Simplification of Markov chains with infinite state space and the mathematical theory of random gene expression bursts

NASA Astrophysics Data System (ADS)

Jia, Chen

2017-09-01

Here we develop an effective approach to simplify two-time-scale Markov chains with infinite state spaces by removal of states with fast leaving rates, which improves the simplification method of finite Markov chains. We introduce the concept of fast transition paths and show that the effective transitions of the reduced chain can be represented as the superposition of the direct transitions and the indirect transitions via all the fast transition paths. Furthermore, we apply our simplification approach to the standard Markov model of single-cell stochastic gene expression and provide a mathematical theory of random gene expression bursts. We give the precise mathematical conditions for the bursting kinetics of both mRNAs and proteins. It turns out that random bursts exactly correspond to the fast transition paths of the Markov model. This helps us gain a better understanding of the physics behind the bursting kinetics as an emergent behavior from the fundamental multiscale biochemical reaction kinetics of stochastic gene expression.

The plumbing of the global biological pump: Efficiency control through leaks, pathways, and time scales

NASA Astrophysics Data System (ADS)

Pasquier, Benoît; Holzer, Mark

2016-08-01

We systematically quantify the pathways and time scales that set the efficiency, Ebio, of the global biological pump by applying Green-function-based diagnostics to a data-assimilated phosphorus cycle embedded in a jointly assimilated ocean circulation. We consider "bio pipes" that consist of phosphorus paths that connect specified regions of last biological utilization with regions where regenerated phosphate first reemerges into the euphotic zone. The bio pipes that contribute most to Ebio connect the Eastern Equatorial Pacific (EEqP) and Equatorial Atlantic to the Southern Ocean ((21 ± 3)% of Ebio), as well as the Southern Ocean to itself ((15 ± 3)% of Ebio). The bio pipes with the largest phosphorus flow rates connect the EEqP to itself and the subantarctic Southern Ocean to itself. The global mean sequestration time of the biological pump is 130 ± 70 years, while the sequestration time of the bio pipe from anywhere to the Antarctic region of the Southern Ocean is 430 ± 30 years. The distribution of phosphorus flowing within a given bio pipe is quantified by its transit-time partitioned path density. For the largest bio pipes, ˜1/7 of their phosphorus is carried by thermocline paths with transit times less than ˜300-400 years, while ˜4/7 of their phosphorus is carried by abyssal paths with transit times exceeding ˜700 years. The path density reveals that Antarctic Intermediate Water carries about a third of the regenerated phosphate last utilized in the EEqP that is destined for the Southern Ocean euphotic zone. The Southern Ocean is where (62 ± 2)% of the regenerated inventory and (69 ± 1)% of the preformed inventory first reemerge into the euphotic zone.

Temporal dynamics of catchment transit times from stable isotope data

NASA Astrophysics Data System (ADS)

Klaus, Julian; Chun, Kwok P.; McGuire, Kevin J.; McDonnell, Jeffrey J.

2015-06-01

Time variant catchment transit time distributions are fundamental descriptors of catchment function but yet not fully understood, characterized, and modeled. Here we present a new approach for use with standard runoff and tracer data sets that is based on tracking of tracer and age information and time variant catchment mixing. Our new approach is able to deal with nonstationarity of flow paths and catchment mixing, and an irregular shape of the transit time distribution. The approach extracts information on catchment mixing from the stable isotope time series instead of prior assumptions of mixing or the shape of transit time distribution. We first demonstrate proof of concept of the approach with artificial data; the Nash-Sutcliffe efficiencies in tracer and instantaneous transit times were >0.9. The model provides very accurate estimates of time variant transit times when the boundary conditions and fluxes are fully known. We then tested the model with real rainfall-runoff flow and isotope tracer time series from the H.J. Andrews Watershed 10 (WS10) in Oregon. Model efficiencies were 0.37 for the 18O modeling for a 2 year time series; the efficiencies increased to 0.86 for the second year underlying the need of long time tracer time series with a long overlap of tracer input and output. The approach was able to determine time variant transit time of WS10 with field data and showed how it follows the storage dynamics and related changes in flow paths where wet periods with high flows resulted in clearly shorter transit times compared to dry low flow periods.

Path Flow Estimation Using Time Varying Coefficient State Space Model

NASA Astrophysics Data System (ADS)

Jou, Yow-Jen; Lan, Chien-Lun

2009-08-01

The dynamic path flow information is very crucial in the field of transportation operation and management, i.e., dynamic traffic assignment, scheduling plan, and signal timing. Time-dependent path information, which is important in many aspects, is nearly impossible to be obtained. Consequently, researchers have been seeking estimation methods for deriving valuable path flow information from less expensive traffic data, primarily link traffic counts of surveillance systems. This investigation considers a path flow estimation problem involving the time varying coefficient state space model, Gibbs sampler, and Kalman filter. Numerical examples with part of a real network of the Taipei Mass Rapid Transit with real O-D matrices is demonstrated to address the accuracy of proposed model. Results of this study show that this time-varying coefficient state space model is very effective in the estimation of path flow compared to time-invariant model.

Quantum circuit dynamics via path integrals: Is there a classical action for discrete-time paths?

NASA Astrophysics Data System (ADS)

Penney, Mark D.; Enshan Koh, Dax; Spekkens, Robert W.

2017-07-01

It is straightforward to compute the transition amplitudes of a quantum circuit using the sum-over-paths methodology when the gates in the circuit are balanced, where a balanced gate is one for which all non-zero transition amplitudes are of equal magnitude. Here we consider the question of whether, for such circuits, the relative phases of different discrete-time paths through the configuration space can be defined in terms of a classical action, as they are for continuous-time paths. We show how to do so for certain kinds of quantum circuits, namely, Clifford circuits where the elementary systems are continuous-variable systems or discrete systems of odd-prime dimension. These types of circuit are distinguished by having phase-space representations that serve to define their classical counterparts. For discrete systems, the phase-space coordinates are also discrete variables. We show that for each gate in the generating set, one can associate a symplectomorphism on the phase-space and to each of these one can associate a generating function, defined on two copies of the configuration space. For discrete systems, the latter association is achieved using tools from algebraic geometry. Finally, we show that if the action functional for a discrete-time path through a sequence of gates is defined using the sum of the corresponding generating functions, then it yields the correct relative phases for the path-sum expression. These results are likely to be relevant for quantizing physical theories where time is fundamentally discrete, characterizing the classical limit of discrete-time quantum dynamics, and proving complexity results for quantum circuits.

Exploring the Dynamics of Transit Times and Subsurface Mixing in a Small Agricultural Catchment

NASA Astrophysics Data System (ADS)

Yang, Jie; Heidbüchel, Ingo; Musolff, Andreas; Reinstorf, Frido; Fleckenstein, Jan H.

2018-03-01

The analysis of transit/residence time distributions (TTDs and RTDs) provides important insights into the dynamics of stream-water ages and subsurface mixing. These insights have significant implications for water quality. For a small agricultural catchment in central Germany, we use a 3D fully coupled surface-subsurface hydrological model to simulate water flow and perform particle tracking to determine flow paths and transit times. The TTDs of discharge, RTDs of storage and fractional StorAge Selection (fSAS) functions are computed and analyzed on daily basis for a period of 10 years. Results show strong seasonal fluctuations of the median transit time of discharge and the median residence time, with the former being strongly related to the catchment wetness. Computed fSAS functions suggest systematic shifts of the discharge selection preference over four main periods: In the wet period, the youngest water in storage is preferentially selected, and this preference shifts gradually toward older ages of stored water when the catchment transitions into the drying, dry and wetting periods. These changes are driven by distinct shifts in the dominance of deeper flow paths and fast shallow flow paths. Changes in the shape of the fSAS functions can be captured by changes in the two parameters of the approximating Beta distributions, allowing the generation of continuous fSAS functions representing the general catchment behavior. These results improve our understanding of the seasonal dynamics of TTDs and fSAS functions for a complex real-world catchment and are important for interpreting solute export to the stream in a spatially implicit manner.

Scan path entropy and arrow plots: capturing scanning behavior of multiple observers

PubMed Central

Hooge, Ignace; Camps, Guido

2013-01-01

Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures (1) “scan path entropy” to quantify gaze guidance and (2) the “arrow plot” to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50). The new measures were tested in an eye tracking study (48 observers, 39 advertisements). Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place. PMID:24399993

Energy management during the space shuttle transition

NASA Technical Reports Server (NTRS)

Stengel, R. F.

1972-01-01

An approach to calculating optimal, gliding flight paths of the type associated with the space shuttle's transition from entry to cruising flight is presented. Kinetic energy and total energy (per unit weight) replace velocity and time in the dynamic equations, reducing the dimension and complexity of the problem. The capability for treating integral and terminal penalties (as well as Mach number effects) is retained in the numerical optimization; hence, stability and control boundaries can be observed as trajectories to the desired final energy, flight path angle, and range are determined. Numerical results show that the jump to the front-side of the L/D curve need not be made until the end of the transition and that the dynamic model provides a conservative range estimate. Alternatives for real time trajectory control are discussed.

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

PubMed Central

Chandrasekaran, Srinivas Niranj; Das, Jhuma; Dokholyan, Nikolay V.; Carter, Charles W.

2016-01-01

PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. PMID:26958584

Examination about the effects of future career choice on time perspective in Japanese high school students.

PubMed

Tsuzuki, Manabu

2015-03-30

This study investigated types of career choice in high school students and examined the effects of career paths on time perspective development. The participants were 4,756 third grade students from nine public high schools in Tokyo. The high school questionnaire survey was conducted throughout autumn of 2008, 2009, and 2010. One year later, 962 graduates participated in the follow-up questionnaire survey by post. Distinguishing gender difference among career paths was found. Girls tend to choose significantly shorter learning careers (p < .01), for example junior college or vocational school in comparison to boys. Career indecision, i.e., students who could not set a concrete future career in high school, had significantly more negative time perspective than other groups (p < .05), which was caused by a deficiency of their basic cognitive ability. Longitudinal data showed different patterns of fluctuation in time perspective between "school to school transition" and "school to work transition". It is suggested that the "school to work transition" tends to be more critical for adolescents and has negative effects on time perspective. These results suggest that the goal content in careers may promote or inhibit the formation of time perspectives during the graduation transition.

Foundations and latest advances in replica exchange transition interface sampling.

PubMed

Cabriolu, Raffaela; Skjelbred Refsnes, Kristin M; Bolhuis, Peter G; van Erp, Titus S

2017-10-21

Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations.

Foundations and latest advances in replica exchange transition interface sampling

NASA Astrophysics Data System (ADS)

Cabriolu, Raffaela; Skjelbred Refsnes, Kristin M.; Bolhuis, Peter G.; van Erp, Titus S.

2017-10-01

Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations.

Method and apparatus for ultrasonic characterization through the thickness direction of a moving web

DOEpatents

Jackson, Theodore; Hall, Maclin S.

2001-01-01

A method and apparatus for determining the caliper and/or the ultrasonic transit time through the thickness direction of a moving web of material using ultrasonic pulses generated by a rotatable wheel ultrasound apparatus. The apparatus includes a first liquid-filled tire and either a second liquid-filled tire forming a nip or a rotatable cylinder that supports a thin moving web of material such as a moving web of paper and forms a nip with the first liquid-filled tire. The components of ultrasonic transit time through the tires and fluid held within the tires may be resolved and separately employed to determine the separate contributions of the two tire thicknesses and the two fluid paths to the total path length that lies between two ultrasonic transducer surfaces contained within the tires in support of caliper measurements. The present invention provides the benefit of obtaining a transit time and caliper measurement at any point in time as a specimen passes through the nip of rotating tires and eliminates inaccuracies arising from nonuniform tire circumferential thickness by accurately retaining point-to-point specimen transit time and caliper variation information, rather than an average obtained through one or more tire rotations. Morever, ultrasonic transit time through the thickness direction of a moving web may be determined independent of small variations in the wheel axle spacing, tire thickness, and liquid and tire temperatures.

Parameter optimization on the convergence surface of path simulations

NASA Astrophysics Data System (ADS)

Chandrasekaran, Srinivas Niranj

Computational treatments of protein conformational changes tend to focus on the trajectories themselves, despite the fact that it is the transition state structures that contain information about the barriers that impose multi-state behavior. PATH is an algorithm that computes a transition pathway between two protein crystal structures, along with the transition state structure, by minimizing the Onsager-Machlup action functional. It is rapid but depends on several unknown input parameters whose range of different values can potentially generate different transition-state structures. Transition-state structures arising from different input parameters cannot be uniquely compared with those generated by other methods. I outline modifications that I have made to the PATH algorithm that estimates these input parameters in a manner that circumvents these difficulties, and describe two complementary tests that validate the transition-state structures found by the PATH algorithm. First, I show that although the PATH algorithm and two other approaches to computing transition pathways produce different low-energy structures connecting the initial and final ground-states with the transition state, all three methods agree closely on the configurations of their transition states. Second, I show that the PATH transition states are close to the saddle points of free-energy surfaces connecting initial and final states generated by replica-exchange Discrete Molecular Dynamics simulations. I show that aromatic side-chain rearrangements create similar potential energy barriers in the transition-state structures identified by PATH for a signaling protein, a contractile protein, and an enzyme. Finally, I observed, but cannot account for, the fact that trajectories obtained for all-atom and Calpha-only simulations identify transition state structures in which the Calpha atoms are in essentially the same positions. The consistency between transition-state structures derived by different algorithms for unrelated protein systems argues that although functionally important protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. In the end, I outline the strategies that could enhance the efficiency and applicability of PATH.

H theorem for generalized entropic forms within a master-equation framework

NASA Astrophysics Data System (ADS)

Casas, Gabriela A.; Nobre, Fernando D.; Curado, Evaldo M. F.

2016-03-01

The H theorem is proven for generalized entropic forms, in the case of a discrete set of states. The associated probability distributions evolve in time according to a master equation, for which the corresponding transition rates depend on these entropic forms. An important equation describing the time evolution of the transition rates and probabilities in such a way as to drive the system towards an equilibrium state is found. In the particular case of Boltzmann-Gibbs entropy, it is shown that this equation is satisfied in the microcanonical ensemble only for symmetric probability transition rates, characterizing a single path to the equilibrium state. This equation fulfils the proof of the H theorem for generalized entropic forms, associated with systems characterized by complex dynamics, e.g., presenting nonsymmetric probability transition rates and more than one path towards the same equilibrium state. Some examples considering generalized entropies of the literature are discussed, showing that they should be applicable to a wide range of natural phenomena, mainly those within the realm of complex systems.

Signs and stability in higher-derivative gravity

NASA Astrophysics Data System (ADS)

Narain, Gaurav

2018-02-01

Perturbatively renormalizable higher-derivative gravity in four space-time dimensions with arbitrary signs of couplings has been considered. Systematic analysis of the action with arbitrary signs of couplings in Lorentzian flat space-time for no-tachyons, fixes the signs. Feynman + i𝜖 prescription for these signs further grants necessary convergence in path-integral, suppressing the field modes with large action. This also leads to a sensible wick rotation where quantum computation can be performed. Running couplings for these sign of parameters make the massive tensor ghost innocuous leading to a stable and ghost-free renormalizable theory in four space-time dimensions. The theory has a transition point arising from renormalization group (RG) equations, where the coefficient of R2 diverges without affecting the perturbative quantum field theory (QFT). Redefining this coefficient gives a better handle over the theory around the transition point. The flow equations push the flow of parameters across the transition point. The flow beyond the transition point is analyzed using the one-loop RG equations which shows that the regime beyond the transition point has unphysical properties: there are tachyons, the path-integral loses positive definiteness, Newton’s constant G becomes negative and large, and perturbative parameters become large. These shortcomings indicate a lack of completeness beyond the transition point and need of a nonperturbative treatment of the theory beyond the transition point.

The Bulgarian Academic Profession in Transition.

ERIC Educational Resources Information Center

Slantcheva, Snejana

2003-01-01

Analyzes the current status of the academic profession in Bulgaria at a time of difficult socioeconomic transition. After providing a brief overview of the historical development of Bulgarian academia, discusses faculty working conditions, the career path within the profession, and the legal framework for the professoriate. Highlights future key…

Ultrafast electron crystallography of the cooperative reaction path in vanadium dioxide

PubMed Central

Yang, Ding-Shyue; Baum, Peter; Zewail, Ahmed H.

