens slowly; then, after reaching a critical size, the rupture accelerates. A transversal wave is excited along the membrane surface. The characteristic signature of each opening dynamics on the acoustic emission is described.

Multipinhole SPECT helical scan parameters and imaging volume

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

Yao, Rutao, E-mail: rutaoyao@buffalo.edu; Deng, Xiao; Wei, Qingyang

Purpose: The authors developed SPECT imaging capability on an animal PET scanner using a multiple-pinhole collimator and step-and-shoot helical data acquisition protocols. The objective of this work was to determine the preferred helical scan parameters, i.e., the angular and axial step sizes, and the imaging volume, that provide optimal imaging performance. Methods: The authors studied nine helical scan protocols formed by permuting three rotational and three axial step sizes. These step sizes were chosen around the reference values analytically calculated from the estimated spatial resolution of the SPECT system and the Nyquist sampling theorem. The nine helical protocols were evaluatedmore » by two figures-of-merit: the sampling completeness percentage (SCP) and the root-mean-square (RMS) resolution. SCP was an analytically calculated numerical index based on projection sampling. RMS resolution was derived from the reconstructed images of a sphere-grid phantom. Results: The RMS resolution results show that (1) the start and end pinhole planes of the helical scheme determine the axial extent of the effective field of view (EFOV), and (2) the diameter of the transverse EFOV is adequately calculated from the geometry of the pinhole opening, since the peripheral region beyond EFOV would introduce projection multiplexing and consequent effects. The RMS resolution results of the nine helical scan schemes show optimal resolution is achieved when the axial step size is the half, and the angular step size is about twice the corresponding values derived from the Nyquist theorem. The SCP results agree in general with that of RMS resolution but are less critical in assessing the effects of helical parameters and EFOV. Conclusions: The authors quantitatively validated the effective FOV of multiple pinhole helical scan protocols and proposed a simple method to calculate optimal helical scan parameters.« less

How quantizable matter gravitates: A practitioner's guide

NASA Astrophysics Data System (ADS)

Schuller, Frederic P.; Witte, Christof

2014-05-01

We present the practical step-by-step procedure for constructing canonical gravitational dynamics and kinematics directly from any previously specified quantizable classical matter dynamics, and then illustrate the application of this recipe by way of two completely worked case studies. Following the same procedure, any phenomenological proposal for fundamental matter dynamics must be supplemented with a suitable gravity theory providing the coefficients and kinematical interpretation of the matter theory, before any of the two theories can be meaningfully compared to experimental data.

Composite grain size sensitive and grain size insensitive creep of bischofite, carnallite and mixed bischofite-carnallite-halite salt rock

NASA Astrophysics Data System (ADS)

Muhammad, Nawaz; de Bresser, Hans; Peach, Colin; Spiers, Chris

2016-04-01

Deformation experiments have been conducted on rock samples of the valuable magnesium and potassium salts bischofite and carnallite, and on mixed bischofite-carnallite-halite rocks. The samples have been machined from a natural core from the northern part of the Netherlands. Main aim was to produce constitutive flow laws that can be applied at the in situ conditions that hold in the undissolved wall rock of caverns resulting from solution mining. The experiments were triaxial compression tests carried out at true in situ conditions of 70° C temperature and 40 MPa confining pressure. A typical experiment consisted of a few steps at constant strain rate, in the range 10-5 to 10-8 s-1, interrupted by periods of stress relaxation. During the constant strain rate part of the test, the sample was deformed until a steady (or near steady) state of stress was reached. This usually required about 2-4% of shortening. Then the piston was arrested and the stress on the sample was allowed to relax until the diminishing force on the sample reached the limits of the load cell resolution, usually at a strain rate in the order of 10-9 s-1. The duration of each relaxation step was a few days. Carnallite was found to be 4-5 times stronger than bischofite. The bischofite-carnallite-halite mixtures, at their turn, were stronger than carnallite, and hence substantially stronger than pure bischofite. For bischofite as well as carnallite, we observed that during stress relaxation, the stress exponent nof a conventional power law changed from ˜5 at strain rate 10-5 s-1 to ˜1 at 10-9 s-1. The absolute strength of both materials remained higher if relaxation started at a higher stress, i.e. at a faster strain rate. We interpret this as indicating a difference in microstructure at the initiation of the relaxation, notably a smaller grain size related to dynamical recrystallization during the constant strain rate step. The data thus suggest that there is a gradual change in deformation mechanism with decreasing strain rate for both bischofite and carnallite, from grain size insensitive (GSI) dislocation creep at the higher strain rates to grain size sensitive (GSS, i.e. pressure solution) creep at slow strain rate. We can speculate about the composite GSI-GSS nature of the constitutive laws describing the creep of the salt materials.

Introducing the North Water: Histories of exploration, ice dynamics, living resources, and human settlement in the Thule Region.

PubMed

Hastrup, Kirsten; Mosbech, Anders; Grønnow, Bjarne

2018-04-01

The North Water is a recurrent polynya in the High Arctic situated between Northwest Greenland and Ellesmere Island of Canada. The North Water makes a dynamic space, where various processes may enhance or obstruct each other, accelerating or halting particular modes of human-animal relations in the region, where life itself depends on the North Water. This will be discussed in four steps. The first step posits the North Water as a perceived oasis for explorers and whalers hailing from Europe or America in the nineteenth century. The second step concentrates on the diverse rhythms inherent in the ice conditions, as affected by trends that are set in motion elsewhere. The third step highlights the implications of the dynamics of the ice and sea currents for animal life in the region. The fourth step gives an overview of human settlement patterns around the North Water across the ages. The article shows how natural and social features are deeply implicated in each other, even if they are not directly co-variant.

A kinetic Monte Carlo approach to diffusion-controlled thermal desorption spectroscopy

NASA Astrophysics Data System (ADS)

Schablitzki, T.; Rogal, J.; Drautz, R.

2017-06-01

Atomistic simulations of thermal desorption spectra for effusion from bulk materials to characterize binding or trapping sites are a challenging task as large system sizes as well as extended time scales are required. Here, we introduce an approach where we combine kinetic Monte Carlo with an analytic approximation of the superbasins within the framework of absorbing Markov chains. We apply our approach to the effusion of hydrogen from BCC iron, where the diffusion within bulk grains is coarse grained using absorbing Markov chains, which provide an exact solution of the dynamics within a superbasin. Our analytic approximation to the superbasin is transferable with respect to grain size and elliptical shapes and can be applied in simulations with constant temperature as well as constant heating rate. The resulting thermal desorption spectra are in close agreement with direct kinetic Monte Carlo simulations, but the calculations are computationally much more efficient. Our approach is thus applicable to much larger system sizes and provides a first step towards an atomistic understanding of the influence of structural features on the position and shape of peaks in thermal desorption spectra. This article is part of the themed issue 'The challenges of hydrogen and metals'.

Ligament Mediated Fragmentation of Viscoelastic Liquids

NASA Astrophysics Data System (ADS)

Keshavarz, Bavand; Houze, Eric C.; Moore, John R.; Koerner, Michael R.; McKinley, Gareth H.

2016-10-01

The breakup and atomization of complex fluids can be markedly different than the analogous processes in a simple Newtonian fluid. Atomization of paint, combustion of fuels containing antimisting agents, as well as physiological processes such as sneezing are common examples in which the atomized liquid contains synthetic or biological macromolecules that result in viscoelastic fluid characteristics. Here, we investigate the ligament-mediated fragmentation dynamics of viscoelastic fluids in three different canonical flows. The size distributions measured in each viscoelastic fragmentation process show a systematic broadening from the Newtonian solvent. In each case, the droplet sizes are well described by Gamma distributions which correspond to a fragmentation-coalescence scenario. We use a prototypical axial step strain experiment together with high-speed video imaging to show that this broadening results from the pronounced change in the corrugated shape of viscoelastic ligaments as they separate from the liquid core. These corrugations saturate in amplitude and the measured distributions for viscoelastic liquids in each process are given by a universal probability density function, corresponding to a Gamma distribution with nmin=4 . The breadth of this size distribution for viscoelastic filaments is shown to be constrained by a geometrical limit which can not be exceeded in ligament-mediated fragmentation phenomena.

Ligament Mediated Fragmentation of Viscoelastic Liquids.

PubMed

Keshavarz, Bavand; Houze, Eric C; Moore, John R; Koerner, Michael R; McKinley, Gareth H

2016-10-07

The breakup and atomization of complex fluids can be markedly different than the analogous processes in a simple Newtonian fluid. Atomization of paint, combustion of fuels containing antimisting agents, as well as physiological processes such as sneezing are common examples in which the atomized liquid contains synthetic or biological macromolecules that result in viscoelastic fluid characteristics. Here, we investigate the ligament-mediated fragmentation dynamics of viscoelastic fluids in three different canonical flows. The size distributions measured in each viscoelastic fragmentation process show a systematic broadening from the Newtonian solvent. In each case, the droplet sizes are well described by Gamma distributions which correspond to a fragmentation-coalescence scenario. We use a prototypical axial step strain experiment together with high-speed video imaging to show that this broadening results from the pronounced change in the corrugated shape of viscoelastic ligaments as they separate from the liquid core. These corrugations saturate in amplitude and the measured distributions for viscoelastic liquids in each process are given by a universal probability density function, corresponding to a Gamma distribution with n_{min}=4. The breadth of this size distribution for viscoelastic filaments is shown to be constrained by a geometrical limit which can not be exceeded in ligament-mediated fragmentation phenomena.

Dynamic response of ultrathin highly dense ZIF-8 nanofilms.

PubMed

Cookney, Joanna; Ogieglo, Wojciech; Hrabanek, Pavel; Vankelecom, Ivo; Fila, Vlastimil; Benes, Nieck E

2014-10-11

Ultrathin ZIF-8 nanofilms are prepared by facile step-by-step dip coating. A critical withdrawal speed allows for films with a very uniform minimum thickness. The high refractive index of the films denotes the absence of mesopores. The dynamic response of the films to CO2 exposure resembles behaviour observed for non-equilibrium organic polymers.

Dynamic Emotional Processing in Experiential Therapy: Two Steps Forward, One Step Back

ERIC Educational Resources Information Center

Pascual-Leone, Antonio

2009-01-01

The study of dynamic and nonlinear change has been a valuable development in psychotherapy process research. However, little advancement has been made in describing how moment-by-moment affective processes contribute to larger units of change. The purpose of this study was to examine observable moment-by-moment sequences in emotional processing as…

Determination of the structures of small gold clusters on stepped magnesia by density functional calculations.

PubMed

Damianos, Konstantina; Ferrando, Riccardo

2012-02-21

The structural modifications of small supported gold clusters caused by realistic surface defects (steps) in the MgO(001) support are investigated by computational methods. The most stable gold cluster structures on a stepped MgO(001) surface are searched for in the size range up to 24 Au atoms, and locally optimized by density-functional calculations. Several structural motifs are found within energy differences of 1 eV: inclined leaflets, arched leaflets, pyramidal hollow cages and compact structures. We show that the interaction with the step clearly modifies the structures with respect to adsorption on the flat defect-free surface. We find that leaflet structures clearly dominate for smaller sizes. These leaflets are either inclined and quasi-horizontal, or arched, at variance with the case of the flat surface in which vertical leaflets prevail. With increasing cluster size pyramidal hollow cages begin to compete against leaflet structures. Cage structures become more and more favourable as size increases. The only exception is size 20, at which the tetrahedron is found as the most stable isomer. This tetrahedron is however quite distorted. The comparison of two different exchange-correlation functionals (Perdew-Burke-Ernzerhof and local density approximation) show the same qualitative trends. This journal is © The Royal Society of Chemistry 2012

The effect of external forces on discrete motion within holographic optical tweezers.

PubMed

Eriksson, E; Keen, S; Leach, J; Goksör, M; Padgett, M J

2007-12-24

Holographic optical tweezers is a widely used technique to manipulate the individual positions of optically trapped micron-sized particles in a sample. The trap positions are changed by updating the holographic image displayed on a spatial light modulator. The updating process takes a finite time, resulting in a temporary decrease of the intensity, and thus the stiffness, of the optical trap. We have investigated this change in trap stiffness during the updating process by studying the motion of an optically trapped particle in a fluid flow. We found a highly nonlinear behavior of the change in trap stiffness vs. changes in step size. For step sizes up to approximately 300 nm the trap stiffness is decreasing. Above 300 nm the change in trap stiffness remains constant for all step sizes up to one particle radius. This information is crucial for optical force measurements using holographic optical tweezers.