2016-01-01

Time-resolved electron diffraction with atomic-scale spatial and temporal resolution was used to unravel the transformation pathway in the photoinduced structural phase transition of vanadium dioxide. Results from bulk crystals and single-crystalline thin-films reveal a common, stepwise mechanism: First, there is a femtosecond V−V bond dilation within 300 fs, second, an intracell adjustment in picoseconds and, third, a nanoscale shear motion within tens of picoseconds. Experiments at different ambient temperatures and pump laser fluences reveal a temperature-dependent excitation threshold required to trigger the transitional reaction path of the atomic motions. PMID:27376103

Assessment of Crack Path Prediction in Non-Proportional Mixed-Mode Fatigue

NASA Technical Reports Server (NTRS)

Highsmith, Shelby, Jr.; Johnson, Steve; Swanson, Gregory; Sayyah, Tarek; Pettit, Richard

2008-01-01

Non-proportional mixed-mode loading is present in many systems and a growing crack can experience any manner of mixed-mode loading. Prediction of the resulting crack path is important when assessing potential failure modes or when performing a failure investigation. Current crack path selection criteria are presented along with data for Inconel 718 under non-proportional mixed-mode loading. Mixed-mode crack growth can transition between path deflection mechanisms with very different orientations. Non-proportional fatigue loadings lack a single parameter for input to current crack path criteria. Crack growth transitions were observed in proportional and non-proportional FCG tests. Different paths displayed distinct fracture surface morphologies. New crack path drivers & transition criteria must be developed.

Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.

PubMed

Ovchinnikov, Victor; Karplus, Martin

2012-07-26

The popular targeted molecular dynamics (TMD) method for generating transition paths in complex biomolecular systems is revisited. In a typical TMD transition path, the large-scale changes occur early and the small-scale changes tend to occur later. As a result, the order of events in the computed paths depends on the direction in which the simulations are performed. To identify the origin of this bias, and to propose a method in which the bias is absent, variants of TMD in the restraint formulation are introduced and applied to the complex open ↔ closed transition in the protein calmodulin. Due to the global best-fit rotation that is typically part of the TMD method, the simulated system is guided implicitly along the lowest-frequency normal modes, until the large spatial scales associated with these modes are near the target conformation. The remaining portion of the transition is described progressively by higher-frequency modes, which correspond to smaller-scale rearrangements. A straightforward modification of TMD that avoids the global best-fit rotation is the locally restrained TMD (LRTMD) method, in which the biasing potential is constructed from a number of TMD potentials, each acting on a small connected portion of the protein sequence. With a uniform distribution of these elements, transition paths that lack the length-scale bias are obtained. Trajectories generated by steered MD in dihedral angle space (DSMD), a method that avoids best-fit rotations altogether, also lack the length-scale bias. To examine the importance of the paths generated by TMD, LRTMD, and DSMD in the actual transition, we use the finite-temperature string method to compute the free energy profile associated with a transition tube around a path generated by each algorithm. The free energy barriers associated with the paths are comparable, suggesting that transitions can occur along each route with similar probabilities. This result indicates that a broad ensemble of paths needs to be calculated to obtain a full description of conformational changes in biomolecules. The breadth of the contributing ensemble suggests that energetic barriers for conformational transitions in proteins are offset by entropic contributions that arise from a large number of possible paths.

Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells.

PubMed

Ohta, Yoshihiro; Nishiyama, Akinobu; Wada, Yoichiro; Ruan, Yijun; Kodama, Tatsuhiko; Tsuboi, Takashi; Tokihiro, Tetsuji; Ihara, Sigeo

2012-08-01

We all use path routing everyday as we take shortcuts to avoid traffic jams, or by using faster traffic means. Previous models of traffic flow of RNA polymerase II (RNAPII) during transcription, however, were restricted to one dimension along the DNA template. Here we report the modeling and application of traffic flow in transcription that allows preferential paths of different dimensions only restricted to visit some transit points, as previously introduced between the 5' and 3' end of the gene. According to its position, an RNAPII protein molecule prefers paths obeying two types of time-evolution rules. One is an asymmetric simple exclusion process (ASEP) along DNA, and the other is a three-dimensional jump between transit points in DNA where RNAPIIs are staying. Simulations based on our model, and comparison experimental results, reveal how RNAPII molecules are distributed at the DNA-loop-formation-related protein binding sites as well as CTCF insulator proteins (or exons). As time passes after the stimulation, the RNAPII density at these sites becomes higher. Apparent far-distance jumps in one dimension are realized by short-range three-dimensional jumps between DNA loops. We confirm the above conjecture by applying our model calculation to the SAMD4A gene by comparing the experimental results. Our probabilistic model provides possible scenarios for assembling RNAPII molecules into transcription factories, where RNAPII and related proteins cooperatively transcribe DNA.

Sunrise effects on VLF signals propagating over a long north-south path

NASA Astrophysics Data System (ADS)

Clilverd, Mark A.; Thomson, Neil R.; Rodger, Craig J.

1999-07-01

We present a detailed study of the times of amplitude minima observed on the 12-Mm path from NAA (24 kHz, 1 MW, Cutler, Maine) to Faraday, Antarctica, during the period 1990-1995. (NAA is a naval transmitter call sign.) This study represents the first account of the effect of the sunrise terminator when it is parallel to a propagation path at some times of the year. Since the NAA-Faraday path is within 3° of the north-south meridian, parallel orientation happens close to the equinoxes, while the maximum angle of incidence occurs during the solstices. During the solstices the terminator takes a significant length of time to cross the entire propagation path, so modal conversion effects are observed over a range of hours. During the equinoxes, however, the leading edge of the night-day transition region crosses the whole propagation path within 20 min. The interpretation of the timing of minima is consistent with modal conversion taking place as the sunrise terminator crosses the NAA-Faraday transmission path at specific, consistent locations. The timing of minima is remarkably consistent from year to year. Long wave propagation modeling is used to show that the location of nightside minima at an altitude of 45-75 km in the subionospheric waveguide represents the location of the sunrise terminator on the great circle path when dayside minima occur.

The Effects of Barycentric and Asymmetric Transverse Velocities on Eclipse and Transit Times

NASA Astrophysics Data System (ADS)

Conroy, Kyle E.; Prša, Andrej; Horvat, Martin; Stassun, Keivan G.

2018-02-01

It has long been recognized that the finite speed of light can affect the observed time of an event. For example, as a source moves radially toward or away from an observer, the path length and therefore the light travel time to the observer decreases or increases, causing the event to appear earlier or later than otherwise expected, respectively. This light travel time effect has been applied to transits and eclipses for a variety of purposes, including studies of eclipse timing variations and transit timing variations that reveal the presence of additional bodies in the system. Here we highlight another non-relativistic effect on eclipse or transit times arising from the finite speed of light—caused by an asymmetry in the transverse velocity of the two eclipsing objects, relative to the observer. This asymmetry can be due to a non-unity mass ratio or to the presence of external barycentric motion. Although usually constant, this barycentric and asymmetric transverse velocity (BATV) effect can vary between sequential eclipses if either the path length between the two objects or the barycentric transverse velocity varies in time. We discuss this BATV effect and estimate its magnitude for both time-dependent and time-independent cases. For the time-dependent cases, we consider binaries that experience a change in orbital inclination, eccentric systems with and without apsidal motion, and hierarchical triple systems. We also consider the time-independent case which, by affecting the primary and secondary eclipses differently, can influence the inferred system parameters, such as the orbital eccentricity.

Autogenerator of beams of charged particles

DOEpatents

Adler, Richard J.; Mazarakis, Michael G.; Miller, Robert B.; Shope, Steven L.; Smith, David L.

1986-01-01

An autogenerating apparatus provides secondary intense relativistic current beam pulses in response to an injected beam pulse. One or more electromagnetic energy storage devices are provided in conjunction with gaps along a beam propagation path for the injected beam pulse. For injected beam pulses which are no longer than double the transit time of electromagnetic waves within the storage devices (which may be resonant cavities), distinct secondary beam pulses are generated by each of the energy storage devices. The beam propagation path, together with the one or more gaps provided therein, operates as a pulse forming transmission line cavity, in which the separate cavities associated with the gaps provide delays for electromagnetic waves generated at the gaps. After doubly traversing the cavity, the electromagnetic waves cause the gap to generate the secondary beam pulses, which are thus delayed by a time interval equal to the double transit time for the induced wave within the cavity.

Autogenerator of beams of charged particles

DOEpatents

Adler, R.J.; Mazarakis, M.G.; Miller, R.M.; Shope, S.L.; Smith, D.L.

1983-10-31

An autogenerating apparatus provides secondary intense relativistic current beam pulses in response to an injected beam pulse. One or more electromagnetic energy storage devices are provided in conjunction with gaps along a beam propagation path for the injected beam pulse. For injected beam pulses which are no longer than double the transit time of electromagnetic waves within the storage devices (which may be resonant cavities), distinct secondary beam pulses are generated by each of the energy storage devices. The beam propagation path, together with the one or more gaps provided therein, operates as a pulse forming transmission line cavity, in which the separate cavities associated with the gaps provide delays for electromagnetic waves generated at the gaps. After doubly traversing the cavity, the electromagnetic waves cause the gap to generate the secondary beam pulses, which are thus delayed by a time interval equal to the double transit time for the induced wave within the cavity.

Transition path theory analysis of c-Src kinase activation

PubMed Central

Meng, Yilin; Shukla, Diwakar; Pande, Vijay S.; Roux, Benoît

2016-01-01

Nonreceptor tyrosine kinases of the Src family are large multidomain allosteric proteins that are crucial to cellular signaling pathways. In a previous study, we generated a Markov state model (MSM) to simulate the activation of c-Src catalytic domain, used as a prototypical tyrosine kinase. The long-time kinetics of transition predicted by the MSM was in agreement with experimental observations. In the present study, we apply the framework of transition path theory (TPT) to the previously constructed MSM to characterize the main features of the activation pathway. The analysis indicates that the activating transition, in which the activation loop first opens up followed by an inward rotation of the αC-helix, takes place via a dense set of intermediate microstates distributed within a fairly broad “transition tube” in a multidimensional conformational subspace connecting the two end-point conformations. Multiple microstates with negligible equilibrium probabilities carry a large transition flux associated with the activating transition, which explains why extensive conformational sampling is necessary to accurately determine the kinetics of activation. Our results suggest that the combination of MSM with TPT provides an effective framework to represent conformational transitions in complex biomolecular systems. PMID:27482115

Path Finding on High-Dimensional Free Energy Landscapes

NASA Astrophysics Data System (ADS)

Díaz Leines, Grisell; Ensing, Bernd

2012-07-01

We present a method for determining the average transition path and the free energy along this path in the space of selected collective variables. The formalism is based upon a history-dependent bias along a flexible path variable within the metadynamics framework but with a trivial scaling of the cost with the number of collective variables. Controlling the sampling of the orthogonal modes recovers the average path and the minimum free energy path as the limiting cases. The method is applied to resolve the path and the free energy of a conformational transition in alanine dipeptide.

Computation of rare transitions in the barotropic quasi-geostrophic equations

NASA Astrophysics Data System (ADS)

Laurie, Jason; Bouchet, Freddy

2015-01-01

We investigate the theoretical and numerical computation of rare transitions in simple geophysical turbulent models. We consider the barotropic quasi-geostrophic and two-dimensional Navier-Stokes equations in regimes where bistability between two coexisting large-scale attractors exist. By means of large deviations and instanton theory with the use of an Onsager-Machlup path integral formalism for the transition probability, we show how one can directly compute the most probable transition path between two coexisting attractors analytically in an equilibrium (Langevin) framework and numerically otherwise. We adapt a class of numerical optimization algorithms known as minimum action methods to simple geophysical turbulent models. We show that by numerically minimizing an appropriate action functional in a large deviation limit, one can predict the most likely transition path for a rare transition between two states. By considering examples where theoretical predictions can be made, we show that the minimum action method successfully predicts the most likely transition path. Finally, we discuss the application and extension of such numerical optimization schemes to the computation of rare transitions observed in direct numerical simulations and experiments and to other, more complex, turbulent systems.

Combined Cycle Engine Large-Scale Inlet for Mode Transition Experiments: System Identification Rack Hardware Design

NASA Technical Reports Server (NTRS)

Thomas, Randy; Stueber, Thomas J.

2013-01-01

The System Identification (SysID) Rack is a real-time hardware-in-the-loop data acquisition (DAQ) and control instrument rack that was designed and built to support inlet testing in the NASA Glenn Research Center 10- by 10-Foot Supersonic Wind Tunnel. This instrument rack is used to support experiments on the Combined-Cycle Engine Large-Scale Inlet for Mode Transition Experiment (CCE? LIMX). The CCE?LIMX is a testbed for an integrated dual flow-path inlet configuration with the two flow paths in an over-and-under arrangement such that the high-speed flow path is located below the lowspeed flow path. The CCE?LIMX includes multiple actuators that are designed to redirect airflow from one flow path to the other; this action is referred to as "inlet mode transition." Multiple phases of experiments have been planned to support research that investigates inlet mode transition: inlet characterization (Phase-1) and system identification (Phase-2). The SysID Rack hardware design met the following requirements to support Phase-1 and Phase-2 experiments: safely and effectively move multiple actuators individually or synchronously; sample and save effector control and position sensor feedback signals; automate control of actuator positioning based on a mode transition schedule; sample and save pressure sensor signals; and perform DAQ and control processes operating at 2.5 KHz. This document describes the hardware components used to build the SysID Rack including their function, specifications, and system interface. Furthermore, provided in this document are a SysID Rack effectors signal list (signal flow); system identification experiment setup; illustrations indicating a typical SysID Rack experiment; and a SysID Rack performance overview for Phase-1 and Phase-2 experiments. The SysID Rack described in this document was a useful tool to meet the project objectives.

The Relationship between School Connectedness and Mental Health during the Transition to Secondary School: A Path Analysis

ERIC Educational Resources Information Center

Lester, Leanne; Waters, Stacey; Cross, Donna

2013-01-01

During the transition from primary to secondary school, students typically experience a new social environment, moving from primary school with small intact classes throughout the day with one main teacher, to a larger secondary school with teachers, classrooms and often classmates changing throughout the day. During this time, students report a…

Stochastic Cell Fate Progression in Embryonic Stem Cells

NASA Astrophysics Data System (ADS)

Zou, Ling-Nan; Doyle, Adele; Jang, Sumin; Ramanathan, Sharad

2013-03-01

Studies on the directed differentiation of embryonic stem (ES) cells suggest that some early developmental decisions may be stochastic in nature. To identify the sources of this stochasticity, we analyzed the heterogeneous expression of key transcription factors in single ES cells as they adopt distinct germ layer fates. We find that under sufficiently stringent signaling conditions, the choice of lineage is unambiguous. ES cells flow into differentiated fates via diverging paths, defined by sequences of transitional states that exhibit characteristic co-expression of multiple transcription factors. These transitional states have distinct responses to morphogenic stimuli; by sequential exposure to multiple signaling conditions, ES cells are steered towards specific fates. However, the rate at which cells travel down a developmental path is stochastic: cells exposed to the same signaling condition for the same amount of time can populate different states along the same path. The heterogeneity of cell states seen in our experiments therefore does not reflect the stochastic selection of germ layer fates, but the stochastic rate of progression along a chosen developmental path. Supported in part by the Jane Coffin Childs Fund

A benchmark for reaction coordinates in the transition path ensemble

PubMed Central

2016-01-01

The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. PMID:27059559

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

PubMed Central

Seyler, Sean L.; Kumar, Avishek; Thorpe, M. F.; Beckstein, Oliver

2015-01-01

Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that the geometry-based FRODA occasionally sampled the pathway space of force field-based DIMS MD. For the AdK transition, the new concept of a Hausdorff-pair map enabled us to extract the molecular structural determinants responsible for differences in pathways, namely a set of conserved salt bridges whose charge-charge interactions are fully modelled in DIMS MD but not in FRODA. PSA has the potential to enhance our understanding of transition path sampling methods, validate them, and to provide a new approach to analyzing conformational transitions. PMID:26488417

The 16.6 Ma Steens Mountain Geomagnetic Polarity Reversal: Additional Complexity From a Composite Record of Five Stratigraphic Sections.

NASA Astrophysics Data System (ADS)

Jarboe, N. A.; Coe, R. S.; Glen, J. M.; Paul, R. R.