Finite-difference modeling with variable grid-size and adaptive time-step in porous media

NASA Astrophysics Data System (ADS)

Liu, Xinxin; Yin, Xingyao; Wu, Guochen

2014-04-01

Forward modeling of elastic wave propagation in porous media has great importance for understanding and interpreting the influences of rock properties on characteristics of seismic wavefield. However, the finite-difference forward-modeling method is usually implemented with global spatial grid-size and time-step; it consumes large amounts of computational cost when small-scaled oil/gas-bearing structures or large velocity-contrast exist underground. To overcome this handicap, combined with variable grid-size and time-step, this paper developed a staggered-grid finite-difference scheme for elastic wave modeling in porous media. Variable finite-difference coefficients and wavefield interpolation were used to realize the transition of wave propagation between regions of different grid-size. The accuracy and efficiency of the algorithm were shown by numerical examples. The proposed method is advanced with low computational cost in elastic wave simulation for heterogeneous oil/gas reservoirs.

Rock sampling. [method for controlling particle size distribution

NASA Technical Reports Server (NTRS)

Blum, P. (Inventor)

1971-01-01

A method for sampling rock and other brittle materials and for controlling resultant particle sizes is described. The method involves cutting grooves in the rock surface to provide a grouping of parallel ridges and subsequently machining the ridges to provide a powder specimen. The machining step may comprise milling, drilling, lathe cutting or the like; but a planing step is advantageous. Control of the particle size distribution is effected primarily by changing the height and width of these ridges. This control exceeds that obtainable by conventional grinding.

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

Lee, Jonghun; Jiang, Zhang; Wang, Jin

Using high resolution in situ small angle x-ray scattering in conjunction with oscillatory shear on highly monodisperse silica suspensions, we demonstrate that an order-to-disorder transition leads to a dynamic shear thickening in a lower stress regime than the standard steady shear thickening. We show that the order-to-disorder transition is controlled by strain, which is distinguishably different from steady shear thickening which is a stress related phenomenon. The appearance of this two-step shear thinning and thickening transition is also influenced by particle size, monodispersity and measurement conditions (i.e. oscillatory shear vs. steady shear). Our results show definitively that the order-to-disorder transitionmore » induced thickening is completely unrelated to the mechanism that drives the steady shear thickening.« less

Unraveling the Role of Order-to-Disorder Transition in Shear Thickening Suspensions

NASA Astrophysics Data System (ADS)

Lee, Jonghun; Jiang, Zhang; Wang, Jin; Sandy, Alec R.; Narayanan, Suresh; Lin, Xiao-Min

2018-01-01

Using high-resolution in situ small angle x-ray scattering in conjunction with oscillatory shear on highly monodisperse silica suspensions, we demonstrate that an order-to-disorder transition leads to a dynamic shear thickening in a lower stress regime than the standard steady shear thickening. We show that the order-to-disorder transition is controlled by strain, which is distinguishably different from steady shear thickening, which is a stress-related phenomenon. The appearance of this two-step shear thinning and thickening transition is also influenced by the particle size, monodispersity, and measurement conditions (i.e., oscillatory shear versus steady shear). Our results show definitively that the order-to-disorder transition-induced thickening is completely unrelated to the mechanism that drives steady shear thickening.

Design study of an ultra-compact superconducting cyclotron for isotope production

NASA Astrophysics Data System (ADS)

Smirnov, V.; Vorozhtsov, S.; Vincent, J.

2014-11-01

A 12.5 MeV, 25 μA, proton compact superconducting cyclotron for medical isotope production has been designed and is currently in fabrication. The machine is initially aimed at producing 13N ammonia for Positron Emission Tomography (PET) cardiology applications. With an ultra-compact size and cost-effective price point, this system will offer clinicians unprecedented access to the preferred radiopharmaceutical isotope for cardiac PET imaging. A systems approach that carefully balanced the subsystem requirements coupled to precise beam dynamics calculations was followed. The system is designed to irradiate a liquid target internal to the cyclotron and to minimize the need for radiation shielding. The main parameters of the cyclotron, its design, and principal steps of the development work are presented here.

A particle-in-cell method for the simulation of plasmas based on an unconditionally stable field solver

DOE PAGES

Wolf, Eric M.; Causley, Matthew; Christlieb, Andrew; ...

2016-08-09

Here, we propose a new particle-in-cell (PIC) method for the simulation of plasmas based on a recently developed, unconditionally stable solver for the wave equation. This method is not subject to a CFL restriction, limiting the ratio of the time step size to the spatial step size, typical of explicit methods, while maintaining computational cost and code complexity comparable to such explicit schemes. We describe the implementation in one and two dimensions for both electrostatic and electromagnetic cases, and present the results of several standard test problems, showing good agreement with theory with time step sizes much larger than allowedmore » by typical CFL restrictions.« less

Antisymmetric vortex interactions in the wake behind a step cylinder

NASA Astrophysics Data System (ADS)

Tian, Cai; Jiang, Fengjian; Pettersen, Bjørnar; Andersson, Helge I.

2017-10-01

Flow around a step cylinder at the Reynolds number 150 was simulated by directly solving the full Navier-Stokes equations. The configuration was adopted from the work of Morton and Yarusevych ["Vortex shedding in the wake of a step cylinder," Phys. Fluids 22, 083602 (2010)], in which the wake dynamics were systematically described. A more detailed investigation of the vortex dislocation process has now been performed. Two kinds of new loop vortex structures were identified. Additionally, antisymmetric vortex interactions in two adjacent vortex dislocation processes were observed and explained. The results in this letter serve as a supplement for a more thorough understanding of the vortex dynamics in the step cylinder wake.

Continuous track paths reveal additive evidence integration in multistep decision making.

PubMed

Buc Calderon, Cristian; Dewulf, Myrtille; Gevers, Wim; Verguts, Tom

2017-10-03

Multistep decision making pervades daily life, but its underlying mechanisms remain obscure. We distinguish four prominent models of multistep decision making, namely serial stage, hierarchical evidence integration, hierarchical leaky competing accumulation (HLCA), and probabilistic evidence integration (PEI). To empirically disentangle these models, we design a two-step reward-based decision paradigm and implement it in a reaching task experiment. In a first step, participants choose between two potential upcoming choices, each associated with two rewards. In a second step, participants choose between the two rewards selected in the first step. Strikingly, as predicted by the HLCA and PEI models, the first-step decision dynamics were initially biased toward the choice representing the highest sum/mean before being redirected toward the choice representing the maximal reward (i.e., initial dip). Only HLCA and PEI predicted this initial dip, suggesting that first-step decision dynamics depend on additive integration of competing second-step choices. Our data suggest that potential future outcomes are progressively unraveled during multistep decision making.

Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory.

PubMed

Kooijman, S A L M; Troost, T A

2007-02-01

The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.

Variable effects of climate on forest growth in relation to climate extremes, disturbance, and forest dynamics.

PubMed

Itter, Malcolm S; Finley, Andrew O; D'Amato, Anthony W; Foster, Jane R; Bradford, John B

2017-06-01

Changes in the frequency, duration, and severity of climate extremes are forecast to occur under global climate change. The impacts of climate extremes on forest productivity and health remain difficult to predict due to potential interactions with disturbance events and forest dynamics-changes in forest stand composition, density, size and age structure over time. Such interactions may lead to non-linear forest growth responses to climate involving thresholds and lag effects. Understanding how forest dynamics influence growth responses to climate is particularly important given stand structure and composition can be modified through management to increase forest resistance and resilience to climate change. To inform such adaptive management, we develop a hierarchical Bayesian state space model in which climate effects on tree growth are allowed to vary over time and in relation to past climate extremes, disturbance events, and forest dynamics. The model is an important step toward integrating disturbance and forest dynamics into predictions of forest growth responses to climate extremes. We apply the model to a dendrochronology data set from forest stands of varying composition, structure, and development stage in northeastern Minnesota that have experienced extreme climate years and forest tent caterpillar defoliation events. Mean forest growth was most sensitive to water balance variables representing climatic water deficit. Forest growth responses to water deficit were partitioned into responses driven by climatic threshold exceedances and interactions with insect defoliation. Forest growth was both resistant and resilient to climate extremes with the majority of forest growth responses occurring after multiple climatic threshold exceedances across seasons and years. Interactions between climate and disturbance were observed in a subset of years with insect defoliation increasing forest growth sensitivity to water availability. Forest growth was particularly sensitive to climate extremes during periods of high stem density following major regeneration events when average inter-tree competition was high. Results suggest the resistance and resilience of forest growth to climate extremes can be increased through management steps such as thinning to reduce competition during early stages of stand development and small-group selection harvests to maintain forest structures characteristic of older, mature stands. © 2017 by the Ecological Society of America.

Tracking the Spatiotemporal Neural Dynamics of Real-world Object Size and Animacy in the Human Brain.

PubMed

Khaligh-Razavi, Seyed-Mahdi; Cichy, Radoslaw Martin; Pantazis, Dimitrios; Oliva, Aude

2018-06-07

Animacy and real-world size are properties that describe any object and thus bring basic order into our perception of the visual world. Here, we investigated how the human brain processes real-world size and animacy. For this, we applied representational similarity to fMRI and MEG data to yield a view of brain activity with high spatial and temporal resolutions, respectively. Analysis of fMRI data revealed that a distributed and partly overlapping set of cortical regions extending from occipital to ventral and medial temporal cortex represented animacy and real-world size. Within this set, parahippocampal cortex stood out as the region representing animacy and size stronger than most other regions. Further analysis of the detailed representational format revealed differences among regions involved in processing animacy. Analysis of MEG data revealed overlapping temporal dynamics of animacy and real-world size processing starting at around 150 msec and provided the first neuromagnetic signature of real-world object size processing. Finally, to investigate the neural dynamics of size and animacy processing simultaneously in space and time, we combined MEG and fMRI with a novel extension of MEG-fMRI fusion by representational similarity. This analysis revealed partly overlapping and distributed spatiotemporal dynamics, with parahippocampal cortex singled out as a region that represented size and animacy persistently when other regions did not. Furthermore, the analysis highlighted the role of early visual cortex in representing real-world size. A control analysis revealed that the neural dynamics of processing animacy and size were distinct from the neural dynamics of processing low-level visual features. Together, our results provide a detailed spatiotemporal view of animacy and size processing in the human brain.

Critical behavior of a two-step contagion model with multiple seeds

NASA Astrophysics Data System (ADS)

Choi, Wonjun; Lee, Deokjae; Kahng, B.

2017-06-01

A two-step contagion model with a single seed serves as a cornerstone for understanding the critical behaviors and underlying mechanism of discontinuous percolation transitions induced by cascade dynamics. When the contagion spreads from a single seed, a cluster of infected and recovered nodes grows without any cluster merging process. However, when the contagion starts from multiple seeds of O (N ) where N is the system size, a node weakened by a seed can be infected more easily when it is in contact with another node infected by a different pathogen seed. This contagion process can be viewed as a cluster merging process in a percolation model. Here we show analytically and numerically that when the density of infectious seeds is relatively small but O (1 ) , the epidemic transition is hybrid, exhibiting both continuous and discontinuous behavior, whereas when it is sufficiently large and reaches a critical point, the transition becomes continuous. We determine the full set of critical exponents describing the hybrid and the continuous transitions. Their critical behaviors differ from those in the single-seed case.

Towards quality by design in pharmaceutical manufacturing: modelling and control of air jet mills

NASA Astrophysics Data System (ADS)

Bhonsale, Satyajeet; Telen, Dries; Stokbroekx, Bard; Van Impe, Jan

2017-06-01

Milling is an important step in pharmaceutical manufacturing as it not only determines the final formulation of the drug product, but also influences the bioavailability and dissolution rate of the active pharmaceutical ingredient (API). In this respect, the air jet mill (AJM) is most commonly used in the pharmaceutical industry as it is a non-contaminating and non-degrading self-classifying process capable of delivering narrow particle size distributions (PSD). Keeping the principles of Quality by Design in mind, the Critical Process Parameters (CPPs) of the AJM have been identified to be the pressures at the grinding nozzles, and the feed rate which affect the PSD, surface charge and the morphology of the product (i.e. the Critical Material Attributes (CMAs)). For the purpose of this research, the PSD is considered to be the only relevant CMA. A population balance based model is proposed to simulate the dynamics milling operation by utilizing the concept of breakage functions. This model agrees qualitatively with experimental observations of the air jet mill unit present at Janssen Pharmaceutica but further steps for model validation need to be carried out.

An illustration of new methods in machine condition monitoring, Part I: stochastic resonance

NASA Astrophysics Data System (ADS)

Worden, K.; Antoniadou, I.; Marchesiello, S.; Mba, C.; Garibaldi, L.