2007-05-01

The best known record of the earth's magnetic field behavior during a geomagnetic polarity reversal preserved in volcanic rock is the reverse to normal (R-N) polarity reversal found in the Steens Basalts of SE Oregon. At three locations where reverse to normal sections are found (Steens Mountain, Catlow Peak, and Poker Jim Ridge), four high precision 40Ar/39Ar plateau ages of plagioclase separates from transitionally magnetized rocks were determined. The ages are the same within error and have a weighted mean age of 16.58 ± 0.14 Ma. Errors are two sigma. A more precise constraint on the youngest possible age of the reversal is 16.548 ± 0.050 Ma determined from the normally magnetized Oregon Canyon tuff capping the Catlow Peak section. Comparison of these ages to the new geomagnetic polarity time scale of Gradstein et al. (A Geologic Time Scale 2004, 589 pp., Cambridge University Press, 2004.), after adjustments due to differences in Fish Canyon sanidine (FCs) standard ages (28.02 Ma, this study; 28.24 Ma, Gradstein et al.), shows that the Steens reversal is uniquely identified as the top of the C5Cr chron. The high precision of the ages and the Steens' reversal location in the geomagnetic polarity timescale convincingly demonstrate that these stratigraphically uncorrelated transitional sections were erupted during the same transition and their transitional paths should be combined. The high-quality, detailed benchmark record of this reversal (Mankinen et al., JGR, 90(B), 10.393-10.416, 1985; Prevot et al., Nature, 316, 230-234, 1985) is a composite derived from two sampled sections 2 km apart on Steens Mountain that overlapped significantly, Steens A above and Steens B below. This study showed that the magnetic field during the reversal moved from reverse to normal and then bounced back to transitional before finally returning to normal (a R-T-N-T-N path). The unexamined upper part of the Steens B section was later sampled and revealed an additional bounce of the field during the transition (Camps et al., JGR, 104(B8), 17747- 58, 1999). This increased the reversal's complexity to a R-T-N-T-N-T-N pattern. We have studied a R-N volcanic section at Catlow Peak 70 km SSE of Steens Mountain with 32 flows erupted during the transition. The transitional directions trace a path very close to the Steens A and B reversal path but contain an additional large swing through the reversed field direction, demonstrating an even more complex R-T-N-T-N-T-R-T-N path. We will also report on two R-N sections recently sampled at Poker Jim Ridge 80 km west of Steens Mountain that add new directions to the Steens record. The complex composite Steens reversal path recorded in these high fidelity lavas gives some credence to suggestions of very complex magnetic field behavior during reversals, previously seen only in sediment records where the acquisition of magnetization is less well understood.

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant

PubMed Central

2013-01-01

The free-energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. Here, we construct the optimal coordinate and the associated free-energy profile for all-helical proteins HP35 and its norleucine (Nle/Nle) double mutant, based on realistic equilibrium folding simulations [Piana et al. Proc. Natl. Acad. Sci. U.S.A.2012, 109, 17845]. From the obtained profiles, we directly determine such basic properties of folding dynamics as the configurations of the minima and transition states (TS), the formation of secondary structure and hydrophobic core during the folding process, the value of the pre-exponential factor and its relation to the transition path times, the relation between the autocorrelation times in TS and minima. We also present an investigation of the accuracy of the pre-exponential factor estimation based on the transition-path times. Four different estimations of the pre-exponential factor for both proteins give k0–1 values of approximately a few tens of nanoseconds. Our analysis gives detailed information about folding of the proteins and can serve as a rigorous common language for extensive comparison between experiment and simulation. PMID:24348206

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.

PubMed

Banushkina, Polina V; Krivov, Sergei V

2013-12-10

The free-energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. Here, we construct the optimal coordinate and the associated free-energy profile for all-helical proteins HP35 and its norleucine (Nle/Nle) double mutant, based on realistic equilibrium folding simulations [Piana et al. Proc. Natl. Acad. Sci. U.S.A. 2012 , 109 , 17845]. From the obtained profiles, we directly determine such basic properties of folding dynamics as the configurations of the minima and transition states (TS), the formation of secondary structure and hydrophobic core during the folding process, the value of the pre-exponential factor and its relation to the transition path times, the relation between the autocorrelation times in TS and minima. We also present an investigation of the accuracy of the pre-exponential factor estimation based on the transition-path times. Four different estimations of the pre-exponential factor for both proteins give k 0 -1 values of approximately a few tens of nanoseconds. Our analysis gives detailed information about folding of the proteins and can serve as a rigorous common language for extensive comparison between experiment and simulation.

Testing the paradigms of the glass transition in colloids

NASA Astrophysics Data System (ADS)

Zia, Roseanna; Wang, Jialun; Peng, Xiaoguang; Li, Qi; McKenna, Gregory

2017-11-01

Many molecular liquids freeze upon fast enough cooling. This so-called glass state is path dependent and out of equilibrium, as measured by the Kovacs signature experiments, i.e. intrinsic isotherms, asymmetry of approach and memory effect. The reasons for this path- and time-dependence are not fully understood, due to fast molecular relaxations. Colloids provide a natural way to model such behavior, owing to disparity in colloidal versus solvent time scales that can slow dynamics. To shed light on the ambiguity of glass transition, we study via large-scale dynamic simulation of hard-sphere colloidal glass after volume-fraction jumps, where particle size increases at fixed system volume followed by protocols of the McKenna-Kovacs signature experiments. During and following each jump, the positions, velocities, and particle-phase stress are tracked and utilized to characterize relaxation time scales. The impact of both quench depth and quench rate on arrested dynamics and ``state'' variables is explored. In addition, we expand our view to various structural signatures, and rearrangement mechanism is proposed. The results provide insight into not only the existence of an ``ideal'' glass transition, but also the role of structure in such a dense amorphous system.

Heterogeneous path ensembles for conformational transitions in semi–atomistic models of adenylate kinase

PubMed Central

Bhatt, Divesh; Zuckerman, Daniel M.

2010-01-01

We performed “weighted ensemble” path–sampling simulations of adenylate kinase, using several semi–atomistic protein models. The models have an all–atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single–processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semi–atomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways. PMID:21660120

Transitioning DARPA Technology

DTIC Science & Technology

2001-05-01

logo suggests, the Institute’s work reflects the summation of technology’s effects on business and government. With a reputation for fierce objectivity... effective for "customerpull" strategies. b. Products moved along the DIS path 30 percent of the time. This path was particularlysuccessful for small...must often be "waited out." But DARPA ha s few effective mechanisms for continuing to "market" its products after the prog ram is over- particularly

Raising the Bar: An Examination of Career Pathways among Women Working in the Child Welfare System

ERIC Educational Resources Information Center

Williams, Vera L.

2013-01-01

In today's society, women who return back to school seeking an advancement within their career is a transition within the lives of women that occurs in various contexts, including the women's ages at the time of their transition, which can define both their expectations and opportunities along their life stages and career paths. In the past, women…

Path-length-resolved dynamic light scattering in highly scattering random media: The transition to diffusing wave spectroscopy

NASA Astrophysics Data System (ADS)

Bizheva, Kostadinka K.; Siegel, Andy M.; Boas, David A.

1998-12-01

We used low coherence interferometry to measure Brownian motion within highly scattering random media. A coherence gate was applied to resolve the optical path-length distribution and to separate ballistic from diffusive light. Our experimental analysis provides details on the transition from single scattering to light diffusion and its dependence on the system parameters. We found that the transition to the light diffusion regime occurs at shorter path lengths for media with higher scattering anisotropy or for larger numerical aperture of the focusing optics.

Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory

NASA Astrophysics Data System (ADS)

Richter, Martin; Fingerhut, Benjamin P.

2017-06-01

The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.

CosmoTransitions: Computing cosmological phase transition temperatures and bubble profiles with multiple fields

NASA Astrophysics Data System (ADS)

Wainwright, Carroll L.

2012-09-01

I present a numerical package (CosmoTransitions) for analyzing finite-temperature cosmological phase transitions driven by single or multiple scalar fields. The package analyzes the different vacua of a theory to determine their critical temperatures (where the vacuum energy levels are degenerate), their supercooling temperatures, and the bubble wall profiles which separate the phases and describe their tunneling dynamics. I introduce a new method of path deformation to find the profiles of both thin- and thick-walled bubbles. CosmoTransitions is freely available for public use.Program summaryProgram Title: CosmoTransitionsCatalogue identifier: AEML_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEML_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 8775No. of bytes in distributed program, including test data, etc.: 621096Distribution format: tar.gzProgramming language: Python.Computer: Developed on a 2009 MacBook Pro. No computer-specific optimization was performed.Operating system: Designed and tested on Mac OS X 10.6.8. Compatible with any OS with Python installed.RAM: Approximately 50 MB, mostly for loading plotting packages.Classification: 1.9, 11.1.External routines: SciPy, NumPy, matplotLibNature of problem: I describe a program to analyze early-Universe finite-temperature phase transitions with multiple scalar fields. The goal is to analyze the phase structure of an input theory, determine the amount of supercooling at each phase transition, and find the bubble-wall profiles of the nucleated bubbles that drive the transitions.Solution method: To find the bubble-wall profile, the program assumes that tunneling happens along a fixed path in field space. This reduces the equations of motion to one dimension, which can then be solved using the overshoot/undershoot method. The path iteratively deforms in the direction opposite the forces perpendicular to the path until the perpendicular forces vanish (or become very small). To find the phase structure, the program finds and integrates the change in a phase's minimum with respect to temperature.Running time: Approximately 1 minute for full analysis of the two-scalar-field test model on a 2.5 GHz CPU.

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2008-01-01

We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the protein maintains its compact configuration, while a (de)increase of secondary structure is observed. The calculated folding rate agrees reasonably with experiment, while the unfolding rate is 10 times higher. We discuss possible origins for this mismatch. We recomputed the rates with the forward flux sampling method, and found a discrepancy of four orders of magnitude, probably caused by the method's higher sensitivity to the choice of order parameter with respect to transition interface sampling. Finally, we used the previously computed transition path-sampling ensemble to screen combinations of many order parameters for the best model of the reaction coordinate by employing likelihood maximization. We found that a combination of the root mean-square deviation of the helix and of the entire protein was, of the set of tried order parameters, the one that best describes the reaction coordination. PMID:18676648

A two-beam acoustic system for tissue analysis.

PubMed

Sachs, T D; Janney, C D

1977-03-01

In the 'thermo-acoustic sensing technique' (TAST), a burst of sound, called the 'thermometer' beam is passed through tissue and its transit time is measured. A focused sound field, called the heating field, then warms a small volume in the path of the therometer beam, in proportion to the absorption. Finally, the therometer beam burst is repeated and its transit time subtracted from that of the initial thermometer burst. This difference measures the velocity perturbation in the tissue produced by the heating field. The transit time difference is td = K integral of infinity-infinity IP dchi where K is the instrument constant, I the heating field intensity, and P a perturbation factor which characterizes the tissues. The integration is carried out along the path of the thermometer beam. The perturbation factor is P = (formula: see text) where C is the specific heat, rho the denisty, V the velocity of sound, (formula: see text) the temperature coefficient of velocity and alpha the heating field absorption coefficient which is apparently sensitive to tissue structure and condition. Experiments on a fixed human brain showed an ability to distinguish between various tissue types combined with a spatial resolution of better than 3 mm. Should predictions based on the data and theory prove correct, TAST may become a non-invasive alternative to biopsy.

Guidance of a Solar Sail Spacecraft to the Sun - L(2) Point.

NASA Astrophysics Data System (ADS)

Hur, Sun Hae

The guidance of a solar sail spacecraft along a minimum-time path from an Earth orbit to a region near the Sun-Earth L_2 libration point is investigated. Possible missions to this point include a spacecraft "listening" for possible extra-terrestrial electromagnetic signals and a science payload to study the geomagnetic tail. A key advantage of the solar sail is that it requires no fuel. The control variables are the sail angles relative to the Sun-Earth line. The thrust is very small, on the order of 1 mm/s^2, and its magnitude and direction are highly coupled. Despite this limited controllability, the "free" thrust can be used for a wide variety of terminal conditions including halo orbits. If the Moon's mass is lumped with the Earth, there are quasi-equilibrium points near L_2. However, they are unstable so that some form of station keeping is required, and the sail can provide this without any fuel usage. In the two-dimensional case, regulating about a nominal orbit is shown to require less control and result in smaller amplitude error response than regulating about a quasi-equilibrium point. In the three-dimensional halo orbit case, station keeping using periodically varying gains is demonstrated. To compute the minimum-time path, the trajectory is divided into two segments: the spiral segment and the transition segment. The spiral segment is computed using a control law that maximizes the rate of energy increase at each time. The transition segment is computed as the solution of the time-optimal control problem from the endpoint of the spiral to the terminal point. It is shown that the path resulting from this approximate strategy is very close to the exact optimal path. For the guidance problem, the approximate strategy in the spiral segment already gives a nonlinear full-state feedback law. However, for large perturbations, follower guidance using an auxiliary propulsion is used for part of the spiral. In the transition segment, neighboring extremal feedback guidance using the solar sail, with feedforward control only near the terminal point, is used to correct perturbations in the initial conditions.

Movement Path Tortuosity Predicts Compliance With Therapeutic Behavioral Prompts in Patients With Traumatic Brain Injury.

PubMed

Kearns, William D; Fozard, James L; Ray, Roger D; Scott, Steven; Jasiewicz, Jan M; Craighead, Jeffrey D; Pagano, Craig V

2016-01-01

Rehabilitation of patients with traumatic brain injury typically includes therapeutic prompts for keeping appointments and adhering to medication regimens. Level of cognitive impairment may significantly affect a traumatic brain injury victim's ability to benefit from text-based prompting. We tested the hypothesis that spatial disorientation as measured by movement path tortuosity during ambulation would be associated with poorer compliance with automated prompts by veterans actively being treated for traumatic brain injury. Clinical polytrauma center. Ten (1 female) veteran patients mean age = 35.4 (SD = 12.4) years. Small group correlational study without random assignment. Fractal Dimension, a measure of movement path tortuosity derived from a GPS logging device used to record casual outdoor ambulation at the start of the study. Compliance with smart home machine-generated therapeutic prompts received during rehabilitation at the James A. Haley Veterans Administration Hospital Polytrauma Transitional Rehabilitation Program. A patient was compliant with a prompt if they transited from where the prompt was presented to the prescribed destination (both within the Polytrauma Transitional Rehabilitation Program) within 30 minutes. Noncompliance was failure to appear at the destination within the allotted time. Fractal dimension was significantly inversely related to overall prompt compliance (r = -0.603, n = 10, P = .032; 1-tailed). The findings support the hypothesis that increased spatial disorientation adversely impacts compliance with automated prompts throughout therapy. The results are consistent with previous studies linking elevated path tortuosity to cognitive impairment and increased risk for falls in assisted living facility residents.

Survey of Retired Military Pharmacist's Transition to a Civilian Pharmacy Career Path.

PubMed

Bennett, David; Wellman, Greg; Mahmood, Maysaa; Freye, Ryan; Remund, Daniel; Samples, Phil L

2015-12-01

To explore variables relevant to transition to civilian pharmacy career path for retiring military pharmacists. A cross-sectional survey was designed to collect information from retired military pharmacists including demographics, military service information, postretirement employment and perceptions of transition, satisfaction, level of responsibility, work environment, rewards (level of financial compensation, opportunities for professional development and career advancement, health benefits), and level of supervisory support. The questionnaire also included additional items asking about their perception of their military experience, transition to civilian work and the impact the military career had on their personal and family life. Respondents included 140 retired pharmacists from the U.S. Army, Navy, Air Force, or Coast Guard. Factors found to be significant predictors of transition to civilian career included: bureaucracy in current job, time elapsed since retirement, extent to which an individual misses military structure and chain of command, access to military facilities and Veterans Administration benefits, and reporting little or no stress in committed long-term personal relationship while in the military. Findings suggest that the majority of retired military pharmacists perceived the transition to civilian professional sector was about what they expected or easier than expected. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Transitions amongst synchronous solutions in the stochastic Kuramoto model

NASA Astrophysics Data System (ADS)

DeVille, Lee

2012-05-01

We consider the Kuramoto model of coupled oscillators with nearest-neighbour coupling and additive white noise. We show that synchronous solutions which are stable without the addition of noise become metastable and that we have transitions amongst synchronous solutions on long timescales. We compute these timescales and, moreover, compute the most likely path in phase space that transitions will follow. We show that these transition timescales do not increase as the number of oscillators in the system increases, and are roughly constant in the system size. Finally, we show that the transitions correspond to a splitting of one synchronous solution into two communities which move independently for some time and which rejoin to form a different synchronous solution.

Time-of-flight dependency on transducer separation distance in a reflective-path guided-wave ultrasonic flow meter at zero flow conditions.

PubMed

Aanes, Magne; Kippersund, Remi Andre; Lohne, Kjetil Daae; Frøysa, Kjell-Eivind; Lunde, Per

2017-08-01

Transit-time flow meters based on guided ultrasonic wave propagation in the pipe spool have several advantages compared to traditional inline ultrasonic flow metering. The extended interrogation field, obtained by continuous leakage from guided waves traveling in the pipe wall, increases robustness toward entrained particles or gas in the flow. In reflective-path guided-wave ultrasonic flow meters (GW-UFMs), the flow equations are derived from signals propagating solely in the pipe wall and from signals passing twice through the fluid. In addition to the time-of-flight (TOF) through the fluid, the fluid path experiences an additional time delay upon reflection at the opposite pipe wall due to specular and non-specular reflections. The present work investigates the influence of these reflections on the TOF in a reflective-path GW-UFM as a function of transducer separation distance at zero flow conditions. Two models are used to describe the signal propagation through the system: (i) a transient full-wave finite element model, and (ii) a combined plane-wave and ray-tracing model. The study shows that a range-dependent time delay is associated with the reflection of the fluid path, introducing transmitter-receiver distance dependence. Based on these results, the applicability of the flow equations derived using model (ii) is discussed.

Open Quantum Random Walks on the Half-Line: The Karlin-McGregor Formula, Path Counting and Foster's Theorem

NASA Astrophysics Data System (ADS)

Jacq, Thomas S.; Lardizabal, Carlos F.

2017-11-01

In this work we consider open quantum random walks on the non-negative integers. By considering orthogonal matrix polynomials we are able to describe transition probability expressions for classes of walks via a matrix version of the Karlin-McGregor formula. We focus on absorbing boundary conditions and, for simpler classes of examples, we consider path counting and the corresponding combinatorial tools. A non-commutative version of the gambler's ruin is studied by obtaining the probability of reaching a certain fortune and the mean time to reach a fortune or ruin in terms of generating functions. In the case of the Hadamard coin, a counting technique for boundary restricted paths in a lattice is also presented. We discuss an open quantum version of Foster's Theorem for the expected return time together with applications.

Workforce Development.

ERIC Educational Resources Information Center

1999

This document contains four symposium papers on work force development. "Effects of Two Different Learning Paths on School-to-Work Transition" (Esther Van Der Schoot) discusses a Dutch study documenting that the following items make a difference in the school-to-work transition: learning path, curriculum characteristics, individual…

Location Prediction Based on Transition Probability Matrices Constructing from Sequential Rules for Spatial-Temporal K-Anonymity Dataset

PubMed Central

Liu, Zhao; Zhu, Yunhong; Wu, Chenxue

2016-01-01

Spatial-temporal k-anonymity has become a mainstream approach among techniques for protection of users’ privacy in location-based services (LBS) applications, and has been applied to several variants such as LBS snapshot queries and continuous queries. Analyzing large-scale spatial-temporal anonymity sets may benefit several LBS applications. In this paper, we propose two location prediction methods based on transition probability matrices constructing from sequential rules for spatial-temporal k-anonymity dataset. First, we define single-step sequential rules mined from sequential spatial-temporal k-anonymity datasets generated from continuous LBS queries for multiple users. We then construct transition probability matrices from mined single-step sequential rules, and normalize the transition probabilities in the transition matrices. Next, we regard a mobility model for an LBS requester as a stationary stochastic process and compute the n-step transition probability matrices by raising the normalized transition probability matrices to the power n. Furthermore, we propose two location prediction methods: rough prediction and accurate prediction. The former achieves the probabilities of arriving at target locations along simple paths those include only current locations, target locations and transition steps. By iteratively combining the probabilities for simple paths with n steps and the probabilities for detailed paths with n-1 steps, the latter method calculates transition probabilities for detailed paths with n steps from current locations to target locations. Finally, we conduct extensive experiments, and correctness and flexibility of our proposed algorithm have been verified. PMID:27508502

Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions.

PubMed

Zheng, Jingjing; Truhlar, Donald G

2012-01-01

Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

PubMed

Molloy, Kevin; Shehu, Amarda

2013-01-01

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.

Relating hyporheic fluxes, residence times, and redox-sensitive biogeochemical processes upstream of beaver dams

USGS Publications Warehouse

Briggs, Martin A.; Lautz, Laura; Hare, Danielle K.

2013-01-01

¨hler number seemed to overestimate the actual transition as indicated by multiple secondary electron acceptors, illustrating the gradient nature of anaerobic transition. Temporal flux variability in low-flux morphologies generated a much greater range in hyporheic redox conditions compared to high-flux zones, and chemical responses to changing flux rates were consistent with those predicted from the empirical relationship between redox condition and residence time. The Raz tracer revealed that hyporheic flow paths have strong net aerobic respiration, particularly at higher residence time, but this reactive exchange did not affect the net stream signal at the reach scale.

Optical and Casimir effects in topological materials

NASA Astrophysics Data System (ADS)

Wilson, Justin H.

Two major electromagnetic phenomena, magneto-optical effects and the Casimir effect, have seen much theoretical and experimental use for many years. On the other hand, recently there has been an explosion of theoretical and experimental work on so-called topological materials, and a natural question to ask is how such electromagnetic phenomena change with these novel materials. Specifically, we will consider are topological insulators and Weyl semimetals. When Dirac electrons on the surface of a topological insulator are gapped or Weyl fermions in the bulk of a Weyl semimetal appear due to time-reversal symmetry breaking, there is a resulting quantum anomalous Hall effect (2D in one case and bulk 3D in the other, respectively). For topological insulators, we investigate the role of localized in-gap states which can leave their own fingerprints on the magneto-optics and can therefore be probed. We have shown that these states resonantly contribute to the Hall conductivity and are magneto-optically active. For Weyl semimetals we investigate the Casimir force and show that with thickness, chemical potential, and magnetic field, a repulsive and tunable Casimir force can be obtained. Additionally, various values of the parameters can give various combinations of traps and antitraps. We additionally probe the topological transition called a Lifshitz transition in the band structure of a material and show that in a Casimir experiment, one can observe a non-analytic "kink'' in the Casimir force across such a transition. The material we propose is a spin-orbit coupled semiconductor with large g-factor that can be magnetically tuned through such a transition. Additionally, we propose an experiment with a two-dimensional metal where weak localization is tuned with an applied field in order to definitively test the effect of diffusive electrons on the Casimir force---an issue that is surprisingly unresolved to this day. Lastly, we show how the time-continuous coherent state path integral breaks down for both the single-site Bose-Hubbard model and the spin path integral. Specifically, when the Hamiltonian is quadratic in a generator of the algebra used to construct coherent states, the path integral fails to produce correct results following from an operator approach. We note that the problems do not arise in the time-discretized version of the path integral, as expected.

Double-path acquisition of pulse wave transit time and heartbeat using self-mixing interferometry

NASA Astrophysics Data System (ADS)

Wei, Yingbin; Huang, Wencai; Wei, Zheng; Zhang, Jie; An, Tong; Wang, Xiulin; Xu, Huizhen

2017-06-01

We present a technique based on self-mixing interferometry for acquiring the pulse wave transit time (PWTT) and heartbeat. A signal processing method based on Continuous Wavelet Transform and Hilbert Transform is applied to extract potentially useful information in the self-mixing interference (SMI) signal, including PWTT and heartbeat. Then, some cardiovascular characteristics of the human body are easily acquired without retrieving the SMI signal by complicated algorithms. Experimentally, the PWTT is measured on the finger and the toe of the human body using double-path self-mixing interferometry. Experimental statistical data show the relation between the PWTT and blood pressure, which can be used to estimate the systolic pressure value by fitting. Moreover, the measured heartbeat shows good agreement with that obtained by a photoplethysmography sensor. The method that we demonstrate, which is based on self-mixing interferometry with significant advantages of simplicity, compactness and non-invasion, effectively illustrates the viability of the SMI technique for measuring other cardiovascular signals.

A quality assurance device for measuring afterloader performance and transit dose for nasobiliary high-dose-rate brachytherapy.

PubMed

Deufel, Christopher L; Mullins, John P; Zakhary, Mark J

2018-05-17

Nasobiliary high-dose-rate (HDR) brachytherapy has emerged as an effective tool to boost the radiation dose for patients with unresectable perihilar cholangiocarcinoma. This work describes a quality assurance (QA) tool for measuring the HDR afterloader's performance, including the transit dose, when the source wire travels through a tortuous nasobiliary catheter path. The nasobiliary QA device was designed to mimic the anatomical path of a nasobiliary catheter, including the nasal, stomach, duodenum, and bile duct loops. Two of these loops, the duodenum and bile duct loops, have adjustable radii of curvature, resulting in the ability to maximize stress on the source wire in transit. The device was used to measure the performance over time for the HDR afterloader and the differences between intraluminal catheter lots. An upper limit on the transit dose was also measured using radiochromic film and compared with a simple theoretical model. The QA device was capable of detecting performance variations among nasobiliary catheter lots and following radioactive source replacement. The transit dose from a nasobiliary treatment increased by up to one order of magnitude when the source wire encountered higher than normal friction. Three distinct travel speeds of the source wire were observed: 5.2, 17.4, and 54.7 cm/s. The maximum transit dose was 0.3 Gy at a radial distance of 5 mm from a 40.3 kU 192 Ir source. The source wire encounters substantially greater friction when it navigates through the nasobiliary brachytherapy catheter. A QA tool that mimics the nasal, stomach, duodenum, and bile duct loops may be used to evaluate transit dose and the afterloader's performance over time. Copyright © 2018 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Reliability and feasibility of gait initiation centre-of-pressure excursions using a Wii® Balance Board in older adults at risk of falling.

PubMed

Lee, James; Webb, Graham; Shortland, Adam P; Edwards, Rebecca; Wilce, Charlotte; Jones, Gareth D

2018-04-17

Impairments in dynamic balance have a detrimental effect in older adults at risk of falls (OARF). Gait initiation (GI) is a challenging transitional movement. Centre of pressure (COP) excursions using force plates have been used to measure GI performance. The Nintendo Wii Balance Board (WBB) offers an alternative to a standard force plate for the measurement of CoP excursion. To determine the reliability of COP excursions using the WBB, and its feasibility within a 4-week strength and balance intervention (SBI) treating OARF. Ten OARF subjects attending SBI and ten young healthy adults, each performed three GI trials after 10 s of quiet stance from a standardised foot position (shoulder width) before walking forward 3 m to pick up an object. Averaged COP mediolateral (ML) and anteroposterior (AP) excursions (distance) and path-length time (GI-onset to first toe-off) were analysed. WBB ML (0.866) and AP COP excursion (0.895) reliability (ICC 3,1 ) was excellent, and COP path-length reliability was fair (0.517). Compared to OARF, healthy subjects presented with larger COP excursion in both directions and shorter COP path length. OARF subjects meaningfully improved their timed-up-and-go and ML COP excursion between weeks 1-4, while AP COP excursions, path length, and confidence-in-balance remained stable. COP path length and excursion directions probably measure different GI postural control attributes. Limitations in WBB accuracy and precision in transition tasks needs to be established before it can be used clinically to measure postural aspects of GI viably. The WBB could provide valuable clinical evaluation of balance function in OARF.

Asymmetry and basic pathways in sleep-stage transitions

NASA Astrophysics Data System (ADS)

Lo, Chung-Chuan; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2013-04-01

We study dynamical aspects of sleep micro-architecture. We find that sleep dynamics exhibits a high degree of asymmetry, and that the entire class of sleep-stage transition pathways underlying the complexity of sleep dynamics throughout the night can be characterized by two independent asymmetric transition paths. These basic pathways remain stable under sleep disorders, even though the degree of asymmetry is significantly reduced. Our findings demonstrate an intriguing temporal organization in sleep micro-architecture at short time scales that is typical for physical systems exhibiting self-organized criticality (SOC), and indicates nonequilibrium critical dynamics in brain activity during sleep.

Turn-Directed α-β Conformational Transition of α-syn12 Peptide at Different pH Revealed by Unbiased Molecular Dynamics Simulations

PubMed Central

Liu, Lei; Cao, Zanxia

2013-01-01

The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH. PMID:23708094

An efficient General Transit Feed Specification (GTFS) enabled algorithm for dynamic transit accessibility analysis.

PubMed

Fayyaz S, S Kiavash; Liu, Xiaoyue Cathy; Zhang, Guohui

2017-01-01

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George's transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis.

An efficient General Transit Feed Specification (GTFS) enabled algorithm for dynamic transit accessibility analysis

PubMed Central

Fayyaz S., S. Kiavash; Zhang, Guohui

2017-01-01

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George’s transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis. PMID:28981544

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

PubMed Central

2013-01-01

Background Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. Methods We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Results and conclusions Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers. PMID:24565158

Drift-Induced Selection Between Male and Female Heterogamety.

PubMed

Veller, Carl; Muralidhar, Pavitra; Constable, George W A; Nowak, Martin A

2017-10-01

Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of "drift-induced selection" operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems. Copyright © 2017 by the Genetics Society of America.

Dynamic Testing of the NASA Hypersonic Project Combined Cycle Engine Testbed for Mode Transition Experiments

NASA Technical Reports Server (NTRS)

2011-01-01

NASA is interested in developing technology that leads to more routine, safe, and affordable access to space. Access to space using airbreathing propulsion systems has potential to meet these objectives based on Airbreathing Access to Space (AAS) system studies. To this end, the NASA Fundamental Aeronautics Program (FAP) Hypersonic Project is conducting fundamental research on a Turbine Based Combined Cycle (TBCC) propulsion system. The TBCC being studied considers a dual flow-path inlet system. One flow-path includes variable geometry to regulate airflow to a turbine engine cycle. The turbine cycle provides propulsion from take-off to supersonic flight. The second flow-path supports a dual-mode scramjet (DMSJ) cycle which would be initiated at supersonic speed to further accelerate the vehicle to hypersonic speed. For a TBCC propulsion system to accelerate a vehicle from supersonic to hypersonic speed, a critical enabling technology is the ability to safely and effectively transition from the turbine to the DMSJ-referred to as mode transition. To experimentally test methods of mode transition, a Combined Cycle Engine (CCE) Large-scale Inlet testbed was designed with two flow paths-a low speed flow-path sized for a turbine cycle and a high speed flow-path designed for a DMSJ. This testbed system is identified as the CCE Large-Scale Inlet for Mode Transition studies (CCE-LIMX). The test plan for the CCE-LIMX in the NASA Glenn Research Center (GRC) 10- by 10-ft Supersonic Wind Tunnel (10x10 SWT) is segmented into multiple phases. The first phase is a matrix of inlet characterization (IC) tests to evaluate the inlet performance and establish the mode transition schedule. The second phase is a matrix of dynamic system identification (SysID) experiments designed to support closed-loop control development at mode transition schedule operating points for the CCE-LIMX. The third phase includes a direct demonstration of controlled mode transition using a closed loop control system developed with the data obtained from the first two phases. Plans for a fourth phase include mode transition experiments with a turbine engine. This paper, focusing on the first two phases of experiments, presents developed operational and analysis tools for streamlined testing and data reduction procedures.

California PATH : 1997 annual report

DOT National Transportation Integrated Search

1997-01-01

The California Partners for Advanced Transit and Highways Program (PATH) has been leading the way in ITS (Intelligent Transportation Systems) research since PATHs founding in 1986, before the term ITS or its predecessor IVHS (Intelligent Vehicle H...

California PATH : 1996 annual report

DOT National Transportation Integrated Search

1996-01-01

The California Partners for Advanced Transit and Highways Program (PATH ) has been leading the way in ITS (Intelligent Transportation Systems) research since PATH's founding in 1986, before the term ITS or its predecessor IVHS (Intelligent Vehicle Hi...

Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.

PubMed

Yu, Tang-Qing; Lapelosa, Mauro; Vanden-Eijnden, Eric; Abrams, Cameron F

2015-03-04

We use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the collective variable space for CO localization in myoglobin to estimate the kinetics of entry, exit, and internal site-hopping. The tessellation is determined by analysis of the free-energy surface in that space using transition-path theory (TPT), which provides criteria for defining optimal milestones, allowing short, independent, cell-constrained MD simulations to provide properly weighted kinetic data. We coarse grain the resulting kinetic model at two levels: first, using crystallographically relevant internal cavities and their predicted interconnections and solvent portals; and second, as a three-state side-path scheme inspired by similar models developed from geminate recombination experiments. We show semiquantitative agreement with experiment on entry and exit rates and in the identification of the so-called "histidine gate" at position 64 through which ≈90% of flux between solvent and the distal pocket passes. We also show with six-dimensional calculations that the minimum free-energy pathway of escape through the histidine gate is a "knock-on" mechanism in which motion of the ligand and the gate are sequential and interdependent. In total, these results suggest that such TPT simulations are indeed a promising approach to overcome the practical time-scale limitations of MD to allow reliable estimation of transition mechanisms and rates among metastable states.