2017-05-01

There have been many recent developments in the application of data-based methods to machine condition monitoring. A powerful methodology based on machine learning has emerged, where diagnostics are based on a two-step procedure: extraction of damage-sensitive features, followed by unsupervised learning (novelty detection) or supervised learning (classification). The objective of the current pair of papers is simply to illustrate one state-of-the-art procedure for each step, using synthetic data representative of reality in terms of size and complexity. The first paper in the pair will deal with feature extraction. Although some papers have appeared in the recent past considering stochastic resonance as a means of amplifying damage information in signals, they have largely relied on ad hoc specifications of the resonator used. In contrast, the current paper will adopt a principled optimisation-based approach to the resonator design. The paper will also show that a discrete dynamical system can provide all the benefits of a continuous system, but also provide a considerable speed-up in terms of simulation time in order to facilitate the optimisation approach.

Evidence of a two-step process and pathway dependency in the thermodynamics of poly(diallyldimethylammonium chloride)/poly(sodium acrylate) complexation.

PubMed

Vitorazi, L; Ould-Moussa, N; Sekar, S; Fresnais, J; Loh, W; Chapel, J-P; Berret, J-F

2014-12-21

Recent studies have pointed out the importance of polyelectrolyte assembly in the elaboration of innovative nanomaterials. Beyond their structures, many important questions on the thermodynamics of association remain unanswered. Here, we investigate the complexation between poly(diallyldimethylammonium chloride) (PDADMAC) and poly(sodium acrylate) (PANa) chains using a combination of three techniques: isothermal titration calorimetry (ITC), static and dynamic light scattering and electrophoresis. Upon addition of PDADMAC to PANa or vice-versa, the results obtained by the different techniques agree well with each other, and reveal a two-step process. The primary process is the formation of highly charged polyelectrolyte complexes of size 100 nm. The secondary process is the transition towards a coacervate phase made of rich and poor polymer droplets. The binding isotherms measured are accounted for using a phenomenological model that provides the thermodynamic parameters for each reaction. Small positive enthalpies and large positive entropies consistent with a counterion release scenario are found throughout this study. Furthermore, this work stresses the importance of the underestimated formulation pathway or mixing order in polyelectrolyte complexation.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene

NASA Astrophysics Data System (ADS)

Sand, Andrew M.; Truhlar, Donald G.; Gagliardi, Laura

2017-01-01

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Precision Linear Actuator for Space Interferometry Mission (SIM) Siderostat Pointing

NASA Technical Reports Server (NTRS)

Cook, Brant; Braun, David; Hankins, Steve; Koenig, John; Moore, Don

2008-01-01

'SIM PlanetQuest will exploit the classical measuring tool of astrometry (interferometry) with unprecedented precision to make dramatic advances in many areas of astronomy and astrophysics'(1). In order to obtain interferometric data two large steerable mirrors, or Siderostats, are used to direct starlight into the interferometer. A gimbaled mechanism actuated by linear actuators is chosen to meet the unprecedented pointing and angle tracking requirements of SIM. A group of JPL engineers designed, built, and tested a linear ballscrew actuator capable of performing submicron incremental steps for 10 years of continuous operation. Precise, zero backlash, closed loop pointing control requirements, lead the team to implement a ballscrew actuator with a direct drive DC motor and a precision piezo brake. Motor control commutation using feedback from a precision linear encoder on the ballscrew output produced an unexpected incremental step size of 20 nm over a range of 120 mm, yielding a dynamic range of 6,000,000:1. The results prove linear nanometer positioning requires no gears, levers, or hydraulic converters. Along the way many lessons have been learned and will subsequently be shared.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene.

PubMed

Sand, Andrew M; Truhlar, Donald G; Gagliardi, Laura

2017-01-21

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H 2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Step and Kink Dynamics in Inorganic and Protein Crystallization

NASA Technical Reports Server (NTRS)

Chernov, A. A.; Rashkovich, L. N.; Vekilov, P. G.; DeYoreo, J. J.

2004-01-01

Behavior of low-kink-density steps in solution growth and consequences for general understanding of spiral crystal growth processes will be overviewed. Also, influence of turbulence on step bunching and possibility to diminish this bunching will be presented.

Age-related differences in the maintenance of frontal plane dynamic stability while stepping to targets

PubMed Central

Hurt, Christopher P.; Grabiner, Mark D.

2015-01-01

Older adults may be vulnerable to frontal plane dynamic instability, which is of clinical significance. The purpose of the current investigation was to examine the age-related differences in frontal plane dynamic stability by quantifying the margin of stability and hip abductor moment generation of subjects performing a single crossover step and sidestep to targets that created three different step widths during forward locomotion. Nineteen young adults (9 males, age: 22.9±3.1 years, height: 174.3±10.2 cm, mass: 71.7±13.0 kg) and 18 older adults (9 males, age: 72.8±5.2 years, height: 174.9±8.6 cm, mass: 78.0±16.3 kg) participated. For each walking trial, subjects performed a single laterally-directed step to a target on a force plate. Subjects were instructed to “perform the lateral step and keep walking forward”. The peak hip abductor moment of the stepping limb was 42% larger by older adults compared to younger adults (p<0.001). Older adults were also more stable than younger adults at all step targets (p<0.001). Older adults executed the lateral step with slower forward-directed and lateral-directed velocity despite similar step widths. Age-related differences in hip abduction moments may reflect greater muscular effort by older adults to reduce the likelihood of becoming unstable. The results of this investigation, in which subjects performed progressively larger lateral-directed steps, provide evidence that older adults may not be more laterally unstable than younger adults. However, age-related differences in this study could also reflect a compensatory strategy by older adults to ensure stability while performing this task. PMID:25627870

Age-related differences in the maintenance of frontal plane dynamic stability while stepping to targets.

PubMed

Hurt, Christopher P; Grabiner, Mark D

2015-02-26

Older adults may be vulnerable to frontal plane dynamic instability, which is of clinical significance. The purpose of the current investigation was to examine the age-related differences in frontal plane dynamic stability by quantifying the margin of stability and hip abductor moment generation of subjects performing a single crossover step and sidestep to targets that created three different step widths during forward locomotion. Nineteen young adults (9 males, age: 22.9±3.1 years, height: 174.3±10.2cm, mass: 71.7±13.0kg) and 18 older adults (9 males, age: 72.8±5.2 years, height: 174.9±8.6cm, mass: 78.0±16.3kg) participated. For each walking trial, subjects performed a single laterally-directed step to a target on a force plate. Subjects were instructed to "perform the lateral step and keep walking forward". The peak hip abductor moment of the stepping limb was 42% larger by older adults compared to younger adults (p<0.001). Older adults were also more stable than younger adults at all step targets (p<0.001). Older adults executed the lateral step with slower forward-directed and lateral-directed velocity despite similar step widths. Age-related differences in hip abduction moments may reflect greater muscular effort by older adults to reduce the likelihood of becoming unstable. The results of this investigation, in which subjects performed progressively larger lateral-directed steps, provide evidence that older adults may not be more laterally unstable than younger adults. However, age-related differences in this study could also reflect a compensatory strategy by older adults to ensure stability while performing this task. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Surface treated carbon catalysts produced from waste tires for fatty acids to biofuel conversion

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

Hood, Zachary D.; Adhikari, Shiba P.; Wright, Marcus W.

A method of making solid acid catalysts includes the step of sulfonating waste tire pieces in a first sulfonation step. The sulfonated waste tire pieces are pyrolyzed to produce carbon composite pieces having a pore size less than 10 nm. The carbon composite pieces are then ground to produce carbon composite powders having a size less than 50 .mu.m. The carbon composite particles are sulfonated in a second sulfonation step to produce sulfonated solid acid catalysts. A method of making biofuels and solid acid catalysts are also disclosed.

Method and apparatus for sizing and separating warp yarns using acoustical energy

DOEpatents

Sheen, Shuh-Haw; Chien, Hual-Te; Raptis, Apostolos C.; Kupperman, David S.

1998-01-01

A slashing process for preparing warp yarns for weaving operations including the steps of sizing and/or desizing the yarns in an acoustic resonance box and separating the yarns with a leasing apparatus comprised of a set of acoustically agitated lease rods. The sizing step includes immersing the yarns in a size solution contained in an acoustic resonance box. Acoustic transducers are positioned against the exterior of the box for generating an acoustic pressure field within the size solution. Ultrasonic waves that result from the acoustic pressure field continuously agitate the size solution to effect greater mixing and more uniform application and penetration of the size onto the yarns. The sized yarns are then separated by passing the warp yarns over and under lease rods. Electroacoustic transducers generate acoustic waves along the longitudinal axis of the lease rods, creating a shearing motion on the surface of the rods for splitting the yarns.

Control Software for Piezo Stepping Actuators

NASA Technical Reports Server (NTRS)

Shields, Joel F.

2013-01-01

A control system has been developed for the Space Interferometer Mission (SIM) piezo stepping actuator. Piezo stepping actuators are novel because they offer extreme dynamic range (centimeter stroke with nanometer resolution) with power, thermal, mass, and volume advantages over existing motorized actuation technology. These advantages come with the added benefit of greatly reduced complexity in the support electronics. The piezo stepping actuator consists of three fully redundant sets of piezoelectric transducers (PZTs), two sets of brake PZTs, and one set of extension PZTs. These PZTs are used to grasp and move a runner attached to the optic to be moved. By proper cycling of the two brake and extension PZTs, both forward and backward moves of the runner can be achieved. Each brake can be configured for either a power-on or power-off state. For SIM, the brakes and gate of the mechanism are configured in such a manner that, at the end of the step, the actuator is in a parked or power-off state. The control software uses asynchronous sampling of an optical encoder to monitor the position of the runner. These samples are timed to coincide with the end of the previous move, which may consist of a variable number of steps. This sampling technique linearizes the device by avoiding input saturation of the actuator and makes latencies of the plant vanish. The software also estimates, in real time, the scale factor of the device and a disturbance caused by cycling of the brakes. These estimates are used to actively cancel the brake disturbance. The control system also includes feedback and feedforward elements that regulate the position of the runner to a given reference position. Convergence time for smalland medium-sized reference positions (less than 200 microns) to within 10 nanometers can be achieved in under 10 seconds. Convergence times for large moves (greater than 1 millimeter) are limited by the step rate.

Auto- and cross-power spectral analysis of dual trap optical tweezer experiments using Bayesian inference.

PubMed

von Hansen, Yann; Mehlich, Alexander; Pelz, Benjamin; Rief, Matthias; Netz, Roland R

2012-09-01

The thermal fluctuations of micron-sized beads in dual trap optical tweezer experiments contain complete dynamic information about the viscoelastic properties of the embedding medium and-if present-macromolecular constructs connecting the two beads. To quantitatively interpret the spectral properties of the measured signals, a detailed understanding of the instrumental characteristics is required. To this end, we present a theoretical description of the signal processing in a typical dual trap optical tweezer experiment accounting for polarization crosstalk and instrumental noise and discuss the effect of finite statistics. To infer the unknown parameters from experimental data, a maximum likelihood method based on the statistical properties of the stochastic signals is derived. In a first step, the method can be used for calibration purposes: We propose a scheme involving three consecutive measurements (both traps empty, first one occupied and second empty, and vice versa), by which all instrumental and physical parameters of the setup are determined. We test our approach for a simple model system, namely a pair of unconnected, but hydrodynamically interacting spheres. The comparison to theoretical predictions based on instantaneous as well as retarded hydrodynamics emphasizes the importance of hydrodynamic retardation effects due to vorticity diffusion in the fluid. For more complex experimental scenarios, where macromolecular constructs are tethered between the two beads, the same maximum likelihood method in conjunction with dynamic deconvolution theory will in a second step allow one to determine the viscoelastic properties of the tethered element connecting the two beads.

CFD simulation of a screw compressor including leakage flows and rotor heating

NASA Astrophysics Data System (ADS)

Spille-Kohoff, Andreas, Dr.; Hesse, Jan; El Shorbagy, Ahmed

2015-08-01

Computational Fluid Dynamics (CFD) simulations have promising potential to become an important part in the development process of positive displacement (PD) machines. CFD delivers deep insights into the flow and thermodynamic behaviour of PD machines. However, the numerical simulation of such machines is more complex compared to dynamic pumps like turbines or fans. The fluid transport in size-changing chambers with very small clearances between the rotors, and between rotors and casing, demands complex meshes that change with each time step. Additionally, the losses due to leakage flows and the heat transfer to the rotors need high-quality meshes so that automatic remeshing is almost impossible. In this paper, setup steps and results for the simulation of a dry screw compressor are shown. The rotating parts are meshed with TwinMesh, a special hexahedral meshing program for gear pumps, gerotors, lobe pumps and screw compressors. In particular, these meshes include axial and radial clearances between housing and rotors, and beside the fluid volume the rotor solids are also meshed. The CFD simulation accounts for gas flow with compressibility and turbulence effects, heat transfer between gas and rotors, and leakage flows through the clearances. We show time- resolved results for torques, forces, interlobe pressure, mass flow, and heat flow between gas and rotors, as well as time- and space-resolved results for pressure, velocity, temperature etc. for different discharge ports and working points of the screw compressor. These results are also used as thermal loads for deformation simulations of the rotors.