Using isotopes to investigate hydrological flow pathways and sources in a remote Arctic catchment

NASA Astrophysics Data System (ADS)

Lessels, Jason; Tetzlaff, Doerthe; Dinsmore, Kerry; Street, Lorna; Billet, Mike; Baxter, Robert; Subke, Jens-Arne; Wookey, Phillip

2014-05-01

Stable water isotopes allow for the identification of flow paths and stream water sources. This ability is beneficial in improving the understanding in catchments with dynamic spatial and temporal sources. Arctic catchments are characterised with strong seasonality where the dominant flow paths change throughout the short summer season. Therefore, the identification of stream water sources through time and space is necessary in order to accurately quantify these dynamics. Stable isotope tracers are incredibly useful tools which integrate processes of time and space and therefore, particularly useful in identifying flow pathways and runoff sources at remote sites. This work presents stable isotope data collected from a small (1km2) catchment in Northwest Canada. The aims of this study are to 1) identify sources of stream water through time and space, 2) provide information which will be incorporated into hydrological and transit time models Sampling of snowmelt, surface runoff, ice-wedge polygons, stream and soil water was undertaken throughout the 2013 summer. The results of this sampling reveal the dominant flow paths in the catchment and the strong influence of aspect in controlling these processes. After the spring freshet, late lying snow packs on north facing slopes and thawing permafrost on south facing slopes are the dominant sources of stream water. Progressively through the season the thawing permafrost and precipitation become the largest contributing sources. The depth of the thawing aspect layer and consequently the contribution to the stream is heavily dependent on aspect. The collection of precipitation, soil and stream isotope samples throughout the summer period provide valuable information for transit time estimates. The combination of spatial and temporal sampling of stable isotopes has revealed clear differences between the main stream sources in the studied catchment and reinforced the importance of slope aspect in these catchments.

Potential energy landscape of the apparent first-order phase transition between low-density and high-density amorphous ice.

PubMed

Giovambattista, Nicolas; Sciortino, Francesco; Starr, Francis W; Poole, Peter H

2016-12-14

The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics to describe supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that low-density liquid (LDL) configurations are located in the same megabasin as LDA, and that high-density liquid (HDL) configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid is different from the path followed by the amorphous solid. At higher pressure, we also study the liquid-to-ice-VII first-order phase transition, and find that the behavior of the PEL properties across this transition is qualitatively similar to the changes found during the LDA-HDA transformation. This similarity supports the interpretation that the LDA-HDA transformation is a first-order phase transition between out-of-equilibrium states. Finally, we compare the PEL properties explored during the LDA-HDA transformations in ST2 water with those reported previously for SPC/E water, for which the LDA-HDA transformations are rather smooth. This comparison illuminates the previous work showing that, at accessible computer times scales, a liquid-liquid phase transition occurs in the case of ST2 water, but not for SPC/E water.

Potential energy landscape of the apparent first-order phase transition between low-density and high-density amorphous ice

NASA Astrophysics Data System (ADS)

Giovambattista, Nicolas; Sciortino, Francesco; Starr, Francis W.; Poole, Peter H.

2016-12-01

The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics to describe supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that low-density liquid (LDL) configurations are located in the same megabasin as LDA, and that high-density liquid (HDL) configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid is different from the path followed by the amorphous solid. At higher pressure, we also study the liquid-to-ice-VII first-order phase transition, and find that the behavior of the PEL properties across this transition is qualitatively similar to the changes found during the LDA-HDA transformation. This similarity supports the interpretation that the LDA-HDA transformation is a first-order phase transition between out-of-equilibrium states. Finally, we compare the PEL properties explored during the LDA-HDA transformations in ST2 water with those reported previously for SPC/E water, for which the LDA-HDA transformations are rather smooth. This comparison illuminates the previous work showing that, at accessible computer times scales, a liquid-liquid phase transition occurs in the case of ST2 water, but not for SPC/E water.

A General, Adaptive, Roadmap-Based Algorithm for Protein Motion Computation.

PubMed

Molloy, Kevin; Shehu, Amarda

2016-03-01

Precious information on protein function can be extracted from a detailed characterization of protein equilibrium dynamics. This remains elusive in wet and dry laboratories, as function-modulating transitions of a protein between functionally-relevant, thermodynamically-stable and meta-stable structural states often span disparate time scales. In this paper we propose a novel, robotics-inspired algorithm that circumvents time-scale challenges by drawing analogies between protein motion and robot motion. The algorithm adapts the popular roadmap-based framework in robot motion computation to handle the more complex protein conformation space and its underlying rugged energy surface. Given known structures representing stable and meta-stable states of a protein, the algorithm yields a time- and energy-prioritized list of transition paths between the structures, with each path represented as a series of conformations. The algorithm balances computational resources between a global search aimed at obtaining a global view of the network of protein conformations and their connectivity and a detailed local search focused on realizing such connections with physically-realistic models. Promising results are presented on a variety of proteins that demonstrate the general utility of the algorithm and its capability to improve the state of the art without employing system-specific insight.

Improved transition path sampling methods for simulation of rare events

NASA Astrophysics Data System (ADS)

Chopra, Manan; Malshe, Rohit; Reddy, Allam S.; de Pablo, J. J.

2008-04-01

The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

NASA Astrophysics Data System (ADS)

Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher

2014-01-01

We have developed a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. In this paper, we set the theoretical framework for employing nonequilibrium work relations to estimate the relative reaction rates associated with different classes of transition pathways. Particularly, we derive an extension of Crook's transient fluctuation theorem, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements (e.g., in Steered Molecular Dynamics). The formalism presented here can be combined with Transition Path Theory to relate the equilibrium and driven transition rates. The usefulness of this framework is illustrated by means of a Gaussian model and a driven proline dimer.

Turbine system

DOEpatents

McMahan, Kevin Weston; Dillard, Daniel Jackson

2016-05-03

A turbine system is disclosed. The turbine system includes a transition duct having an inlet, an outlet, and a passage extending between the inlet and the outlet and defining a longitudinal axis, a radial axis, and a tangential axis. The outlet of the transition duct is offset from the inlet along the longitudinal axis and the tangential axis. The turbine system further includes a turbine section connected to the transition duct. The turbine section includes a plurality of shroud blocks at least partially defining a hot gas path, a plurality of buckets at least partially disposed in the hot gas path, and a plurality of nozzles at least partially disposed in the hot gas path. At least one of a shroud block, a bucket, or a nozzle includes means for withstanding high temperatures.

Integral transforms of the quantum mechanical path integral: Hit function and path-averaged potential.

PubMed

Edwards, James P; Gerber, Urs; Schubert, Christian; Trejo, Maria Anabel; Weber, Axel

2018-04-01

We introduce two integral transforms of the quantum mechanical transition kernel that represent physical information about the path integral. These transforms can be interpreted as probability distributions on particle trajectories measuring respectively the relative contribution to the path integral from paths crossing a given spatial point (the hit function) and the likelihood of values of the line integral of the potential along a path in the ensemble (the path-averaged potential).

Integral transforms of the quantum mechanical path integral: Hit function and path-averaged potential

NASA Astrophysics Data System (ADS)

Edwards, James P.; Gerber, Urs; Schubert, Christian; Trejo, Maria Anabel; Weber, Axel

2018-04-01

We introduce two integral transforms of the quantum mechanical transition kernel that represent physical information about the path integral. These transforms can be interpreted as probability distributions on particle trajectories measuring respectively the relative contribution to the path integral from paths crossing a given spatial point (the hit function) and the likelihood of values of the line integral of the potential along a path in the ensemble (the path-averaged potential).

Mechanical induction of transitions into mesenchymal and amoeboid states

NASA Astrophysics Data System (ADS)

Liphardt, Jan

One of the fundamental mysteries of biology lies in the ability of cells to convert from one phenotype to another in response to external control inputs. We have been studying the Epithelial-to-Mesenchymal Transition (EMT), which allows organized assemblies of epithelial cells to scatter into lone mesenchymal cells. EMT is critical for normal development and wound healing, and may be important for cancer metastasis. I'll present recent data on disorganizing mammary epithelial structures. We have used CRISPR to insert fluorescent tags directly into eight EMT-related genes (such as E-cadherin and Vimentin), which allows us to monitor the dynamics of the transition in real time, subject only to delays imposed by fluorophore folding/maturation times. With this information, we can begin to order events in time (temporal resolution 30 minutes), starting with external signal inputs and proceeding through a secession of intracellular changes of gene expression on the path to the mesenchymal state.

Do reciprocal relationships between academic workload and self-regulated learning predict medical freshmen's achievement? A longitudinal study on the educational transition from secondary school to medical school.

PubMed

Barbosa, Joselina; Silva, Álvaro; Ferreira, Maria Amélia; Severo, Milton

2018-04-16

One of the most important factors that makes the transition from secondary school to medical school challenging is the inability to put in the study time that a medical school curriculum demands. The implementation of regulated learning is essential for students to cope with medical course environment and succeed. This study aimed to investigate the reciprocal relationships between self-regulated learning skills (SRLS) and academic workload (AW) across secondary school to medical school transition. Freshmen enrolled in medical school (N = 102) completed questionnaires at the beginning and at the end of their academic year, assessing AW (measured as study time hours and perceived workload), SRLS (planning and strategies for learning assessment, motivation and action to learning and self-directedness) and academic achievement. An exploratory factor analysis (EFA) and a longitudinal path analysis were performed. According to the EFA, study time and perceived workload revealed two factors of AW: students who had a high perceived workload also demonstrated increased study time (tandem AW); and those who had a low perceived workload also demonstrated increased study time (inverse AW). Only a longitudinal relationship between SRLS and AW was found in the path analysis: prior self-directedness was related to later tandem AW. Moreover, success during the first year of medical school is dependent on exposure to motivation, self-directedness and high study time without overload during secondary school and medical school, and prior academic achievement. By better understanding these relationships, teachers can create conditions that support academic success during the first year medical school.

Assessing the Mental Health of Adolescents: A Guide for Out-of-School Time Program Practitioners. Research-to-Results Brief. Publication #2007-07

ERIC Educational Resources Information Center

Martin, Laurie; Milot, Alyssa

2007-01-01

Mental health problems can develop at any point in life and may be influenced by a variety of factors, including genetics or family history of a disorder, chemical imbalances in the brain, or stressors in the environment. Adolescence is a time of great change and transition, when youth are starting to make decisions about career paths, further…

Does timing and sequencing of transitions to adulthood make a difference? Stress, smoking, and physical activity among young Australian women.

PubMed

Bell, Sandra; Lee, Christina

2006-01-01

The major changes of the transition to adulthood are argued to be stressful, and health-related behaviors such as smoking and physical activity may be adopted, consolidated, or abandoned at this time. On the other hand, research has suggested that the normative transitions of emerging adulthood, although involving considerable change, may be associated with low stress because they are perceived as both positive and normal at this life stage. This article examines relations between the timing and sequencing of life transitions and stress and health-related behaviors, focusing on the transition to young adulthood among Australian women. A total of 853 women aged 22 to 27 provided information about the timing and sequencing of 6 life transitions: moving out of home, stopping full-time education, starting full-time work, having the first live-in relationship, marriage, and motherhood-and stress, smoking, and physical activity. Most had moved out of home, stopped full-time education, and started full-time work, but only 14% had undertaken all 6 transitions. Overall, 70% of participants had made transitions "in order." Overall, the findings suggest that the relations between timing and sequencing of transitions, and indicators of health, are moderate for smoking, but small for stress and for physical activity. These effects remained after controlling for socioeconomic status of the participants' families of origin. Matching current social norms for the timing and sequencing of life changes may be of less importance for women's well-being than is commonly believed. Although the significant relations between early or "out of order" transitions and smoking are of concern, the smaller relations with stress and with sedentariness suggest that such transitions may have limited negative consequences, and support the view that individuals are active in choosing the life path that is appropriate for them and their circumstances.

Complexity in Matuyama-Brunhes polarity transitions from North Atlantic IODP/ODP deep-sea sites

NASA Astrophysics Data System (ADS)

Channell, J. E. T.

2017-06-01

Integrated Ocean Drilling Program (IODP) Expedition 303 to the North Atlantic provided 16 records of the Matuyama-Brunhes polarity transition (MBT), based on u-channel and discrete samples, from holes drilled at three sites (Sites U1304, U1305 and U1306) that have mean Brunhes sedimentation rates of 16-18 cm/kyr. The MBT occurs during the transition from marine isotope stage (MIS) 19c to MIS 18e, with mid-point at ∼773 ka, and a transition duration of ∼8 kyr. Combining the new MBT records, including one new record for the top Jaramillo, with previously published North Atlantic MBT records (ODP Sites 983, 984 and 1063) yields a total of more than 20 high-sedimentation-rate polarity transition records. The MBT yields a repetitive pattern of transitional field states as virtual geomagnetic poles (VGPs) move from high southern latitudes to loop over the Pacific, group in NE Asia, and transit into the mid-latitude South Atlantic before reaching high latitudes in the Northern Hemisphere. The VGPs for the top Jaramillo transition feature a loop over the Pacific, then a NE Asia group before transit over the Indian Ocean to high southerly latitudes. The North Atlantic MBT records described here contrast with longitudinally-constrained VGP paths for the MBT, indicating that relatively low sedimentation rate (∼4 cm/kyr) records of the MBT are heavily smoothed by the remanence acquisition process and do not adequately represent the MBT field. The VGPs at the MBT and top Jaramillo, as measured in the North Atlantic, have similarities with excursion (Iceland Basin) VGP paths, and were apparently guided by maxima in downward vertical flux similar to those seen in the modern non-dipole (ND) field, implying longevity in ND features through time.

High power regenerative laser amplifier

DOEpatents

Miller, John L.; Hackel, Lloyd A.; Dane, Clifford B.; Zapata, Luis E.

1994-01-01

A regenerative amplifier design capable of operating at high energy per pulse, for instance, from 20-100 Joules, at moderate repetition rates, for instance from 5-20 Hertz is provided. The laser amplifier comprises a gain medium and source of pump energy coupled with the gain medium; a Pockels cell, which rotates an incident beam in response to application of a control signal; an optical relay system defining a first relay plane near the gain medium and a second relay plane near the rotator; and a plurality of reflectors configured to define an optical path through the gain medium, optical relay and Pockels cell, such that each transit of the optical path includes at least one pass through the gain medium and only one pass through the Pockels cell. An input coupler, and an output coupler are provided, implemented by a single polarizer. A control circuit coupled to the Pockels cell generates the control signal in timed relationship with the input pulse so that the input pulse is captured by the input coupler and proceeds through at least one transit of the optical path, and then the control signal is applied to cause rotation of the pulse to a polarization reflected by the polarizer, after which the captured pulse passes through the gain medium at least once more and is reflected out of the optical path by the polarizer before passing through the rotator again to provide an amplified pulse.

High power regenerative laser amplifier

DOEpatents

Miller, J.L.; Hackel, L.A.; Dane, C.B.; Zapata, L.E.

1994-02-08

A regenerative amplifier design capable of operating at high energy per pulse, for instance, from 20-100 Joules, at moderate repetition rates, for instance from 5-20 Hertz is provided. The laser amplifier comprises a gain medium and source of pump energy coupled with the gain medium; a Pockels cell, which rotates an incident beam in response to application of a control signal; an optical relay system defining a first relay plane near the gain medium and a second relay plane near the rotator; and a plurality of reflectors configured to define an optical path through the gain medium, optical relay and Pockels cell, such that each transit of the optical path includes at least one pass through the gain medium and only one pass through the Pockels cell. An input coupler, and an output coupler are provided, implemented by a single polarizer. A control circuit coupled to the Pockels cell generates the control signal in timed relationship with the input pulse so that the input pulse is captured by the input coupler and proceeds through at least one transit of the optical path, and then the control signal is applied to cause rotation of the pulse to a polarization reflected by the polarizer, after which the captured pulse passes through the gain medium at least once more and is reflected out of the optical path by the polarizer before passing through the rotator again to provide an amplified pulse. 7 figures.

Path-sum solution of the Weyl quantum walk in 3 + 1 dimensions

NASA Astrophysics Data System (ADS)

D'Ariano, G. M.; Mosco, N.; Perinotti, P.; Tosini, A.

2017-10-01

We consider the Weyl quantum walk in 3+1 dimensions, that is a discrete-time walk describing a particle with two internal degrees of freedom moving on a Cayley graph of the group , which in an appropriate regime evolves according to Weyl's equation. The Weyl quantum walk was recently derived as the unique unitary evolution on a Cayley graph of that is homogeneous and isotropic. The general solution of the quantum walk evolution is provided here in the position representation, by the analytical expression of the propagator, i.e. transition amplitude from a node of the graph to another node in a finite number of steps. The quantum nature of the walk manifests itself in the interference of the paths on the graph joining the given nodes. The solution is based on the binary encoding of the admissible paths on the graph and on the semigroup structure of the walk transition matrices. This article is part of the themed issue `Second quantum revolution: foundational questions'.