Cognitive mechanisms for explaining dynamics of aesthetic appreciation

PubMed Central

Carbon, Claus-Christian

2011-01-01

For many domains aesthetic appreciation has proven to be highly reliable. Evaluations of facial attractiveness, for instance, show high internal consistencies and impressively high inter-rater reliabilities, even across cultures. This indicates general mechanisms underlying such evaluations. It is, however, also obvious that our taste for specific objects is not always stable—in some realms such stability is hardly conceivable at all since aesthetic domains such as fashion, design, or art are inherently very dynamic. Gaining insights into the cognitive mechanisms that trigger and enable corresponding changes of aesthetic appreciation is of particular interest for psychologists as this will probably reveal essential mechanisms of aesthetic evaluations per se. The present paper develops a two-step model, dynamically adapting itself, which accounts for typical dynamics of aesthetic appreciation found in different research areas such as art history, philosophy, and psychology. The first step assumes singular creative sources creating and establishing innovative material towards which, in a second step, people adapt by integrating it into their visual habits. This inherently leads to dynamic changes of the beholders— aesthetic appreciation. PMID:23145254

A Neural Dynamic Model Generates Descriptions of Object-Oriented Actions.

PubMed

Richter, Mathis; Lins, Jonas; Schöner, Gregor

2017-01-01

Describing actions entails that relations between objects are discovered. A pervasively neural account of this process requires that fundamental problems are solved: the neural pointer problem, the binding problem, and the problem of generating discrete processing steps from time-continuous neural processes. We present a prototypical solution to these problems in a neural dynamic model that comprises dynamic neural fields holding representations close to sensorimotor surfaces as well as dynamic neural nodes holding discrete, language-like representations. Making the connection between these two types of representations enables the model to describe actions as well as to perceptually ground movement phrases-all based on real visual input. We demonstrate how the dynamic neural processes autonomously generate the processing steps required to describe or ground object-oriented actions. By solving the fundamental problems of neural pointing, binding, and emergent discrete processing, the model may be a first but critical step toward a systematic neural processing account of higher cognition. Copyright © 2017 The Authors. Topics in Cognitive Science published by Wiley Periodicals, Inc. on behalf of Cognitive Science Society.

Second Wind: Handbook for Happy Retirement.

ERIC Educational Resources Information Center

Kelly, Philip J.

Reflecting 10 years of actual retirement experience, the author attempts to prove that older people can live interesting dynamic lives right to the last moment. The book, with its conversational, step-by-step style, has been written for anybody over 50. It presents retirement as a "stepping out" rather than a "stepping down"; the solid realities…

Dynamic code block size for JPEG 2000

NASA Astrophysics Data System (ADS)

Tsai, Ping-Sing; LeCornec, Yann

2008-02-01

Since the standardization of the JPEG 2000, it has found its way into many different applications such as DICOM (digital imaging and communication in medicine), satellite photography, military surveillance, digital cinema initiative, professional video cameras, and so on. The unified framework of the JPEG 2000 architecture makes practical high quality real-time compression possible even in video mode, i.e. motion JPEG 2000. In this paper, we present a study of the compression impact using dynamic code block size instead of fixed code block size as specified in the JPEG 2000 standard. The simulation results show that there is no significant impact on compression if dynamic code block sizes are used. In this study, we also unveil the advantages of using dynamic code block sizes.

Modeling Zone-3 Protection with Generic Relay Models for Dynamic Contingency Analysis

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

Huang, Qiuhua; Vyakaranam, Bharat GNVSR; Diao, Ruisheng

This paper presents a cohesive approach for calculating and coordinating the settings of multiple zone-3 protections for dynamic contingency analysis. The zone-3 protections are represented by generic distance relay models. A two-step approach for determining zone-3 relay settings is proposed. The first step is to calculate settings, particularly, the reach, of each zone-3 relay individually by iteratively running line open-end fault short circuit analysis; the blinder is also employed and properly set to meet the industry standard under extreme loading conditions. The second step is to systematically coordinate the protection settings of the zone-3 relays. The main objective of thismore » coordination step is to address the over-reaching issues. We have developed a tool to automate the proposed approach and generate the settings of all distance relays in a PSS/E dyr format file. The calculated zone-3 settings have been tested on a modified IEEE 300 system using a dynamic contingency analysis tool (DCAT).« less

Tracking control of air-breathing hypersonic vehicles with non-affine dynamics via improved neural back-stepping design.

PubMed

Bu, Xiangwei; He, Guangjun; Wang, Ke

2018-04-01

This study considers the design of a new back-stepping control approach for air-breathing hypersonic vehicle (AHV) non-affine models via neural approximation. The AHV's non-affine dynamics is decomposed into velocity subsystem and altitude subsystem to be controlled separately, and robust adaptive tracking control laws are developed using improved back-stepping designs. Neural networks are applied to estimate the unknown non-affine dynamics, which guarantees the addressed controllers with satisfactory robustness against uncertainties. In comparison with the existing control methodologies, the special contributions are that the non-affine issue is handled by constructing two low-pass filters based on model transformations, and virtual controllers are treated as intermediate variables such that they aren't needed for back-stepping designs any more. Lyapunov techniques are employed to show the uniformly ultimately boundedness of all closed-loop signals. Finally, simulation results are presented to verify the tracking performance and superiorities of the investigated control strategy. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Optimal subinterval selection approach for power system transient stability simulation

DOE PAGES

Kim, Soobae; Overbye, Thomas J.

2015-10-21

Power system transient stability analysis requires an appropriate integration time step to avoid numerical instability as well as to reduce computational demands. For fast system dynamics, which vary more rapidly than what the time step covers, a fraction of the time step, called a subinterval, is used. However, the optimal value of this subinterval is not easily determined because the analysis of the system dynamics might be required. This selection is usually made from engineering experiences, and perhaps trial and error. This paper proposes an optimal subinterval selection approach for power system transient stability analysis, which is based on modalmore » analysis using a single machine infinite bus (SMIB) system. Fast system dynamics are identified with the modal analysis and the SMIB system is used focusing on fast local modes. An appropriate subinterval time step from the proposed approach can reduce computational burden and achieve accurate simulation responses as well. As a result, the performance of the proposed method is demonstrated with the GSO 37-bus system.« less

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

PubMed

Chotibut, Thiparat; Nelson, David R

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Evolutionary dynamics with fluctuating population sizes and strong mutualism

NASA Astrophysics Data System (ADS)

Chotibut, Thiparat; Nelson, David R.

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

PubMed Central

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

Spacecraft Dynamic Characterization by Strain Energies Method

NASA Astrophysics Data System (ADS)

Bretagne, J.-M.; Fragnito, M.; Massier, S.

2002-01-01

In the last years the significant increase in satellite broadcasting demand, with the wide band communication dawn, has given a great impulse to the telecommunication satellite market. The big demand is translated from operators (such as SES/Astra, Eutelsat, Intelsat, Inmarsat, EuroSkyWay etc.) in an increase of orders of telecom satellite to the world industrials. The largest part of these telecom satellite orders consists of Geostationary platforms which grow more and more in mass (over 5 tons) due to an ever longer demanded lifetime (up to 20 years), and become more complex due to the need of implementing an ever larger number of repeaters, antenna reflectors and feeds, etc... In this frame, the mechanical design and verification of these large spacecraft become difficult and ambitious at the same time, driven by the dry mass limitation objective. By the Finite Element Method (FEM), and on the basis of the telecom satellite heritage of a world leader constructor such as Alcatel Space Industries it is nowadays possible to model these spacecraft in a realistic and confident way in order to identify the main global dynamic aspects such as mode shapes, mass participation and/or dynamic responses. But on the other hand, one of the main aims consists in identifying soon in a program the most critical aspects of the system behavior in the launch dynamic environment, such as possible dynamic coupling between the different subsystems and secondary structures of the spacecraft (large deployable reflectors, thrusters, etc.). To this aim a numerical method has been developed in the frame of the Alcatel SPACEBUS family program, using MSC/Nastran capabilities and it is presented in this paper. The method is based on Spacecraft sub-structuring and strain energy calculation. The method mainly consists of two steps : 1) subsystem modal strain energy ratio (with respect to the global strain energy); 2) subsystem strain energy calculation for each mode according to the base driven forcing direction. The first step consists of the following : for each part the modal strain energy ratio is calculated with respect to the total strain energy of the Spacecraft global model. The results are shown in tabular form : for each mode the parts with a strain energy ratio greater then 1% are reported. The second step can be summarized as follows : for each part or subsystem, in order to compare the relative importance, in terms of dynamic response, among all the modes identified by the percentage method, the subsystem strain energy in Joule is calculated for each axis 1g base driven excitation. Then plots are given where, for each subsystem and for each base forcing direction, the strain energy values are shown in a 0-100 Hz frequency range. Through this method, for each subsystem the sizing eigenfrequencies and associated excitation axis are identified in a clear way, allowing at the same time a better understanding of dynamic responses.

Hierarchical tone mapping for high dynamic range image visualization

NASA Astrophysics Data System (ADS)

Qiu, Guoping; Duan, Jiang

2005-07-01

In this paper, we present a computationally efficient, practically easy to use tone mapping techniques for the visualization of high dynamic range (HDR) images in low dynamic range (LDR) reproduction devices. The new method, termed hierarchical nonlinear linear (HNL) tone-mapping operator maps the pixels in two hierarchical steps. The first step allocates appropriate numbers of LDR display levels to different HDR intensity intervals according to the pixel densities of the intervals. The second step linearly maps the HDR intensity intervals to theirs allocated LDR display levels. In the developed HNL scheme, the assignment of LDR display levels to HDR intensity intervals is controlled by a very simple and flexible formula with a single adjustable parameter. We also show that our new operators can be used for the effective enhancement of ordinary images.

Impact of implementation choices on quantitative predictions of cell-based computational models

NASA Astrophysics Data System (ADS)

Kursawe, Jochen; Baker, Ruth E.; Fletcher, Alexander G.

2017-09-01

'Cell-based' models provide a powerful computational tool for studying the mechanisms underlying the growth and dynamics of biological tissues in health and disease. An increasing amount of quantitative data with cellular resolution has paved the way for the quantitative parameterisation and validation of such models. However, the numerical implementation of cell-based models remains challenging, and little work has been done to understand to what extent implementation choices may influence model predictions. Here, we consider the numerical implementation of a popular class of cell-based models called vertex models, which are often used to study epithelial tissues. In two-dimensional vertex models, a tissue is approximated as a tessellation of polygons and the vertices of these polygons move due to mechanical forces originating from the cells. Such models have been used extensively to study the mechanical regulation of tissue topology in the literature. Here, we analyse how the model predictions may be affected by numerical parameters, such as the size of the time step, and non-physical model parameters, such as length thresholds for cell rearrangement. We find that vertex positions and summary statistics are sensitive to several of these implementation parameters. For example, the predicted tissue size decreases with decreasing cell cycle durations, and cell rearrangement may be suppressed by large time steps. These findings are counter-intuitive and illustrate that model predictions need to be thoroughly analysed and implementation details carefully considered when applying cell-based computational models in a quantitative setting.

Tracker Toolkit

NASA Technical Reports Server (NTRS)

Lewis, Steven J.; Palacios, David M.

2013-01-01

This software can track multiple moving objects within a video stream simultaneously, use visual features to aid in the tracking, and initiate tracks based on object detection in a subregion. A simple programmatic interface allows plugging into larger image chain modeling suites. It extracts unique visual features for aid in tracking and later analysis, and includes sub-functionality for extracting visual features about an object identified within an image frame. Tracker Toolkit utilizes a feature extraction algorithm to tag each object with metadata features about its size, shape, color, and movement. Its functionality is independent of the scale of objects within a scene. The only assumption made on the tracked objects is that they move. There are no constraints on size within the scene, shape, or type of movement. The Tracker Toolkit is also capable of following an arbitrary number of objects in the same scene, identifying and propagating the track of each object from frame to frame. Target objects may be specified for tracking beforehand, or may be dynamically discovered within a tripwire region. Initialization of the Tracker Toolkit algorithm includes two steps: Initializing the data structures for tracked target objects, including targets preselected for tracking; and initializing the tripwire region. If no tripwire region is desired, this step is skipped. The tripwire region is an area within the frames that is always checked for new objects, and all new objects discovered within the region will be tracked until lost (by leaving the frame, stopping, or blending in to the background).