Edgeworth expansions of stochastic trading time

NASA Astrophysics Data System (ADS)

Decamps, Marc; De Schepper, Ann

2010-08-01

Under most local and stochastic volatility models the underlying forward is assumed to be a positive function of a time-changed Brownian motion. It relates nicely the implied volatility smile to the so-called activity rate in the market. Following Young and DeWitt-Morette (1986) [8], we propose to apply the Duru-Kleinert process-cum-time transformation in path integral to formulate the transition density of the forward. The method leads to asymptotic expansions of the transition density around a Gaussian kernel corresponding to the average activity in the market conditional on the forward value. The approximation is numerically illustrated for pricing vanilla options under the CEV model and the popular normal SABR model. The asymptotics can also be used for Monte Carlo simulations or backward integration schemes.

On the assumptions underlying milestoning.

PubMed

Vanden-Eijnden, Eric; Venturoli, Maddalena; Ciccotti, Giovanni; Elber, Ron

2008-11-07

Milestoning is a procedure to compute the time evolution of complicated processes such as barrier crossing events or long diffusive transitions between predefined states. Milestoning reduces the dynamics to transition events between intermediates (the milestones) and computes the local kinetic information to describe these transitions via short molecular dynamics (MD) runs between the milestones. The procedure relies on the ability to reinitialize MD trajectories on the milestones to get the right kinetic information about the transitions. It also rests on the assumptions that the transition events between successive milestones and the time lags between these transitions are statistically independent. In this paper, we analyze the validity of these assumptions. We show that sets of optimal milestones exist, i.e., sets such that successive transitions are indeed statistically independent. The proof of this claim relies on the results of transition path theory and uses the isocommittor surfaces of the reaction as milestones. For systems in the overdamped limit, we also obtain the probability distribution to reinitialize the MD trajectories on the milestones, and we discuss why this distribution is not available in closed form for systems with inertia. We explain why the time lags between transitions are not statistically independent even for optimal milestones, but we show that working with such milestones allows one to compute mean first passage times between milestones exactly. Finally, we discuss some practical implications of our results and we compare milestoning with Markov state models in view of our findings.

Free-end adaptive nudged elastic band method for locating transition states in minimum energy path calculation.

PubMed

Zhang, Jiayong; Zhang, Hongwu; Ye, Hongfei; Zheng, Yonggang

2016-09-07

A free-end adaptive nudged elastic band (FEA-NEB) method is presented for finding transition states on minimum energy paths, where the energy barrier is very narrow compared to the whole paths. The previously proposed free-end nudged elastic band method may suffer from convergence problems because of the kinks arising on the elastic band if the initial elastic band is far from the minimum energy path and weak springs are adopted. We analyze the origin of the formation of kinks and present an improved free-end algorithm to avoid the convergence problem. Moreover, by coupling the improved free-end algorithm and an adaptive strategy, we develop a FEA-NEB method to accurately locate the transition state with the elastic band cut off repeatedly and the density of images near the transition state increased. Several representative numerical examples, including the dislocation nucleation in a penta-twinned nanowire, the twin boundary migration under a shear stress, and the cross-slip of screw dislocation in face-centered cubic metals, are investigated by using the FEA-NEB method. Numerical results demonstrate both the stability and efficiency of the proposed method.

Sampling the kinetic pathways of a micelle fusion and fission transition.

PubMed

Pool, René; Bolhuis, Peter G

2007-06-28

The mechanism and kinetics of micellar breakup and fusion in a dilute solution of a model surfactant are investigated by path sampling techniques. Analysis of the path ensemble gives insight in the mechanism of the transition. For larger, less stable micelles the fission/fusion occurs via a clear neck formation, while for smaller micelles the mechanism is more direct. In addition, path analysis yields an appropriate order parameter to evaluate the fusion and fission rate constants using stochastic transition interface sampling. For the small, stable micelle (50 surfactants) the computed fission rate constant is a factor of 10 lower than the fusion rate constant. The procedure opens the way for accurate calculation of free energy and kinetics for, e.g., membrane fusion, and wormlike micelle endcap formation.

Transition duct system with straight ceramic liner for delivering hot-temperature gases in a combustion turbine engine

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

Wiebe, David J.

A transition duct system (10) for delivering hot-temperature gases from a plurality of combustors in a combustion turbine engine is provided. The system includes an exit piece (16) for each combustor. The exit piece may include a straight path segment (26) for receiving a gas flow from a respective combustor. A straight ceramic liner (40) may be inwardly disposed onto a metal outer shell (38) along the straight path segment of the exit piece. Structural arrangements are provided to securely attach the ceramic liner in the presence of substantial flow path pressurization. Cost-effective serviceability of the transition duct systems ismore » realizable since the liner can be readily removed and replaced as needed.« less

Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins

NASA Astrophysics Data System (ADS)

Seyler, Sean L.

In a typical living cell, millions to billions of proteins--nanomachines that fluctuate and cycle among many conformational states--convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible. Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)--an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project--developing a hybrid atomistic-continuum method--is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.

Circuity analyses of HSR network and high-speed train paths in China

PubMed Central

Zhao, Shuo; Huang, Jie; Shan, Xinghua

2017-01-01

Circuity, defined as the ratio of the shortest network distance to the Euclidean distance between one origin–destination (O-D) pair, can be adopted as a helpful evaluation method of indirect degrees of train paths. In this paper, the maximum circuity of the paths of operated trains is set to be the threshold value of the circuity of high-speed train paths. For the shortest paths of any node pairs, if their circuity is not higher than the threshold value, the paths can be regarded as the reasonable paths. With the consideration of a certain relative or absolute error, we cluster the reasonable paths on the basis of their inclusion relationship and the center path of each class represents a passenger transit corridor. We take the high-speed rail (HSR) network in China at the end of 2014 as an example, and obtain 51 passenger transit corridors, which are alternative sets of train paths. Furthermore, we analyze the circuity distribution of paths of all node pairs in the network. We find that the high circuity of train paths can be decreased with the construction of a high-speed railway line, which indicates that the structure of the HSR network in China tends to be more complete and the HSR network can make the Chinese railway network more efficient. PMID:28945757

Paving the Way to the Future? Education and Young Europeans' Paths to Work and Independence

ERIC Educational Resources Information Center

Lundahl, Lisbeth

2011-01-01

This article discusses young people's transitions from school to work at a time when educational systems have become more closely connected to the economy than ever before. The serious situation of high unemployment, unstable employment conditions and poverty among young people and young adults in Europe is highlighted. Using Sweden as an…

Migrants' Resources: Multilingualism and Transnational Mobility. A Study on Learning Paths and School to Job Transition of Young Portuguese Migrants

ERIC Educational Resources Information Center

Furstenau, Sara

2005-01-01

In this contribution, the results of an empirical study on young immigrants' learning paths and school to job transition are presented. The study focused on the strategies of successful students from the Portuguese immigrant minority in Hamburg. One aim was to find out whether the young people could profit by their migration experiences and…

PyRETIS: A well-done, medium-sized python library for rare events.

PubMed

Lervik, Anders; Riccardi, Enrico; van Erp, Titus S

2017-10-30

Transition path sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, for example, chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present PyRETIS, a Python library for performing TIS and RETIS simulations. PyRETIS directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. PyRETIS is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The Effect of Disorder on the Free-Energy for the Random Walk Pinning Model: Smoothing of the Phase Transition and Low Temperature Asymptotics

NASA Astrophysics Data System (ADS)

Berger, Quentin; Lacoin, Hubert

2011-01-01

We consider the continuous time version of the Random Walk Pinning Model (RWPM), studied in (Berger and Toninelli (Electron. J. Probab., to appear) and Birkner and Sun (Ann. Inst. Henri Poincaré Probab. Stat. 46:414-441, 2010; arXiv:0912.1663). Given a fixed realization of a random walk Y on ℤ d with jump rate ρ (that plays the role of the random medium), we modify the law of a random walk X on ℤ d with jump rate 1 by reweighting the paths, giving an energy reward proportional to the intersection time Lt(X,Y)=int0t {1}_{Xs=Ys} {d}s: the weight of the path under the new measure is exp ( βL t ( X, Y)), β∈ℝ. As β increases, the system exhibits a delocalization/localization transition: there is a critical value β c , such that if β> β c the two walks stick together for almost-all Y realizations. A natural question is that of disorder relevance, that is whether the quenched and annealed systems have the same behavior. In this paper we investigate how the disorder modifies the shape of the free energy curve: (1) We prove that, in dimension d≥3, the presence of disorder makes the phase transition at least of second order. This, in dimension d≥4, contrasts with the fact that the phase transition of the annealed system is of first order. (2) In any dimension, we prove that disorder modifies the low temperature asymptotic of the free energy.

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

PubMed Central

Ovchinnikov, Victor; Karplus, Martin

2014-01-01

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes. PMID:24811667

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

NASA Astrophysics Data System (ADS)

Ovchinnikov, Victor; Karplus, Martin

2014-05-01

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15-20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.

Cell transmission model of dynamic assignment for urban rail transit networks.

PubMed

Xu, Guangming; Zhao, Shuo; Shi, Feng; Zhang, Feilian

2017-01-01

For urban rail transit network, the space-time flow distribution can play an important role in evaluating and optimizing the space-time resource allocation. For obtaining the space-time flow distribution without the restriction of schedules, a dynamic assignment problem is proposed based on the concept of continuous transmission. To solve the dynamic assignment problem, the cell transmission model is built for urban rail transit networks. The priority principle, queuing process, capacity constraints and congestion effects are considered in the cell transmission mechanism. Then an efficient method is designed to solve the shortest path for an urban rail network, which decreases the computing cost for solving the cell transmission model. The instantaneous dynamic user optimal state can be reached with the method of successive average. Many evaluation indexes of passenger flow can be generated, to provide effective support for the optimization of train schedules and the capacity evaluation for urban rail transit network. Finally, the model and its potential application are demonstrated via two numerical experiments using a small-scale network and the Beijing Metro network.

Optimizing Pedestrian-Friendly Walking Path for the First and Last Mile Transit Journey by Using the Analytical Network Process (anp) Decision Model and GIS Network Analysis

NASA Astrophysics Data System (ADS)

Naharudin, N.; Ahamad, M. S. S.; Sadullah, A. F. M.

2017-10-01

Every transit trip begins and ends with pedestrian travel. People need to walk to access the transit services. However, their choice to walk depends on many factors including the connectivity, level of comfort and safety. These factors can influence the pleasantness of riding the transit itself, especially during the first/last mile (FLM) journey. This had triggered few studies attempting to measure the pedestrian-friendliness a walking environment can offer. There were studies that implement the pedestrian experience on walking to assess the pedestrian-friendliness of a walking environment. There were also studies that use spatial analysis to measure it based on the path connectivity and accessibility to public facilities and amenities. Though both are good, but the perception-based studies and spatial analysis can be combined to derive more holistic results. This paper proposes a framework for selecting a pedestrian-friendly path for the FLM transit journey by using the two techniques (perception-based and spatial analysis). First, the degree of importance for the factors influencing a good walking environment will be aggregated by using Analytical Network Process (ANP) decision rules based on people's preferences on those factors. The weight will then be used as attributes in the GIS network analysis. Next, the network analysis will be performed to find a pedestrian-friendly walking route based on the priorities aggregated by ANP. It will choose routes passing through the preferred attributes accordingly. The final output is a map showing pedestrian-friendly walking path for the FLM transit journey.

Transition duct system with metal liners for delivering hot-temperature gases in a combustion turbine engine

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

Wiebe, David J.

A transition duct system (10) for delivering hot-temperature gases from a plurality of combustors in a combustion turbine engine is provided. The system includes an exit piece (16) for each combustor. The exit piece may include a straight path segment (26) and an arcuate connecting segment (36). A respective straight metal liner (92) and an arcuate metal liner (94) may be each inwardly disposed onto a metal outer shell (38) along the straight path segment and the arcuate connecting segment (36) of the exit piece. Structural arrangements are provided to securely attach the respective liners in the presence of substantialmore » flow path pressurization. Cost-effective serviceability of the transition duct systems is realizable since the liners can be readily removed and replaced as needed.« less

SIMULATION FROM ENDPOINT-CONDITIONED, CONTINUOUS-TIME MARKOV CHAINS ON A FINITE STATE SPACE, WITH APPLICATIONS TO MOLECULAR EVOLUTION.

PubMed

Hobolth, Asger; Stone, Eric A

2009-09-01

Analyses of serially-sampled data often begin with the assumption that the observations represent discrete samples from a latent continuous-time stochastic process. The continuous-time Markov chain (CTMC) is one such generative model whose popularity extends to a variety of disciplines ranging from computational finance to human genetics and genomics. A common theme among these diverse applications is the need to simulate sample paths of a CTMC conditional on realized data that is discretely observed. Here we present a general solution to this sampling problem when the CTMC is defined on a discrete and finite state space. Specifically, we consider the generation of sample paths, including intermediate states and times of transition, from a CTMC whose beginning and ending states are known across a time interval of length T. We first unify the literature through a discussion of the three predominant approaches: (1) modified rejection sampling, (2) direct sampling, and (3) uniformization. We then give analytical results for the complexity and efficiency of each method in terms of the instantaneous transition rate matrix Q of the CTMC, its beginning and ending states, and the length of sampling time T. In doing so, we show that no method dominates the others across all model specifications, and we give explicit proof of which method prevails for any given Q, T, and endpoints. Finally, we introduce and compare three applications of CTMCs to demonstrate the pitfalls of choosing an inefficient sampler.

Pathways to the Principalship: An Event History Analysis of the Careers of Teachers with Principal Certification

ERIC Educational Resources Information Center

Davis, Bradley W.; Gooden, Mark A.; Bowers, Alex J.

2017-01-01

Utilizing rich data on nearly 11,000 educators over 17 academic years in a highly diverse context, we examine the career paths of teachers to determine whether and when they transition into the principalship. We utilize a variety of event history analyses, including discrete-time hazard modeling, to determine how an individual's race, gender, and…

Vocabulary Development in Norwegian L1 and L2 Learners in the Kindergarten-School Transition

ERIC Educational Resources Information Center

Karlsen, Jannicke; Lyster, Solveig-Alma Halaas; Lervåg, Arne

2017-01-01

This study examined the vocabulary development of Norwegian second language (L2) learners with Urdu/Punjabi as their first language (L1) at two time-points from kindergarten to primary school, and compared it to the vocabulary development of monolingual Norwegian children. Using path models, the associations between number of picture books in the…

A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

NASA Astrophysics Data System (ADS)

Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

2015-03-01

We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

Transitionless driving on adiabatic search algorithm

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

Oh, Sangchul, E-mail: soh@qf.org.qa; Kais, Sabre, E-mail: kais@purdue.edu; Department of Chemistry, Department of Physics and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907

We study quantum dynamics of the adiabatic search algorithm with the equivalent two-level system. Its adiabatic and non-adiabatic evolution is studied and visualized as trajectories of Bloch vectors on a Bloch sphere. We find the change in the non-adiabatic transition probability from exponential decay for the short running time to inverse-square decay in asymptotic running time. The scaling of the critical running time is expressed in terms of the Lambert W function. We derive the transitionless driving Hamiltonian for the adiabatic search algorithm, which makes a quantum state follow the adiabatic path. We demonstrate that a uniform transitionless driving Hamiltonian,more » approximate to the exact time-dependent driving Hamiltonian, can alter the non-adiabatic transition probability from the inverse square decay to the inverse fourth power decay with the running time. This may open up a new but simple way of speeding up adiabatic quantum dynamics.« less

"Complexity" in Polarity Transitions at the Matuyama-Brunhes Boundary and top Jaramillo in North Atlantic Deep-sea Sediments

NASA Astrophysics Data System (ADS)

Channell, J. E. T.

2016-12-01

Integrated Ocean Drilling Program (IODP) Expedition 303 to the North Atlantic provided 16 records of the Matuyama-Brunhes polarity transition (MBT) and the top Jaramillo transition, based on u-channel and discrete samples, from holes drilled at three sites (Sites U1304, U1305 and U1306) that have mean Brunhes sedimentation rates of 16-18 cm/kyr. The MBT occurs during the transition from marine isotope stage (MIS) 19.3 to MIS 18.4, with mid-point at 773 ka, and a transition duration of 5-8 kyr. The top Jaramillo occurs during MIS 28 at 992 ka with a similar 5 kyr transition duration. Combining the new records with previously published North Atlantic records (ODP Sites 983, 984 and 1063) yields a total of 24 high sedimentation rate records. The MBT yields a repetitive pattern of transitional field states as virtual geomagnetic poles (VGPs) move from high southern latitudes to loop over the Pacific, cluster in NE Asia, and transit into the mid-latitude South Atlantic before reaching high latitudes in the Northern Hemisphere. The VGPs for the top Jaramillo transition feature a loop over the Pacific, then occupation of the NE Asia cluster before transit over the Indian Ocean to high southerly latitudes. The North Atlantic MBT records described here are very different to the longitudinally constrained North Atlantic VGP paths from MBT records that are the basis for a 2007 Bayesian inversion of the MBT field. We conclude that the relatively low sedimentation rate ( 4 cm/kyr) records utilized in the Bayesian inversion have been heavily smoothed by the remanence acquisition process, and do not adequately represent the MBT field. The VGPs at the MBT and top Jaramillo, as measured in the North Atlantic, have similarities with excursion (Iceland Basin) VGP paths, and are apparently guided by maxima in downward vertical flux in the modern non-dipole (ND) field, implying longevity in ND features through time.

VLF modal interference distance and nighttime D region VLF reflection height for west-east and east-west propagation paths to Fiji

NASA Astrophysics Data System (ADS)

Chand, Atishnal Elvin; Kumar, Sushil

2017-08-01

Very low frequency (VLF) signals from navigational transmitters propagate through the Earth-ionosphere waveguide formed by the Earth and the lower conducting ionosphere and show the pronounced minima during solar terminator transition between transmitter and receiver. Pronounced amplitude minima observed on 19.8 kHz (NWC transmitter) and 24.8 kHz (NLK transmitter) signals recorded at Suva (18.149°S, 178.446°E), Fiji, during 2013-2014, have been used to estimate the VLF modal interference distance (DMS) and nighttime D region VLF reflection height (hN). The NWC transmitter signal propagates mostly in west-east direction, and the NLK transmitter follows a transequatorial path propagating significantly in the east-west direction. The values of DMS calculated using midpath terminator speed are 2103 ± 172 km and 2507 ± 373 km for these paths having west-east and east-west components of VLF subionospheric propagation, respectively, which agree with previously published results and within 10% with theoretical values. We have also compared the DMS estimated using a terminator time method with that calculated using terminator speed for a particular day and found both the values to be consistent. The hN values were found to be maximum during winter of Southern Hemisphere for NWC signal and winter of Northern Hemisphere for NLK signal VLF propagation paths to Suva. The hN also shows significant day-to-day and seasonal variabilities with a maximum of about 10 km and 23 km for NWC and NLK signal propagation paths, respectively, which could be due to the atmospheric gravity waves associated with solar terminator transition, as well as meteorological factors such as strong lightnings.

Optimal guidance for the space shuttle transition

NASA Technical Reports Server (NTRS)

Stengel, R. F.

1972-01-01

A guidance method for the space shuttle's transition from hypersonic entry to subsonic cruising flight is presented. The method evolves from a numerical trajectory optimization technique in which kinetic energy and total energy (per unit weight) replace velocity and time in the dynamic equations. This allows the open end-time problem to be transformed to one of fixed terminal energy. In its ultimate form, E-Guidance obtains energy balance (including dynamic-pressure-rate damping) and path length control by angle-of-attack modulation and cross-range control by roll angle modulation. The guidance functions also form the basis for a pilot display of instantaneous maneuver limits and destination. Numerical results illustrate the E-Guidance concept and the optimal trajectories on which it is based.

Selection of NIR H2O absorption transitions for in-cylinder measurement of temperature in IC engines

NASA Astrophysics Data System (ADS)

Zhou, Xin; Liu, Xiang; Jeffries, Jay B.; Hanson, Ronald K.

2005-12-01

The water vapour spectrum in the 1.25-1.65 µm region is systematically analysed to find the best absorption transitions for sensitive measurement of in-cylinder gas temperature over short paths in an internal combustion engine. The strategy to select the optimum wavelength regions and absorption line combinations is developed for the time-varying pressures and temperatures expected during the compression portion of an engine cycle. We have identified 14 transitions of water vapour in this spectral region as promising for this application. From these transitions, 16 potential line pairs were considered for a wavelength-modulated absorption sensor for in-cylinder gas temperature during the compression stroke. Expected performance is modelled for the intake portion of two engine cycles that produce extreme temperature and pressure variations during compression.

Path planning and energy management of solar-powered unmanned ground vehicles

NASA Astrophysics Data System (ADS)

Kaplan, Adam

Many of the applications pertinent to unmanned vehicles, such as environmental research and analysis, communications, and information-surveillance and reconnaissance, benefit from prolonged vehicle operation time. Conventional efforts to increase the operational time of electric-powered unmanned vehicles have traditionally focused on the design of energy-efficient components and the identification of energy efficient search patterns, while little attention has been paid to the vehicle's mission-level path plan and power management. This thesis explores the formulation and generation of integrated motion-plans and power-schedules for solar-panel equipped mobile robots operating under strict energy constraints, which cannot be effectively addressed through conventional motion planning algorithms. Transit problems are considered to design time-optimal paths using both Balkcom-Mason and Pseudo-Dubins curves. Additionally, a more complicated problem to generate mission plans for vehicles which must persistently travel between certain locations, similar to the traveling salesperson problem (TSP), is presented. A comparison between one of the common motion-planning algorithms and experimental results of the prescribed algorithms, made possible by use of a test environment and mobile robot designed and developed specifically for this research, are presented and discussed.

Compact atom interferometer using single laser

NASA Astrophysics Data System (ADS)

Chiow, Sheng-wey; Yu, Nan

2018-06-01

A typical atom interferometer requires vastly different laser frequencies at different stages of operation, e.g., near resonant light for laser cooling and far detuned light for atom optics, such that multiple lasers are typically employed. The number of laser units constrains the achievable minimum size and power in practical devices for resource critical environments such as space. We demonstrate a compact atom interferometer accelerometer operated by a single diode laser. This is achieved by dynamically changing the laser output frequency in GHz range while maintaining spectroscopic reference to an atomic transition via a sideband generated by phase modulation. At the same time, a beam path sharing configuration is also demonstrated for a compact sensor head design, in which atom interferometer beams share the same path as that of the cooling beam. This beam path sharing also significantly simplifies three-axis atomic accelerometry in microgravity using single sensor head.

Sign phase transition in the problem of interfering directed paths

NASA Astrophysics Data System (ADS)

Baldwin, C. L.; Laumann, C. R.; Spivak, B.

2018-01-01

We investigate the statistical properties of interfering directed paths in disordered media. At long distance, the average sign of the sum over paths may tend to zero (sign disordered) or remain finite (sign ordered) depending on dimensionality and the concentration of negative scattering sites x . We show that in two dimensions the sign-ordered phase is unstable even for arbitrarily small x by identifying rare destabilizing events. In three dimensions, we present strong evidence that there is a sign phase transition at a finite xc>0 . These results have consequences for several different physical systems. In two-dimensional insulators at low temperature, the variable-range-hopping magnetoresistance is always negative, while in three dimensions, it changes sign at the point of the sign phase transition. We also show that in the sign-disordered regime a small magnetic field may enhance superconductivity in a random system of D -wave superconducting grains embedded in a metallic matrix. Finally, the existence of the sign phase transition in three dimensions implies new features in the spin-glass phase diagram at high temperature.

The processing of spatial information in short-term memory: insights from eye tracking the path length effect.

PubMed

Guérard, Katherine; Tremblay, Sébastien; Saint-Aubin, Jean

2009-10-01

Serial memory for spatial locations increases as the distance between successive stimuli locations decreases. This effect, known as the path length effect [Parmentier, F. B. R., Elford, G., & Maybery, M. T. (2005). Transitional information in spatial serial memory: Path characteristics affect recall performance. Journal of Experimental Psychology: Learning, Memory & Cognition, 31, 412-427], was investigated in a systematic manner using eye tracking and interference procedures to explore the mechanisms responsible for the processing of spatial information. In Experiment 1, eye movements were monitored during a spatial serial recall task--in which the participants have to remember the location of spatially and temporally separated dots on the screen. In the experimental conditions, eye movements were suppressed by requiring participants to incessantly move their eyes between irrelevant locations. Ocular suppression abolished the path length effect whether eye movements were prevented during item presentation or during a 7s retention interval. In Experiment 2, articulatory suppression was combined with a spatial serial recall task. Although articulatory suppression impaired performance, it did not alter the path length effect. Our results suggest that rehearsal plays a key role in serial memory for spatial information, though the effect of path length seems to involve other processes located at encoding, such as the time spent fixating each location and perceptual organization.

Deep Reductions in Greenhouse Gas Emissions from the California Transportation Sector: Dynamics in Vehicle Fleet and Energy Supply Transitions to Achieve 80% Reduction in Emissions from 1990 Levels by 2050

NASA Astrophysics Data System (ADS)

Leighty, Wayne Waterman

California's "80in50" target for reducing greenhouse gas emissions to 80 percent below 1990 levels by the year 2050 is based on climate science rather than technical feasibility of mitigation. As such, it raises four fundamental questions: is this magnitude of reduction in greenhouse gas emissions possible, what energy system transitions over the next 40 years are necessary, can intermediate policy goals be met on the pathway toward 2050, and does the path of transition matter for the objective of climate change mitigation? Scenarios for meeting the 80in50 goal in the transportation sector are modelled. Specifically, earlier work defining low carbon transport scenarios for the year 2050 is refined by incorporating new information about biofuel supply. Then transition paths for meeting 80in50 scenarios are modelled for the light-duty vehicle sub-sector, with important implications for the timing of action, rate of change, and cumulative greenhouse gas emissions. One aspect of these transitions -- development in the California wind industry to supply low-carbon electricity for plug-in electric vehicles -- is examined in detail. In general, the range of feasible scenarios for meeting the 80in50 target is narrow enough that several common themes are apparent: electrification of light-duty vehicles must occur; continued improvements in vehicle efficiency must be applied to improving fuel economy; and energy carriers must de-carbonize to less than half of the carbon intensity of gasoline and diesel. Reaching the 80in50 goal will require broad success in travel demand reduction, fuel economy improvements and low-carbon fuel supply, since there is little opportunity to increase emission reductions in one area if we experience failure in another. Although six scenarios for meeting the 80in50 target are defined, only one also meets the intermediate target of reducing greenhouse gas emissions to 1990 levels by the year 2020. Furthermore, the transition path taken to reach any one of these scenarios can differ in cumulative emissions by more than 25 percent. Since cumulative emissions are the salient factor for climate change mitigation and the likelihood of success is an important consideration, initiating action immediately to begin the transitions indicated for achieving the 80in50 goal is found to be prudent.

Statistical physics approaches to quantifying sleep-stage transitions

NASA Astrophysics Data System (ADS)

Lo, Chung-Chuan

Sleep can be viewed as a sequence of transitions in a very complex neuronal system. Traditionally, studies of the dynamics of sleep control have focused on the circadian rhythm of sleep-wake transitions or on the ultradian rhythm of the sleep cycle. However, very little is known about the mechanisms responsible for the time structure or even the statistics of the rapid sleep-stage transitions that appear without periodicity. I study the time dynamics of sleep-wake transitions for different species, including humans, rats, and mice, and find that the wake and sleep episodes exhibit completely different behaviors: the durations of wake episodes are characterized by a scale-free power-law distribution, while the durations of sleep episodes have an exponential distribution with a characteristic time scale. The functional forms of the distributions of the sleep and wake durations hold for human subjects of different ages and for subjects with sleep apnea. They also hold for all the species I investigate. Surprisingly, all species have the same power-law exponent for the distribution of wake durations, but the exponential characteristic time of the distribution of sleep durations changes across species. I develop a stochastic model which accurately reproduces our empirical findings. The model suggests that the difference between the dynamics of the sleep and wake states arises from the constraints on the number of microstates in the sleep-wake system. I develop a measure of asymmetry in sleep-stage transitions using a transition probability matrix. I find that both normal and sleep apnea subjects are characterized by two types of asymmetric sleep-stage transition paths, and that the sleep apnea group exhibits less asymmetry in the sleep-stage transitions.

O and temperature in a hydrocarbon-fueled scramjet combustor

NASA Astrophysics Data System (ADS)

Goldenstein, C. S.; Schultz, I. A.; Spearrin, R. M.; Jeffries, J. B.; Hanson, R. K.

2014-09-01

The design and demonstration of a two-color tunable diode laser sensor for measurements of temperature and H2O in an ethylene-fueled model scramjet combustor are presented. This sensor probes multiple H2O transitions in the fundamental vibration bands near 2.5 μm that are up to 20 times stronger than those used by previous near-infrared H2O sensors. In addition, two design measures enabled high-fidelity measurements in the nonuniform flow field. (1) A recently developed calibration-free scanned-wavelength-modulation spectroscopy spectral-fitting strategy was used to infer the integrated absorbance of each transition without a priori knowledge of the absorption lineshape and (2) transitions with strengths that scale near-linearly with temperature were used to accurately determine the H2O column density and the H2O-weighted path-averaged temperature from the integrated absorbance of two transitions.

Longitudinal Proximity Effects in Superconducting Transition-Edge Sensors

NASA Technical Reports Server (NTRS)

Sadlier, John E.; Smith, Stephen J.; Bandler, Simon R.; Chervenak, James A.; Clem, John R.

2009-01-01

We have found experimentally that the critical current of a square thin-film superconducting transition-edge sensor (TES) depends exponentially upon the side length L and the square root of the temperature T, a behavior that has a natural theoretical explanation in terms of longitudinal proximity effects if the TES is regarded as a weak link between superconducting leads. As a consequence, the effective transition temperature T(sub c) of the TES is current-dependent and at fixed current scales as 1/L(sup 2). We also have found that the critical current can show clear Fraunhofer-like oscillations in an applied magnetic field, similar to those found in Josephson junctions. We have observed the longitudinal proximity effect in these devices over extraordinarily long lengths up to 290 micrometers, 1450 times the mean-free path.

Longitudinal Proximity Effects in Superconducting Transition-Edge Sensors

NASA Technical Reports Server (NTRS)

Sadleir, John E.; Smith, Stephen J.; Bandler, Simon R.; Chervenak, James A.; Clem, John R.

2010-01-01

We have found experimentally that the critical current of a square thin-film superconducting transition-edge sensor (TES) depends exponentially upon the side length L and the square root of the temperature T, a behavior that has a natural theoretical explanation in terms of longitudinal proximity effects if the TES is regarded as a weak link between superconducting leads. As a consequence, the effective transition temperature T(sub c) of the TES is current-dependent and at fixed current scales as 1/L(sup 2). We also have found that the critical current can show clear Fraunhofer-like oscillations in an applied magnetic field, similar to those found in Josephson junctions. We have observed the longitudinal proximity effect in these devices over extraordinarily long lengths up to 290 micrometers, 1450 times the mean-free path.

Wetting transition on patterned surfaces: transition states and energy barriers.

PubMed

Ren, Weiqing

2014-03-18

We study the wetting transition on microstructured hydrophobic surfaces. We use the string method [J. Chem. Phys. 2007, 126, 164103; J. Chem. Phys. 2013, 138, 134105] to accurately compute the transition states, the energy barriers, and the minimum energy paths for the wetting transition from the Cassie-Baxter state to the Wenzel state. Numerical results are obtained for the wetting of a hydrophobic surface textured with a square lattice of pillars. It is found that the wetting of the solid substrate occurs via infiltration of the liquid in a single groove, followed by lateral propagation of the liquid front. The propagation of the liquid front proceeds in a stepwise manner, and a zipping mechanism is observed during the infiltration of each layer. The minimum energy path for the wetting transition goes through a sequence of intermediate metastable states, whose wetted areas reflect the microstructure of the patterned surface. We also study the dependence of the energy barrier on the drop size and the gap between the pillars.

Exploring the dynamics of transit times and runoff source zones in a small agricultural catchment using a physically-based water flow model

NASA Astrophysics Data System (ADS)

Fleckenstein, J. H.; Yang, J.; Heidbuchel, I.; Musolff, A.