Direct fluorescent labeling for efficient biological assessment of inhalable particles.

PubMed

Poudel, Bijay Kumar; Park, Jae Hong; Lim, Jiseok; Byeon, Jeong Hoon

2017-10-01

Labeling of aerosol particles with a radioactive, magnetic, or optical tracer has been employed to confirm particle localization in cell compartments, which has provided useful evidence for correlating toxic effects of inhaled particles. However, labeling requires several physicochemical steps to identify functionalities of the inner or outer surfaces of particles, and moreover, these steps can cause changes in size, surface charge, and bioactivity of the particles, resulting in misinterpretations regarding their toxic effects. This study addresses this challenging issue with a goal of introducing an efficient strategy for constantly supplying labeled aerosol particles in a single-pass configuration without any pre- or post-physicochemical batch treatments of aerosol particles. Carbon black (CB, simulating combustion-generated soot) or calcium carbonate (CC, simulating brake-wear fragments) particles were constantly produced via spark ablation or bubble bursting, respectively. These minute particles were incorporated with fluorescein isothiocyanate-poly(ethylene glycol) 2-aminoethyl ether acetic acid solution at the orifice of a collison atomizer to fabricate hybrid droplets. The droplets successively entered a diffusion dryer containing 254-nm UV irradiation; therefore, the droplets were dynamically stiffened by UV to form fluorescent probes on particles during solvent extraction in the dryer. Particle size distributions, morphologies, and surface charges before and after labeling were measured to confirm fluorescence labeling without significant changes in the properties. In vitro assays, including confocal imaging, were conducted to confirm the feasibility of the labeling approach without inducing significant differences in bioactivity compared with untreated CB or CC particles.

A split-step method to include electron–electron collisions via Monte Carlo in multiple rate equation simulations

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

Huthmacher, Klaus; Molberg, Andreas K.; Rethfeld, Bärbel

2016-10-01

A split-step numerical method for calculating ultrafast free-electron dynamics in dielectrics is introduced. The two split steps, independently programmed in C++11 and FORTRAN 2003, are interfaced via the presented open source wrapper. The first step solves a deterministic extended multi-rate equation for the ionization, electron–phonon collisions, and single photon absorption by free-carriers. The second step is stochastic and models electron–electron collisions using Monte-Carlo techniques. This combination of deterministic and stochastic approaches is a unique and efficient method of calculating the nonlinear dynamics of 3D materials exposed to high intensity ultrashort pulses. Results from simulations solving the proposed model demonstrate howmore » electron–electron scattering relaxes the non-equilibrium electron distribution on the femtosecond time scale.« less

Preparatory steps for a robust dynamic model for organically bound tritium dynamics in agricultural crops

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

Melintescu, A.; Galeriu, D.; Diabate, S.

2015-03-15

The processes involved in tritium transfer in crops are complex and regulated by many feedback mechanisms. A full mechanistic model is difficult to develop due to the complexity of the processes involved in tritium transfer and environmental conditions. First, a review of existing models (ORYZA2000, CROPTRIT and WOFOST) presenting their features and limits, is made. Secondly, the preparatory steps for a robust model are discussed, considering the role of dry matter and photosynthesis contribution to the OBT (Organically Bound Tritium) dynamics in crops.

40 CFR 141.81 - Applicability of corrosion control treatment steps to small, medium-size and large water systems.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false Applicability of corrosion control treatment steps to small, medium-size and large water systems. 141.81 Section 141.81 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Control of Lead and Copper...

Effect of time step size and turbulence model on the open water hydrodynamic performance prediction of contra-rotating propellers

NASA Astrophysics Data System (ADS)

Wang, Zhan-zhi; Xiong, Ying

2013-04-01

A growing interest has been devoted to the contra-rotating propellers (CRPs) due to their high propulsive efficiency, torque balance, low fuel consumption, low cavitations, low noise performance and low hull vibration. Compared with the single-screw system, it is more difficult for the open water performance prediction because forward and aft propellers interact with each other and generate a more complicated flow field around the CRPs system. The current work focuses on the open water performance prediction of contra-rotating propellers by RANS and sliding mesh method considering the effect of computational time step size and turbulence model. The validation study has been performed on two sets of contra-rotating propellers developed by David W Taylor Naval Ship R & D center. Compared with the experimental data, it shows that RANS with sliding mesh method and SST k-ω turbulence model has a good precision in the open water performance prediction of contra-rotating propellers, and small time step size can improve the level of accuracy for CRPs with the same blade number of forward and aft propellers, while a relatively large time step size is a better choice for CRPs with different blade numbers.

Dynamic analysis of trapping and escaping in dual beam optical trap

NASA Astrophysics Data System (ADS)

Li, Wenqiang; Hu, Huizhu; Su, Heming; Li, Zhenggang; Shen, Yu

2016-10-01

In this paper, we simulate the dynamic movement of a dielectric sphere in optical trap. This dynamic analysis can be used to calibrate optical forces, increase trapping efficiency and measure viscous coefficient of surrounding medium. Since an accurate dynamic analysis is based on a detailed force calculation, we calculate all forces a sphere receives. We get the forces of dual-beam gradient radiation pressure on a micron-sized dielectric sphere in the ray optics regime and utilize Einstein-Ornstein-Uhlenbeck to deal with its Brownian motion forces. Hydrodynamic viscous force also exists when the sphere moves in liquid. Forces from buoyance and gravity are also taken into consideration. Then we simulate trajectory of a sphere when it is subject to all these forces in a dual optical trap. From our dynamic analysis, the sphere can be trapped at an equilibrium point in static water, although it permanently fluctuates around the equilibrium point due to thermal effects. We go a step further to analyze the effects of misalignment of two optical traps. Trapping and escaping phenomena of the sphere in flowing water are also simulated. In flowing water, the sphere is dragged away from the equilibrium point. This dragging distance increases with the decrease of optical power, which results in escaping of the sphere with optical power below a threshold. In both trapping and escaping process we calculate the forces and position of the sphere. Finally, we analyze a trapping region in dual optical tweezers.

Relaxation dynamics in a binary hard-ellipse liquid.

PubMed

Xu, Wen-Sheng; Sun, Zhao-Yan; An, Li-Jia

2015-01-21

Structural relaxation in binary hard spherical particles has been shown recently to exhibit a wealth of remarkable features when size disparity or mixture composition is varied. In this paper, we test whether or not similar dynamical phenomena occur in glassy systems composed of binary hard ellipses. We demonstrate via event-driven molecular dynamics simulation that a binary hard-ellipse mixture with an aspect ratio of two and moderate size disparity displays characteristic glassy dynamics upon increasing density in both the translational and the rotational degrees of freedom. The rotational glass transition density is found to be close to the translational one for the binary mixtures investigated. More importantly, we assess the influence of size disparity and mixture composition on the relaxation dynamics. We find that an increase of size disparity leads, both translationally and rotationally, to a speed up of the long-time dynamics in the supercooled regime so that both the translational and the rotational glass transition shift to higher densities. By increasing the number concentration of the small particles, the time evolution of both translational and rotational relaxation dynamics at high densities displays two qualitatively different scenarios, i.e., both the initial and the final part of the structural relaxation slow down for small size disparity, while the short-time dynamics still slows down but the final decay speeds up in the binary mixture with large size disparity. These findings are reminiscent of those observed in binary hard spherical particles. Therefore, our results suggest a universal mechanism for the influence of size disparity and mixture composition on the structural relaxation in both isotropic and anisotropic particle systems.

Measurement of Dynamic Viscoelasticity of Full-Size Wood Composite Panels Using a Vibration Testing Method

Treesearch

Cheng Guan; Houjiang Zhang; John F. Hunt; Lujing Zhou; Dan Feng

2016-01-01

The dynamic viscoelasticity of full-size wood composite panels (WCPs) under the free-free vibrational state were determined by a vibration testing method. Vibration detection tests were performed on 194 pieces of three types of full-size WCPs (particleboard, medium density fiberboard, and plywood (PW)). The dynamic viscoelasticity from smaller specimens cut from the...

Two-step size reduction and post-washing of steam exploded corn stover improving simultaneous saccharification and fermentation for ethanol production.

PubMed

Liu, Zhi-Hua; Chen, Hong-Zhang

2017-01-01

The simultaneous saccharification and fermentation (SSF) of corn stover biomass for ethanol production was performed by integrating steam explosion (SE) pretreatment, hydrolysis and fermentation. Higher SE pretreatment severity and two-step size reduction increased the specific surface area, swollen volume and water holding capacity of steam exploded corn stover (SECS) and hence facilitated the efficiency of hydrolysis and fermentation. The ethanol production and yield in SSF increased with the decrease of particle size and post-washing of SECS prior to fermentation to remove the inhibitors. Under the SE conditions of 1.5MPa and 9min using 2.0cm particle size, glucan recovery and conversion to glucose by enzymes were 86.2% and 87.2%, respectively. The ethanol concentration and yield were 45.0g/L and 85.6%, respectively. With this two-step size reduction and post-washing strategy, the water utilization efficiency, sugar recovery and conversion, and ethanol concentration and yield by the SSF process were improved. Copyright © 2016 Elsevier Ltd. All rights reserved.

Predation risk suppresses the positive feedback between size structure and cannibalism.

PubMed

Kishida, Osamu; Trussell, Geoffrey C; Ohno, Ayaka; Kuwano, Shinya; Ikawa, Takuya; Nishimura, Kinya

2011-11-01

1. Cannibalism can play a prominent role in the structuring and dynamics of ecological communities. Previous studies have emphasized the importance of size structure and density of cannibalistic species in shaping short- and long-term cannibalism dynamics, but our understanding of how predators influence cannibalism dynamics is limited. This is despite widespread evidence that many prey species exhibit behavioural and morphological adaptations in response to predation risk. 2. This study examined how the presence and absence of predation risk from larval dragonflies Aeshna nigroflava affected cannibalism dynamics in its prey larval salamanders Hynobius retardatus. 3. We found that feedback dynamics between size structure and cannibalism depended on whether dragonfly predation risk was present. In the absence of dragonfly risk cues, a positive feedback between salamander size structure and cannibalism through time occurred because most of the replicates in this treatment contained at least one salamander larvae having an enlarged gape (i.e. cannibal). In contrast, this feedback and the emergence of cannibalism were rarely observed in the presence of the dragonfly risk cues. Once salamander size divergence occurred, experimental reversals of the presence or absence of dragonfly risk cues did not alter existing cannibalism dynamics as the experiment progressed. Thus, the effects of risk on the mechanisms driving cannibalism dynamics likely operated during the early developmental period of the salamander larvae. 4. The effects of dragonfly predation risk on behavioural aspects of cannibalistic interactions among hatchlings may prohibit the initiation of dynamics between size structure and cannibalism. Our predation trials clearly showed that encounter rates among hatchlings and biting and ingestion rates of prospective prey by prospective cannibals were significantly lower in the presence vs. absence of dragonfly predation risk even though the size asymmetry between cannibals and victims was similar in both risk treatments. These results suggest that dragonfly risk cues first suppress cannibalism among hatchlings and then prevent size variation from increasing through time. 5. We suggest that the positive feedback dynamics between size structure and cannibalism and their modification by predation risk may also operate in other systems to shape the population dynamics of cannibalistic prey species as well as overall community dynamics. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

USE OF THE SDO POINTING CONTROLLERS FOR INSTRUMENT CALIBRATION MANEUVERS

NASA Technical Reports Server (NTRS)

Vess, Melissa F.; Starin, Scott R.; Morgenstern, Wendy M.

2005-01-01

During the science phase of the Solar Dynamics Observatory mission, the three science instruments require periodic instrument calibration maneuvers with a frequency of up to once per month. The command sequences for these maneuvers vary in length from a handful of steps to over 200 steps, and individual steps vary in size from 5 arcsec per step to 22.5 degrees per step. Early in the calibration maneuver development, it was determined that the original attitude sensor complement could not meet the knowledge requirements for the instrument calibration maneuvers in the event of a sensor failure. Because the mission must be single fault tolerant, an attitude determination trade study was undertaken to determine the impact of adding an additional attitude sensor versus developing alternative, potentially complex, methods of performing the maneuvers in the event of a sensor failure. To limit the impact to the science data capture budget, these instrument calibration maneuvers must be performed as quickly as possible while maintaining the tight pointing and knowledge required to obtain valid data during the calibration. To this end, the decision was made to adapt a linear pointing controller by adjusting gains and adding an attitude limiter so that it would be able to slew quickly and still achieve steady pointing once on target. During the analysis of this controller, questions arose about the stability of the controller during slewing maneuvers due to the combination of the integral gain, attitude limit, and actuator saturation. Analysis was performed and a method for disabling the integral action while slewing was incorporated to ensure stability. A high fidelity simulation is used to simulate the various instrument calibration maneuvers.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa

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

Johnson, Quentin R.; Nellas, Ricky B.; Shen, Tongye

2012-07-25

Understanding how organic solvent-stable proteins can function in anhydrous and often complex solutions is essential for the study of the interaction of protein and molecular immiscible interfaces and the design of efficient industrial enzymes in nonaqueous solvents. Using an extremophilic lipase from Pseudomonas aeruginosa as an example, we investigated the conformational dynamics of an organic solvent-tolerant enzyme in complex solvent milieux. Four 100-ns molecular dynamics simulations of the lipase were performed in solvent systems: water, hexane, and two mixtures of hexane and water, 5% and 95% (w/w) hexane. Our results show a solvent-dependent structural change of the protein, especially inmore » the region that regulates the admission of the substrate. We observed that the lipase is much less flexible in hexane than in aqueous solution or at the immiscible interface. Quantified by the size of the accessible channel, the lipase in water has a closed-gate conformation and no access to the active site, while in the hexane-containing systems, the lipase is at various degrees of open-gate state, with the immiscible interface setup being in the widely open conformation ensembles. Furthermore, the composition of explicit solvents in the access channel showed a significant influence on the conformational dynamics of the protein. Interestingly, the slowest step (bottleneck) of the hexane-induced conformational switch seems to be correlated with the slow dehydration dynamics of the channel.« less

Correlation of microstructure with dynamic deformation behavior and penetration performance of tungsten heavy alloys fabricated by mechanical alloying

NASA Astrophysics Data System (ADS)

Kim, Dong-Kuk; Lee, Sunghak; Ryu, Ho Jin; Hyunghong, Soon; Noh, Joon-Woong

2000-10-01

In this study, tungsten heavy alloy specimens were fabricated by mechanical alloying (MA), and their dynamic torsional properties and penetration performance were investigated. Dynamic torsional tests were conducted on the specimens fabricated with different sintering temperatures after MA, and then the test data were compared with those of a conventionally processed specimen. Refinement of tungsten particles was obtained after MA, but contiguity was seriously increased, thereby leading to low ductility and impact energy. Specimens in which both particle size and contiguity were simultaneously reduced by MA and two-step sintering and those having higher matrix fraction by partial MA were successfully fabricated. The dynamic test results indicated that the formation of adiabatic shear bands was expected because of the plastic localization at the central area of the gage section. Upon highspeed impact testing of these specimens, self-sharpening was promoted by the adiabatic shear band formation, but their penetration performance did not improve since much of kinetic energy of the penetrators was consumed for the microcrack formation due to interfacial debonding and cleavage fracture of tungsten particles. In order to improve penetration performance as well as to achieve selfsharpening by applying MA, conditions of MA and sintering process should be established so that alloy densification, particle refinement, and contiguity reduction can be simultaneously achieved.

Dynamic Modeling of the Main Blow in Basic Oxygen Steelmaking Using Measured Step Responses

NASA Astrophysics Data System (ADS)

Kattenbelt, Carolien; Roffel, B.

2008-10-01

In the control and optimization of basic oxygen steelmaking, it is important to have an understanding of the influence of control variables on the process. However, important process variables such as the composition of the steel and slag cannot be measured continuously. The decarburization rate and the accumulation rate of oxygen, which can be derived from the generally measured waste gas flow and composition, are an indication of changes in steel and slag composition. The influence of the control variables on the decarburization rate and the accumulation rate of oxygen can best be determined in the main blow period. In this article, the measured step responses of the decarburization rate and the accumulation rate of oxygen to step changes in the oxygen blowing rate, lance height, and the addition rate of iron ore during the main blow are presented. These measured step responses are subsequently used to develop a dynamic model for the main blow. The model consists of an iron oxide and a carbon balance and an additional equation describing the influence of the lance height and the oxygen blowing rate on the decarburization rate. With this simple dynamic model, the measured step responses can be explained satisfactorily.

Structure Formation in Salt-Free Solutions of Amphiphilic Sulfonated Polyelectrolytes

NASA Astrophysics Data System (ADS)

Bockstaller, Michael; Koehler, Werner

2000-03-01

Self-assembled systems have long attracted attention due to their practical importance in many technical and biological fields. Dodecyl-substituted poly(para-phenylen)sulfonates (abbreviated PPPS) are highly charged polyelectrolytes which in the uncharged state have been investigated extensively and an intrinsic persistence length of 15 nm has been reported. Due to their hydrophobic side chains, PPPS are compatible with water only as micellar aggregates and tend to form supramolecular structures even at concentrations as low as 10-5mol_mon.units/l. Because of the rodlike conformation of PPPS, this self-assembly leads to aggregates of anisotropic shape. Therefore, depolarized light scattering was employed to yield complementary information about structure and dynamics of these complex fluids. Aqueous solutions of PPPS at room temperature undergo a structural transition at a critical concentration of c_crit.=0.016 g/l. This transition is characterized by a strong increase of scattered intensity in forward direction and dynamic depolarized scattering. Above c_crit. the cylindrical micelles (L=310 nm, d=3.1 nm, N_radial=12) self assembly into large ellipsoidal clusters of size in the μ m range. Due to the strong increase of depolarized scattered intensity there has to be a preferential orientation of the micelles inside those clusters, which thus represent a lyotropic mesophase. By combining static and dynamic light scattering for the low q-range as well as small angle x-ray scattering for the higher q-range it is possible to determine size and shape of each aggregation step. Decreasing the molecular weight of the PPPS has profound influence on the micellar length and hence on c_crit. which is close to the overlap concentration (c ~ 1/L^3) allowing for the observation of the polyelectrolyte effect.

Monitoring the Stability of Perfluorocarbon Nanoemulsions by Cryo-TEM Image Analysis and Dynamic Light Scattering

PubMed Central

Grapentin, Christoph; Barnert, Sabine; Schubert, Rolf

2015-01-01

Perfluorocarbon nanoemulsions (PFC-NE) are disperse systems consisting of nanoscale liquid perfluorocarbon droplets stabilized by an emulsifier, usually phospholipids. Perfluorocarbons are chemically inert and non-toxic substances that are exhaled after in vivo administration. The manufacture of PFC-NE can be done in large scales by means of high pressure homogenization or microfluidization. Originally investigated as oxygen carriers for cases of severe blood loss, their application nowadays is more focused on using them as marker agents in 19F Magnetic Resonance Imaging (19F MRI). 19F is scarce in organisms and thus PFC-NE are a promising tool for highly specific and non-invasive imaging of inflammation via 19F MRI. Neutrophils, monocytes and macrophages phagocytize PFC-NE and subsequently migrate to inflamed tissues. This technique has proven feasibility in numerous disease models in mice, rabbits and mini pigs. The translation to clinical trials in human needs the development of a stable nanoemulsion whose droplet size is well characterized over a long storage time. Usually dynamic light scattering (DLS) is applied as the standard method for determining particle sizes in the nanometer range. Our study uses a second method, analysis of transmission electron microscopy images of cryo-fixed samples (Cryo-TEM), to evaluate stability of PFC-NE in comparison to DLS. Four nanoemulsions of different composition are observed for one year. The results indicate that DLS alone cannot reveal the changes in particle size, but can even mislead to a positive estimation of stability. The combination with Cryo-TEM images gives more insight in the particulate evolution, both techniques supporting one another. The study is one further step in the development of analytical tools for the evaluation of a clinically applicable perfluorooctylbromide nanoemulsion. PMID:26098661

Can SNOMED CT be squeezed without losing its shape?

PubMed

López-García, Pablo; Schulz, Stefan

2016-09-21

In biomedical applications where the size and complexity of SNOMED CT become problematic, using a smaller subset that can act as a reasonable substitute is usually preferred. In a special class of use cases-like ontology-based quality assurance, or when performing scaling experiments for real-time performance-it is essential that modules show a similar shape than SNOMED CT in terms of concept distribution per sub-hierarchy. Exactly how to extract such balanced modules remains unclear, as most previous work on ontology modularization has focused on other problems. In this study, we investigate to what extent extracting balanced modules that preserve the original shape of SNOMED CT is possible, by presenting and evaluating an iterative algorithm. We used a graph-traversal modularization approach based on an input signature. To conform to our definition of a balanced module, we implemented an iterative algorithm that carefully bootstraped and dynamically adjusted the signature at each step. We measured the error for each sub-hierarchy and defined convergence as a residual sum of squares <1. Using 2000 concepts as an initial signature, our algorithm converged after seven iterations and extracted a module 4.7 % the size of SNOMED CT. Seven sub-hierarhies were either over or under-represented within a range of 1-8 %. Our study shows that balanced modules from large terminologies can be extracted using ontology graph-traversal modularization techniques under certain conditions: that the process is repeated a number of times, the input signature is dynamically adjusted in each iteration, and a moderate under/over-representation of some hierarchies is tolerated. In the case of SNOMED CT, our results conclusively show that it can be squeezed to less than 5 % of its size without any sub-hierarchy losing its shape more than 8 %, which is likely sufficient in most use cases.

4D x-ray phase contrast tomography for repeatable motion of biological samples

NASA Astrophysics Data System (ADS)

Hoshino, Masato; Uesugi, Kentaro; Yagi, Naoto

2016-09-01

X-ray phase contrast tomography based on a grating interferometer was applied to fast and dynamic measurements of biological samples. To achieve this, the scanning procedure in the tomographic scan was improved. A triangle-shaped voltage signal from a waveform generator to a Piezo stage was used for the fast phase stepping in the grating interferometer. In addition, an optical fiber coupled x-ray scientific CMOS camera was used to achieve fast and highly efficient image acquisitions. These optimizations made it possible to perform an x-ray phase contrast tomographic measurement within an 8 min scan with density resolution of 2.4 mg/cm3. A maximum volume size of 13 × 13 × 6 mm3 was obtained with a single tomographic measurement with a voxel size of 6.5 μm. The scanning procedure using the triangle wave was applied to four-dimensional measurements in which highly sensitive three-dimensional x-ray imaging and a time-resolved dynamic measurement of biological samples were combined. A fresh tendon in the tail of a rat was measured under a uniaxial stretching and releasing condition. To maintain the freshness of the sample during four-dimensional phase contrast tomography, the temperature of the bathing liquid of the sample was kept below 10° using a simple cooling system. The time-resolved deformation of the tendon and each fascicle was measured with a temporal resolution of 5.7 Hz. Evaluations of cross-sectional area size, length of the axis, and mass density in the fascicle during a stretching process provided a basis for quantitative analysis of the deformation of tendon fascicle.

4D x-ray phase contrast tomography for repeatable motion of biological samples.

PubMed

Hoshino, Masato; Uesugi, Kentaro; Yagi, Naoto

2016-09-01

X-ray phase contrast tomography based on a grating interferometer was applied to fast and dynamic measurements of biological samples. To achieve this, the scanning procedure in the tomographic scan was improved. A triangle-shaped voltage signal from a waveform generator to a Piezo stage was used for the fast phase stepping in the grating interferometer. In addition, an optical fiber coupled x-ray scientific CMOS camera was used to achieve fast and highly efficient image acquisitions. These optimizations made it possible to perform an x-ray phase contrast tomographic measurement within an 8 min scan with density resolution of 2.4 mg/cm 3 . A maximum volume size of 13 × 13 × 6 mm 3 was obtained with a single tomographic measurement with a voxel size of 6.5 μm. The scanning procedure using the triangle wave was applied to four-dimensional measurements in which highly sensitive three-dimensional x-ray imaging and a time-resolved dynamic measurement of biological samples were combined. A fresh tendon in the tail of a rat was measured under a uniaxial stretching and releasing condition. To maintain the freshness of the sample during four-dimensional phase contrast tomography, the temperature of the bathing liquid of the sample was kept below 10° using a simple cooling system. The time-resolved deformation of the tendon and each fascicle was measured with a temporal resolution of 5.7 Hz. Evaluations of cross-sectional area size, length of the axis, and mass density in the fascicle during a stretching process provided a basis for quantitative analysis of the deformation of tendon fascicle.

Optimized spray drying process for preparation of one-step calcium-alginate gel microspheres

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

Popeski-Dimovski, Riste

Calcium-alginate micro particles have been used extensively in drug delivery systems. Therefore we establish a one-step method for preparation of internally gelated micro particles with spherical shape and narrow size distribution. We use four types of alginate with different G/M ratio and molar weight. The size of the particles is measured using light diffraction and scanning electron microscopy. Measurements showed that with this method, micro particles with size distribution around 4 micrometers can be prepared, and SEM imaging showed that those particles are spherical in shape.

Shear Melting of a Colloidal Glass

NASA Astrophysics Data System (ADS)

Eisenmann, Christoph; Kim, Chanjoong; Mattsson, Johan; Weitz, David A.

2010-01-01

We use confocal microscopy to explore shear melting of colloidal glasses, which occurs at strains of ˜0.08, coinciding with a strongly non-Gaussian step size distribution. For larger strains, the particle mean square displacement increases linearly with strain and the step size distribution becomes Gaussian. The effective diffusion coefficient varies approximately linearly with shear rate, consistent with a modified Stokes-Einstein relationship in which thermal energy is replaced by shear energy and the length scale is set by the size of cooperatively moving regions consisting of ˜3 particles.

Production of pure indinavir free base nanoparticles by a supercritical anti-solvent (SAS) method.

PubMed

Imperiale, Julieta C; Bevilacqua, Gabriela; Rosa, Paulo de Tarso Vieira E; Sosnik, Alejandro

2014-12-01

This work investigated the production of pure indinavir free base nanoparticles by a supercritical anti-solvent method to improve the drug dissolution in intestine-like medium. To increase the dissolution of the drug by means of a supercritical fluid processing method. Acetone was used as solvent and supercritical CO2 as antisolvent. Products were characterized by dynamic light scattering (size, size distribution), scanning electron microscopy (morphology), differential scanning calorimetry (thermal behaviour) and X-rays diffraction (crystallinity). Processed indinavir resulted in particles of significantly smaller size than the original drug. Particles showed at least one dimension at the nanometer scale with needle or rod-like morphology. Results of X-rays powder diffraction suggested the formation of a mixture of polymorphs. Differential scanning calorimetry analysis showed a main melting endotherm at 152 °C. Less prominent transitions due to the presence of small amounts of bound water (in the raw drug) or an unstable polymorph (in processed IDV) were also visible. Finally, drug particle size reduction significantly increased the dissolution rate with respect to the raw drug. Conversely, the slight increase of the intrinsic solubility of the nanoparticles was not significant. A supercritical anti-solvent method enabled the nanonization of indinavir free base in one single step with high yield. The processing led to faster dissolution that would improve the oral bioavailability of the drug.

Shapiro steps for skyrmion motion on a washboard potential with longitudinal and transverse ac drives

DOE PAGES

Reichhardt, Charles; Reichhardt, Cynthia Jane

2015-12-28

In this work, we numerically study the behavior of two-dimensional skyrmions in the presence of a quasi-one-dimensional sinusoidal substrate under the influence of externally applied dc and ac drives. In the overdamped limit, when both dc and ac drives are aligned in the longitudinal direction parallel to the direction of the substrate modulation, the velocity-force curves exhibit classic Shapiro step features when the frequency of the ac drive matches the washboard frequency that is dynamically generated by the motion of the skyrmions over the substrate, similar to previous observations in superconducting vortex systems. In the case of skyrmions, the additionalmore » contribution to the skyrmion motion from a nondissipative Magnus force shifts the location of the locking steps to higher dc drives, and we find that the skyrmions move at an angle with respect to the direction of the dc drive. For a longitudinal dc drive and a perpendicular or transverse ac drive, the overdamped system exhibits no Shapiro steps; however, when a finite Magnus force is present, we find pronounced transverse Shapiro steps along with complex two-dimensional periodic orbits of the skyrmions in the phase-locked regimes. Both the longitudinal and transverse ac drives produce locking steps whose widths oscillate with increasing ac drive amplitude. We examine the role of collective skyrmion interactions and find that additional fractional locking steps occur for both longitudinal and transverse ac drives. Finally, at higher skyrmion densities, the system undergoes a series of dynamical order-disorder transitions, with the skyrmions forming a moving solid on the phase locking steps and a fluctuating dynamical liquid in regimes between the steps.« less

Grain size evolution and convection regimes of the terrestrial planets

NASA Astrophysics Data System (ADS)

Rozel, A.; Golabek, G. J.; Boutonnet, E.

2011-12-01

A new model of grain size evolution has recently been proposed in Rozel et al. 2010. This new approach stipulates that the grain size dynamics is governed by two additive and simultaneous processes: grain growth and dynamic recrystallization. We use the usual normal grain growth laws for the growth part. For dynamic recrystallization, reducing the mean grain size increases the total area of grain boundaries. Grain boundaries carry some surface tension, so some energy is required to decrease the mean grain size. We consider that this energy is available during mechanical work. It is usually considered to produce some heat via viscous dissipation. A partitioning parameter f is then required to know what amount of energy is dissipated and what part is converted in surface tension. This study gives a new calibration of the partitioning parameter on major Earth materials involved in the dynamic of the terrestrial planets. Our calibration is in adequation with the published piezometric relations available in the literature (equilibrium grain size versus shear stress). We test this new model of grain size evolution in a set of numerical computations of the dynamics of the Earth using stagYY. We show that the grain size evolution has a major effect on the convection regimes of terrestrial planets.

Double-lumen tubes and auto-PEEP during one-lung ventilation.

PubMed

Spaeth, J; Ott, M; Karzai, W; Grimm, A; Wirth, S; Schumann, S; Loop, T

2016-01-01

Double-lumen tubes (DLT) are routinely used to enable one-lung-ventilation (OLV) during thoracic anaesthesia. The flow-dependent resistance of the DLT's bronchial limb may be high as a result of its narrow inner diameter and length, and thus potentially contribute to an unintended increase in positive end-expiratory pressure (auto-PEEP). We therefore studied the impact of adult sized DLTs on the dynamic auto-PEEP during OLV. In this prospective clinical study, dynamic auto-PEEP was determined in 72 patients undergoing thoracic surgery, with right- and left-sided DLTs of various sizes. During OLV, air trapping was provoked by increasing inspiration to expiration ratio from 1:2 to 2:1 (five steps). Based on measured flow rate, airway pressure (Paw) and bronchial pressure (Pbronch), the pressure gradient across the DLT (ΔPDLT) and the total auto-PEEP in the respiratory system (i.e. the lungs, the DLT and the ventilator circuit) were determined. Subsequently the DLT's share in total auto-PEEP was calculated. ΔPDLT was 2.3 (0.7) cm H2O over the entire breathing cycle. At the shortest expiratory time the mean total auto-PEEP was 2.9 (1.5) cm H2O (range 0-5.9 cm H2O). The DLT caused 27 to 31% of the total auto-PEEP. Size and side of the DLT's bronchial limb did not impact auto-PEEP significantly. Although the DLT contributes to the overall auto-PEEP, its contribution is small and independent of size and side of the DLT's bronchial limb. The choice of DLT does not influence the risk of auto-PEEP during OLV to a clinically relevant extent. DRKS00005648. © The Author 2015. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Understanding coupled natural and human systems on fire prone landscapes: integrating wildfire simulation into an agent based planning system.

NASA Astrophysics Data System (ADS)

Barros, Ana; Ager, Alan; Preisler, Haiganoush; Day, Michelle; Spies, Tom; Bolte, John

2015-04-01

Agent-based models (ABM) allow users to examine the long-term effects of agent decisions in complex systems where multiple agents and processes interact. This framework has potential application to study the dynamics of coupled natural and human systems where multiple stimuli determine trajectories over both space and time. We used Envision, a landscape based ABM, to analyze long-term wildfire dynamics in a heterogeneous, multi-owner landscape in Oregon, USA. Landscape dynamics are affected by land management policies, actors decisions, and autonomous processes such as vegetation succession, wildfire, or at a broader scale, climate change. Key questions include: 1) How are landscape dynamics influenced by policies and institutions, and 2) How do land management policies and actor decisions interact to produce intended and unintended consequences with respect to wildfire on fire-prone landscapes. Applying Envision to address these questions required the development of a wildfire module that could accurately simulate wildfires on the heterogeneous landscapes within the study area in terms of replicating historical fire size distribution, spatial distribution and fire intensity. In this paper we describe the development and testing of a mechanistic fire simulation system within Envision and application of the model on a 3.2 million fire prone landscape in central Oregon USA. The core fire spread equations use the Minimum Travel Time algorithm developed by M Finney. The model operates on a daily time step and uses a fire prediction system based on the relationship between energy release component and historical fires. Specifically, daily wildfire probabilities and sizes are generated from statistical analyses of historical fires in relation to daily ERC values. The MTT was coupled with the vegetation dynamics module in Envision to allow communication between the respective subsystem and effectively model fire effects and vegetation dynamics after a wildfire. Canopy and surface fuels are modeled in a state and transition framework that accounts for succession, fire effects, and fuels management. Fire effects are modeled using simulated fire intensity (flame length) to calculate expected vegetation impacts for each vegetation state. This talk will describe the mechanics of the simulation system along with initial results of Envision simulations for the Central Oregon study area that explore the dynamics of wildfire, fuel management, and succession over time.

Automated detection and analysis of particle beams in laser-plasma accelerator simulations

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

Ushizima, Daniela Mayumi; Geddes, C.G.; Cormier-Michel, E.

Numerical simulations of laser-plasma wakefield (particle) accelerators model the acceleration of electrons trapped in plasma oscillations (wakes) left behind when an intense laser pulse propagates through the plasma. The goal of these simulations is to better understand the process involved in plasma wake generation and how electrons are trapped and accelerated by the wake. Understanding of such accelerators, and their development, offer high accelerating gradients, potentially reducing size and cost of new accelerators. One operating regime of interest is where a trapped subset of electrons loads the wake and forms an isolated group of accelerated particles with low spread inmore » momentum and position, desirable characteristics for many applications. The electrons trapped in the wake may be accelerated to high energies, the plasma gradient in the wake reaching up to a gigaelectronvolt per centimeter. High-energy electron accelerators power intense X-ray radiation to terahertz sources, and are used in many applications including medical radiotherapy and imaging. To extract information from the simulation about the quality of the beam, a typical approach is to examine plots of the entire dataset, visually determining the adequate parameters necessary to select a subset of particles, which is then further analyzed. This procedure requires laborious examination of massive data sets over many time steps using several plots, a routine that is unfeasible for large data collections. Demand for automated analysis is growing along with the volume and size of simulations. Current 2D LWFA simulation datasets are typically between 1GB and 100GB in size, but simulations in 3D are of the order of TBs. The increase in the number of datasets and dataset sizes leads to a need for automatic routines to recognize particle patterns as particle bunches (beam of electrons) for subsequent analysis. Because of the growth in dataset size, the application of machine learning techniques for scientific data mining is increasingly considered. In plasma simulations, Bagherjeiran et al. presented a comprehensive report on applying graph-based techniques for orbit classification. They used the KAM classifier to label points and components in single and multiple orbits. Love et al. conducted an image space analysis of coherent structures in plasma simulations. They used a number of segmentation and region-growing techniques to isolate regions of interest in orbit plots. Both approaches analyzed particle accelerator data, targeting the system dynamics in terms of particle orbits. However, they did not address particle dynamics as a function of time or inspected the behavior of bunches of particles. Ruebel et al. addressed the visual analysis of massive laser wakefield acceleration (LWFA) simulation data using interactive procedures to query the data. Sophisticated visualization tools were provided to inspect the data manually. Ruebel et al. have integrated these tools to the visualization and analysis system VisIt, in addition to utilizing efficient data management based on HDF5, H5Part, and the index/query tool FastBit. In Ruebel et al. proposed automatic beam path analysis using a suite of methods to classify particles in simulation data and to analyze their temporal evolution. To enable researchers to accurately define particle beams, the method computes a set of measures based on the path of particles relative to the distance of the particles to a beam. To achieve good performance, this framework uses an analysis pipeline designed to quickly reduce the amount of data that needs to be considered in the actual path distance computation. As part of this process, region-growing methods are utilized to detect particle bunches at single time steps. Efficient data reduction is essential to enable automated analysis of large data sets as described in the next section, where data reduction methods are steered to the particular requirements of our clustering analysis. Previously, we have described the application of a set of algorithms to automate the data analysis and classification of particle beams in the LWFA simulation data, identifying locations with high density of high energy particles. These algorithms detected high density locations (nodes) in each time step, i.e. maximum points on the particle distribution for only one spatial variable. Each node was correlated to a node in previous or later time steps by linking these nodes according to a pruned minimum spanning tree (PMST). We call the PMST representation 'a lifetime diagram', which is a graphical tool to show temporal information of high dense groups of particles in the longitudinal direction for the time series. Electron bunch compactness was described by another step of the processing, designed to partition each time step, using fuzzy clustering, into a fixed number of clusters.« less

Short‐term time step convergence in a climate model

PubMed Central

Rasch, Philip J.; Taylor, Mark A.; Jablonowski, Christiane

2015-01-01

Abstract This paper evaluates the numerical convergence of very short (1 h) simulations carried out with a spectral‐element (SE) configuration of the Community Atmosphere Model version 5 (CAM5). While the horizontal grid spacing is fixed at approximately 110 km, the process‐coupling time step is varied between 1800 and 1 s to reveal the convergence rate with respect to the temporal resolution. Special attention is paid to the behavior of the parameterized subgrid‐scale physics. First, a dynamical core test with reduced dynamics time steps is presented. The results demonstrate that the experimental setup is able to correctly assess the convergence rate of the discrete solutions to the adiabatic equations of atmospheric motion. Second, results from full‐physics CAM5 simulations with reduced physics and dynamics time steps are discussed. It is shown that the convergence rate is 0.4—considerably slower than the expected rate of 1.0. Sensitivity experiments indicate that, among the various subgrid‐scale physical parameterizations, the stratiform cloud schemes are associated with the largest time‐stepping errors, and are the primary cause of slow time step convergence. While the details of our findings are model specific, the general test procedure is applicable to any atmospheric general circulation model. The need for more accurate numerical treatments of physical parameterizations, especially the representation of stratiform clouds, is likely common in many models. The suggested test technique can help quantify the time‐stepping errors and identify the related model sensitivities. PMID:27660669

Dynamic balance and stepping versus tai chi training to improve balance and stepping in at-risk older adults.

PubMed

Nnodim, Joseph O; Strasburg, Debra; Nabozny, Martina; Nyquist, Linda; Galecki, Andrzej; Chen, Shu; Alexander, Neil B

2006-12-01

To compare the effect of two 10-week balance training programs, Combined Balance and Step Training (CBST) versus tai chi (TC), on balance and stepping measures. Prospective intervention trial. Local senior centers and congregate housing facilities. Aged 65 and older with at least mild impairment in the ability to perform unipedal stance and tandem walk. Participants were allocated to TC (n = 107, mean age 78) or CBST, an intervention focused on improving dynamic balance and stepping (n = 106, mean age 78). At baseline and 10 weeks, participants were tested in their static balance (Unipedal Stance and Tandem Stance (TS)), stepping (Maximum Step Length, Rapid Step Test), and Timed Up and Go (TUG). Performance improved more with CBST than TC, ranging from 5% to 10% for the stepping tests (Maximum Step Length and Rapid Step Test) and 9% for TUG. The improvement in TUG represented an improvement of more than 1 second. Greater improvements were also seen in static balance ability (in TS) with CBST than TC. Of the two training programs, in which variants of each program have been proven to reduce falls, CBST results in modest improvements in balance, stepping, and functional mobility versus TC over a 10-week period. Future research should include a prospective comparison of fall rates in response to these two balance training programs.

Algorithm for Training a Recurrent Multilayer Perceptron

NASA Technical Reports Server (NTRS)

Parlos, Alexander G.; Rais, Omar T.; Menon, Sunil K.; Atiya, Amir F.

2004-01-01

An improved algorithm has been devised for training a recurrent multilayer perceptron (RMLP) for optimal performance in predicting the behavior of a complex, dynamic, and noisy system multiple time steps into the future. [An RMLP is a computational neural network with self-feedback and cross-talk (both delayed by one time step) among neurons in hidden layers]. Like other neural-network-training algorithms, this algorithm adjusts network biases and synaptic-connection weights according to a gradient-descent rule. The distinguishing feature of this algorithm is a combination of global feedback (the use of predictions as well as the current output value in computing the gradient at each time step) and recursiveness. The recursive aspect of the algorithm lies in the inclusion of the gradient of predictions at each time step with respect to the predictions at the preceding time step; this recursion enables the RMLP to learn the dynamics. It has been conjectured that carrying the recursion to even earlier time steps would enable the RMLP to represent a noisier, more complex system.

A control system design approach for flexible spacecraft

NASA Technical Reports Server (NTRS)

Silverberg, L. M.

1985-01-01

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

Lipopolysaccharide Membrane Building and Simulation

PubMed Central

Jo, Sunhwan; Wu, Emilia L.; Stuhlsatz, Danielle; Klauda, Jeffery B.; Widmalm, Göran; Im, Wonpil

2015-01-01

Summary While membrane simulations are widely employed to study the structure and dynamics of various lipid bilayers and membrane proteins in the bilayers, simulations of lipopolysaccharides (LPS) in membrane environments have been limited due to its structural complexity, difficulties in building LPS-membrane systems, and lack of appropriate molecular force field. In this work, as a first step to extend CHARMM-GUI Membrane Builder to incorporate LPS molecules and to explore their structures and dynamics in membrane environments using molecular dynamics simulations, we describe step-by-step procedures to build LPS bilayer systems using CHARMM and the recently developed CHARMM carbohydrate and lipid force fields. Such procedures are illustrated by building various bilayers of Escherichia coli O6 LPS and their preliminary simulation results are given in terms of per-LPS area and density distributions of various components along the membrane normal. PMID:25753722

Study of CdTe quantum dots grown using a two-step annealing method

NASA Astrophysics Data System (ADS)

Sharma, Kriti; Pandey, Praveen K.; Nagpal, Swati; Bhatnagar, P. K.; Mathur, P. C.

2006-02-01

High size dispersion, large average radius of quantum dot and low-volume ratio has been a major hurdle in the development of quantum dot based devices. In the present paper, we have grown CdTe quantum dots in a borosilicate glass matrix using a two-step annealing method. Results of optical characterization and the theoretical model of absorption spectra have shown that quantum dots grown using two-step annealing have lower average radius, lesser size dispersion, higher volume ratio and higher decrease in bulk free energy as compared to quantum dots grown conventionally.

An iterative procedure for obtaining maximum-likelihood estimates of the parameters for a mixture of normal distributions

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Walker, H. F.

1978-01-01

This paper addresses the problem of obtaining numerically maximum-likelihood estimates of the parameters for a mixture of normal distributions. In recent literature, a certain successive-approximations procedure, based on the likelihood equations, was shown empirically to be effective in numerically approximating such maximum-likelihood estimates; however, the reliability of this procedure was not established theoretically. Here, we introduce a general iterative procedure, of the generalized steepest-ascent (deflected-gradient) type, which is just the procedure known in the literature when the step-size is taken to be 1. We show that, with probability 1 as the sample size grows large, this procedure converges locally to the strongly consistent maximum-likelihood estimate whenever the step-size lies between 0 and 2. We also show that the step-size which yields optimal local convergence rates for large samples is determined in a sense by the 'separation' of the component normal densities and is bounded below by a number between 1 and 2.

An iterative procedure for obtaining maximum-likelihood estimates of the parameters for a mixture of normal distributions, 2

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Walker, H. F.

1976-01-01

The problem of obtaining numerically maximum likelihood estimates of the parameters for a mixture of normal distributions is addressed. In recent literature, a certain successive approximations procedure, based on the likelihood equations, is shown empirically to be effective in numerically approximating such maximum-likelihood estimates; however, the reliability of this procedure was not established theoretically. Here, a general iterative procedure is introduced, of the generalized steepest-ascent (deflected-gradient) type, which is just the procedure known in the literature when the step-size is taken to be 1. With probability 1 as the sample size grows large, it is shown that this procedure converges locally to the strongly consistent maximum-likelihood estimate whenever the step-size lies between 0 and 2. The step-size which yields optimal local convergence rates for large samples is determined in a sense by the separation of the component normal densities and is bounded below by a number between 1 and 2.

Visually Lossless JPEG 2000 for Remote Image Browsing

PubMed Central

Oh, Han; Bilgin, Ali; Marcellin, Michael

2017-01-01

Image sizes have increased exponentially in recent years. The resulting high-resolution images are often viewed via remote image browsing. Zooming and panning are desirable features in this context, which result in disparate spatial regions of an image being displayed at a variety of (spatial) resolutions. When an image is displayed at a reduced resolution, the quantization step sizes needed for visually lossless quality generally increase. This paper investigates the quantization step sizes needed for visually lossless display as a function of resolution, and proposes a method that effectively incorporates the resulting (multiple) quantization step sizes into a single JPEG2000 codestream. This codestream is JPEG2000 Part 1 compliant and allows for visually lossless decoding at all resolutions natively supported by the wavelet transform as well as arbitrary intermediate resolutions, using only a fraction of the full-resolution codestream. When images are browsed remotely using the JPEG2000 Interactive Protocol (JPIP), the required bandwidth is significantly reduced, as demonstrated by extensive experimental results. PMID:28748112

Multiple stage miniature stepping motor

DOEpatents

Niven, William A.; Shikany, S. David; Shira, Michael L.

1981-01-01

A stepping motor comprising a plurality of stages which may be selectively activated to effect stepping movement of the motor, and which are mounted along a common rotor shaft to achieve considerable reduction in motor size and minimum diameter, whereby sequential activation of the stages results in successive rotor steps with direction being determined by the particular activating sequence followed.

Erosion of a wet/dry granular interface

NASA Astrophysics Data System (ADS)

Jop, Pierre; Lefebvre, Gautier

2013-04-01

To model the dynamic of landslides, the evolution of the interface between the erodible ground and the flowing material is still studied experimentally or numerically (ie. Mangeney et al. 2010, Iverson 2012). In some cases, the basal material is more cohesive than the flowing one. Such situation arises for example due to cementation or humidity. What are the exchange rates between these phases? What is the coupling between the evolution of the interface and the flow? We studied the erosion phenomenon and performed laboratory experiments to focus on the interaction between a cohesive unsaturated granular material and a dry granular flow. Both materials were spherical grains, the cohesion being induced by adding a given mass of liquid to the grains. Two configurations were explored: a circular aggregate submitted to a dry flow in a rotating drum, and a granular flow eroding a wet granular pile. First, we focused on the influence of the cohesion, controlled by the liquid properties, such as the surface tension and the viscosity. Then the flow characteristics were modified by varying the grain size and density. These results allowed us to present a model for the erosion mechanisms, based on the flow and fluid properties. The main results are the need to take into account the whole probability distribution the stress applied on the wet grains and that both the surface tension and the viscosity are important since they play a different roles. The latter is mainly responsible of the time scale of the dynamic of a wet grain, while the former acts as a threshold on the force distribution. In the second configuration, we could also control the inclination of the slope. This system supported the previous model and moreover revealed an interface instability, leading the formation of steep steps, which is a reminiscence of the cyclic-steps observed during river-channel incision (Parker and Izumi 2000). We will present the dynamics of such granular steps. [1] Mangeney, A., O. Roche, O. Hungr, N. Mangold, G. Faccanoni, and A. Lucas (2010), Erosion and mobility in granular collapse over sloping beds, J. Geophys. Res., 115, F03040, doi:10.1029/2009JF001462. [2] Iverson, R. M. (2012), Elementary theory of bed-sediment entrainment by debris flows and avalanches, J. Geophys. Res., 117, F03006, doi:10.1029/2011JF002189. [3] Parker G.and Izumi N., Purely erosional cyclic and solitary steps created by flow over a cohesive bed, J. Fluid Mech. (2000), vol. 419, pp. 203-238.

Planning energy-efficient bipedal locomotion on patterned terrain

NASA Astrophysics Data System (ADS)

Zamani, Ali; Bhounsule, Pranav A.; Taha, Ahmad

2016-05-01

Energy-efficient bipedal walking is essential in realizing practical bipedal systems. However, current energy-efficient bipedal robots (e.g., passive-dynamics-inspired robots) are limited to walking at a single speed and step length. The objective of this work is to address this gap by developing a method of synthesizing energy-efficient bipedal locomotion on patterned terrain consisting of stepping stones using energy-efficient primitives. A model of Cornell Ranger (a passive-dynamics inspired robot) is utilized to illustrate our technique. First, an energy-optimal trajectory control problem for a single step is formulated and solved. The solution minimizes the Total Cost Of Transport (TCOT is defined as the energy used per unit weight per unit distance travelled) subject to various constraints such as actuator limits, foot scuffing, joint kinematic limits, ground reaction forces. The outcome of the optimization scheme is a table of TCOT values as a function of step length and step velocity. Next, we parameterize the terrain to identify the location of the stepping stones. Finally, the TCOT table is used in conjunction with the parameterized terrain to plan an energy-efficient stepping strategy.

Dynamic properties of epidemic spreading on finite size complex networks

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Yang; Shan, Xiu-Ming; Ren, Yong; Jiao, Jian; Qiu, Ben

2005-11-01

The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptible-infected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.