2017-12-01

Catchment-scale transit time distributions (TTDs) for discharge and residence time distributions (RTDs) of the water in storage are promising tools to characterize the discharge and mixing behavior of a catchment. TTDs and RTDs are dynamic in time, influenced by dynamic rainfall and evapotranspiration forcing, as well as changing groundwater storage in the catchment. In order to understand the links between the dynamics of TTDs and catchment mixing in an agricultural catchment in central Germany, a 3D hydrological model was set up using the fully coupled surface-subsurface numerical code HydroGeoSphere. The transient model is calibrated using discharge and groundwater level measurements, and is run for a period of 10 years from 1997 to 2007. A particle tracking tool was implemented in HydroGeoSphere to track the movement of water parcels in the subsurface, outputting TTDs of discharge and RTDs of groundwater storage at daily intervals. Results show the strong variability of the median age of discharge and median age of the water in storage, in response to the overall wetness of the catchment. Computed fractional StorAge Selection (fSAS, van der Velde et al. 2012, Rinaldo et al. 2015) functions suggest systematic changes in the preference of the catchment to discharge water of a certain age ranges from storage over the seasons: In the wet period, youngest water in storage is preferentially selected, and the preference shifts gradually to older water in storage when the catchment transitions into periods of post-wet, dry and pre-wet. Those changes are driven by distinct shifts in the dominant flow paths from deeper, slow flow paths during dry periods to faster shallow flow paths during the wet season. Changes in the shape of the fSAS functions are quantified in terms of changes in the two parameters of the Beta functions, which are used to approximate the fSAS functions. This provides an opportunity to generate quasi-continuous fSAS functions over the course of a year for the catchment. Our results provide new insights into the dynamics of TTDs and fSAS functions for a complex real-world catchment and can help to interpret the associated solute exports to the stream.

Numerical assessment and comparison of pulse wave velocity methods aiming at measuring aortic stiffness.

PubMed

Obeid, Hasan; Soulat, Gilles; Mousseaux, Elie; Laurent, Stéphane; Stergiopulos, Nikos; Boutouyrie, Pierre; Segers, Patrick

2017-10-31

Pulse waveform analyses have become established components of cardiovascular research. Recently several methods have been proposed as tools to measure aortic pulse wave velocity (aPWV). The carotid-femoral pulse wave velocity (cf-PWV), the current clinical gold standard method for the noninvasive assessment of aPWV, uses the carotid-to-femoral pulse transit time difference (cf-PTT) and an estimated path length to derive cf-PWV. The heart-ankle PWV (ha-PWV), brachial-ankle PWV (ba-PWV) and finger-toe (ft-PWV) are also methods presuming to approximate aPWV based on time delays between physiological cardiovascular signals at two locations (~heart-ankle PTT, ha-PTT; ~brachial-ankle PTT, ba-PTT; ~finger-toe PTT, ft-PTT) and a path length typically derived from the subject's height. To test the validity of these methods, we used a detailed 1D arterial network model (143 arterial segments) including the foot and hand circulation. The arterial tree dimensions and properties were taken from the literature and completed with data from patient scans. We calculated PTTs with all the methods mentioned above. The calculated PTTs were compared with the aortic PTT (aPTT), which is considered as the absolute reference method in this study. The correlation between methods and aPTT was good and significant, cf-PTT (R 2   =  0.97; P  <  0.001; mean difference 5  ±  2 ms), ha-PTT (R 2   =  0.96; P  <  0.001; 150  ±  23 ms), ba-PTT (R 2   =  0.96; P  <  0.001; 70  ±  13 ms) and ft-PTT (R 2   =  0.95; P  <  0.001; 14  ±  10 ms). Consequently, good correlation was also observed for the PWV values derived with the tested methods, but absolute values differed because of the different path lengths used. In conclusion, our computer model-based analyses demonstrate that for PWV methods based on peripheral signals, pulse transit time differences closely correlate with the aortic transit time, supporting the use of these methods in clinical practice.

The extent to which path-integral models account for evanescent (tunneling) and complex (near-field) waves

NASA Astrophysics Data System (ADS)

Ranfagni, Anedio; Mugnai, Daniela; Cacciari, Ilaria

2018-05-01

The usefulness of a stochastic approach in determining time scales in tunneling processes (mainly, but not only, in the microwave range) is reconsidered and compared with a different approach to these kinds of processes, based on Feynman's transition elements. This latter method is found to be particularly suitable for interpreting situations in the near field, as results from some experimental cases considered here.

Complex quantum network geometries: Evolution and phase transitions

NASA Astrophysics Data System (ADS)

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

Complex quantum network geometries: Evolution and phase transitions.

PubMed

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

The impact of family structure transitions on youth achievement: evidence from the children of the NLSY79.

PubMed

Aughinbaugh, Alison; Pierret, Charles R; Rothstein, Donna S

2005-08-01

We investigated the sensitivity of measures of cognitive ability and socioemotional development to changes in parents' marital status using data from the National Longitudinal Survey of Youth, 1979. We used several scores for each assessment, taken at different times relative to parents' marital transitions, which allowed us to trace the effects starting up to five years before a parent's change in marital status and continuing for up to six years afterward. It also allowed us to correct for the unobserved heterogeneity of the transition and nontransition samples by controlling for the child's fixed effect in estimating the time path of his or her response to the transition. We found that children from families with both biological parents scored significantly better on the BPI and the PIAT-math and PIAT-reading assessments than did children from nonintact families. However, much of the difference disappeared when we controlled for background variables. Furthermore, when we controlled for child fixed effects, we did not find significant longitudinal variation in these scores over long periods that encompass the marital transition. This finding suggests that most of the variation is due to cross-sectional differences and is not a result of marital transitions per se.

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

PubMed Central

Juraszek, J.; Bolhuis, P. G.

2006-01-01

We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding. PMID:17035504

Near-optimal energy transitions for energy-state trajectories of hypersonic aircraft

NASA Technical Reports Server (NTRS)

Ardema, M. D.; Bowles, J. V.; Terjesen, E. J.; Whittaker, T.

1992-01-01

A problem of the instantaneous energy transition that occurs in energy-state approximation is considered. The transitions are modeled as a sequence of two load-factor bounded paths (either climb-dive or dive-climb). The boundary-layer equations associated with the energy-state dynamic model are analyzed to determine the precise location of the transition.

Reliable Transition State Searches Integrated with the Growing String Method.

PubMed

Zimmerman, Paul

2013-07-09

The growing string method (GSM) is highly useful for locating reaction paths connecting two molecular intermediates. GSM has often been used in a two-step procedure to locate exact transition states (TS), where GSM creates a quality initial structure for a local TS search. This procedure and others like it, however, do not always converge to the desired transition state because the local search is sensitive to the quality of the initial guess. This article describes an integrated technique for simultaneous reaction path and exact transition state search. This is achieved by implementing an eigenvector following optimization algorithm in internal coordinates with Hessian update techniques. After partial convergence of the string, an exact saddle point search begins under the constraint that the maximized eigenmode of the TS node Hessian has significant overlap with the string tangent near the TS. Subsequent optimization maintains connectivity of the string to the TS as well as locks in the TS direction, all but eliminating the possibility that the local search leads to the wrong TS. To verify the robustness of this approach, reaction paths and TSs are found for a benchmark set of more than 100 elementary reactions.

A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

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

Nguyen, Trong-Nghia; Department of Physical Chemistry, Hanoi University of Science and Technology, Hanoi; Putikam, Raghunath

2015-03-28

We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} groupmore » by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.« less

Communication: hybrid femtosecond/picosecond rotational coherent anti-Stokes Raman scattering thermometry using a narrowband time-asymmetric probe pulse.

PubMed

Stauffer, Hans U; Miller, Joseph D; Roy, Sukesh; Gord, James R; Meyer, Terrence R

2012-03-21

A narrowband, time-asymmetric probe pulse is introduced into the hybrid femtosecond/picosecond rotational coherent anti-Stokes Raman scattering (fs/ps RCARS) technique to provide accurate and precise single-shot, high-repetition-rate gas-phase thermometric measurements. This narrowband pulse-generated by inserting a Fabry-Pérot étalon into the probe-pulse beam path-enables frequency-domain detection of pure-rotational transitions. The unique time-asymmetric nature of this pulse, in turn, allows for detection of resonant Raman-active rotational transitions free of signal contamination by nonresonant four-wave-mixing processes while still allowing detection at short probe-pulse delays, where collisional dephasing processes are negligible. We demonstrate that this approach provides excellent single-shot thermometric accuracy (<1% error) and precision (~2.5%) in gas-phase environments. © 2012 American Institute of Physics

Real-time observation of fluctuations at the driven-dissipative Dicke phase transition

PubMed Central

Brennecke, Ferdinand; Mottl, Rafael; Baumann, Kristian; Landig, Renate; Donner, Tobias; Esslinger, Tilman

2013-01-01

We experimentally study the influence of dissipation on the driven Dicke quantum phase transition, realized by coupling external degrees of freedom of a Bose–Einstein condensate to the light field of a high-finesse optical cavity. The cavity provides a natural dissipation channel, which gives rise to vacuum-induced fluctuations and allows us to observe density fluctuations of the gas in real-time. We monitor the divergence of these fluctuations over two orders of magnitude while approaching the phase transition, and observe a behavior that deviates significantly from that expected for a closed system. A correlation analysis of the fluctuations reveals the diverging time scale of the atomic dynamics and allows us to extract a damping rate for the external degree of freedom of the atoms. We find good agreement with our theoretical model including dissipation via both the cavity field and the atomic field. Using a dissipation channel to nondestructively gain information about a quantum many-body system provides a unique path to study the physics of driven-dissipative systems. PMID:23818599

Option volatility and the acceleration Lagrangian

NASA Astrophysics Data System (ADS)

Baaquie, Belal E.; Cao, Yang

2014-01-01

This paper develops a volatility formula for option on an asset from an acceleration Lagrangian model and the formula is calibrated with market data. The Black-Scholes model is a simpler case that has a velocity dependent Lagrangian. The acceleration Lagrangian is defined, and the classical solution of the system in Euclidean time is solved by choosing proper boundary conditions. The conditional probability distribution of final position given the initial position is obtained from the transition amplitude. The volatility is the standard deviation of the conditional probability distribution. Using the conditional probability and the path integral method, the martingale condition is applied, and one of the parameters in the Lagrangian is fixed. The call option price is obtained using the conditional probability and the path integral method.

Enzymatic reaction paths as determined by transition path sampling

NASA Astrophysics Data System (ADS)

Masterson, Jean Emily

Enzymes are biological catalysts capable of enhancing the rates of chemical reactions by many orders of magnitude as compared to solution chemistry. Since the catalytic power of enzymes routinely exceeds that of the best artificial catalysts available, there is much interest in understanding the complete nature of chemical barrier crossing in enzymatic reactions. Two specific questions pertaining to the source of enzymatic rate enhancements are investigated in this work. The first is the issue of how fast protein motions of an enzyme contribute to chemical barrier crossing. Our group has previously identified sub-picosecond protein motions, termed promoting vibrations (PVs), that dynamically modulate chemical transformation in several enzymes. In the case of human heart lactate dehydrogenase (hhLDH), prior studies have shown that a specific axis of residues undergoes a compressional fluctuation towards the active site, decreasing a hydride and a proton donor--acceptor distance on a sub-picosecond timescale to promote particle transfer. To more thoroughly understand the contribution of this dynamic motion to the enzymatic reaction coordinate of hhLDH, we conducted transition path sampling (TPS) using four versions of the enzymatic system: a wild type enzyme with natural isotopic abundance; a heavy enzyme where all the carbons, nitrogens, and non-exchangeable hydrogens were replaced with heavy isotopes; and two versions of the enzyme with mutations in the axis of PV residues. We generated four separate ensembles of reaction paths and analyzed each in terms of the reaction mechanism, time of barrier crossing, dynamics of the PV, and residues involved in the enzymatic reaction coordinate. We found that heavy isotopic substitution of hhLDH altered the sub-picosecond dynamics of the PV, changed the favored reaction mechanism, dramatically increased the time of barrier crossing, but did not have an effect on the specific residues involved in the PV. In the mutant systems, we observed changes in the reaction mechanism and altered contributions of the mutated residues to the enzymatic reaction coordinate, but we did not detect a substantial change in the time of barrier crossing. These results confirm the importance of maintaining the dynamics and structural scaffolding of the hhLDH PV in order to facilitate facile barrier passage. We also utilized TPS to investigate the possible role of fast protein dynamics in the enzymatic reaction coordinate of human dihydrofolate reductase (hsDHFR). We found that sub-picosecond dynamics of hsDHFR do contribute to the reaction coordinate, whereas this is not the case in the E. coli version of the enzyme. This result indicates a shift in the DHFR family to a more dynamic version of catalysis. The second inquiry we addressed in this thesis regarding enzymatic barrier passage concerns the variability of paths through reactive phase space for a given enzymatic reaction. We further investigated the hhLDH-catalyzed reaction using a high-perturbation TPS algorithm. Though we saw that alternate reaction paths were possible, the dominant reaction path we observed corresponded to that previously elucidated in prior hhLDH TPS studies. Since the additional reaction paths we observed were likely high-energy, these results indicate that only the dominant reaction path contributes significantly to the overall reaction rate. In conclusion, we show that the enzymes hhLDH and hsDHFR exhibit paths through reactive phase space where fast protein motions are involved in the enzymatic reaction coordinate and exhibit a non-negligible contribution to chemical barrier crossing.

Prediction of Rare Transitions in Planetary Atmosphere Dynamics Between Attractors with Different Number of Zonal Jets

NASA Astrophysics Data System (ADS)

Bouchet, F.; Laurie, J.; Zaboronski, O.

2012-12-01

We describe transitions between attractors with either one, two or more zonal jets in models of turbulent atmosphere dynamics. Those transitions are extremely rare, and occur over times scales of centuries or millennia. They are extremely hard to observe in direct numerical simulations, because they require on one hand an extremely good resolution in order to simulate accurately the turbulence and on the other hand simulations performed over an extremely long time. Those conditions are usually not met together in any realistic models. However many examples of transitions between turbulent attractors in geophysical flows are known to exist (paths of the Kuroshio, Earth's magnetic field reversal, atmospheric flows, and so on). Their study through numerical computations is inaccessible using conventional means. We present an alternative approach, based on instanton theory and large deviations. Instanton theory provides a way to compute (both numerically and theoretically) extremely rare transitions between turbulent attractors. This tool, developed in field theory, and justified in some cases through the large deviation theory in mathematics, can be applied to models of turbulent atmosphere dynamics. It provides both new theoretical insights and new type of numerical algorithms. Those algorithms can predict transition histories and transition rates using numerical simulations run over only hundreds of typical model dynamical time, which is several order of magnitude lower than the typical transition time. We illustrate the power of those tools in the framework of quasi-geostrophic models. We show regimes where two or more attractors coexist. Those attractors corresponds to turbulent flows dominated by either one or more zonal jets similar to midlatitude atmosphere jets. Among the trajectories connecting two non-equilibrium attractors, we determine the most probable ones. Moreover, we also determine the transition rates, which are several of magnitude larger than a typical time determined from the jet structure. We discuss the medium-term generalization of those results to models with more complexity, like primitive equations or GCMs.

Method and apparatus for upshifting light frequency by rapid plasma creation

DOEpatents

Dawson, John M.; Wilks, Scott C.; Mori, Warren B.; Joshi, Chandrasekhar J.; Sessler, Andrew M.

1990-01-01

Photons of an electromagnetic source wave are frequency-upshifted as a plasma is rapidly created around the path of this propagating source wave. The final frequency can be controlled by adjusting the gas density. A controlled time-varying frequency (chirped) pulse can be produced by using a controlled spatially varying gas density. The plasma must be created in a time which is short compared to the transit time of the light through the plasmas region. For very fast creation over one to at most a few light periods of an overdense plasma, static magnetic fields with short wavelengths are created.

Neural Architectures for Control

NASA Technical Reports Server (NTRS)

Peterson, James K.

1991-01-01

The cerebellar model articulated controller (CMAC) neural architectures are shown to be viable for the purposes of real-time learning and control. Software tools for the exploration of CMAC performance are developed for three hardware platforms, the MacIntosh, the IBM PC, and the SUN workstation. All algorithm development was done using the C programming language. These software tools were then used to implement an adaptive critic neuro-control design that learns in real-time how to back up a trailer truck. The truck backer-upper experiment is a standard performance measure in the neural network literature, but previously the training of the controllers was done off-line. With the CMAC neural architectures, it was possible to train the neuro-controllers on-line in real-time on a MS-DOS PC 386. CMAC neural architectures are also used in conjunction with a hierarchical planning approach to find collision-free paths over 2-D analog valued obstacle fields. The method constructs a coarse resolution version of the original problem and then finds the corresponding coarse optimal path using multipass dynamic programming. CMAC artificial neural architectures are used to estimate the analog transition costs that dynamic programming requires. The CMAC architectures are trained in real-time for each obstacle field presented. The coarse optimal path is then used as a baseline for the construction of a fine scale optimal path through the original obstacle array. These results are a very good indication of the potential power of the neural architectures in control design. In order to reach as wide an audience as possible, we have run a seminar on neuro-control that has met once per week since 20 May 1991. This seminar has thoroughly discussed the CMAC architecture, relevant portions of classical control, back propagation through time, and adaptive critic designs.

Interference between two resonant transitions with distinct initial and final states connected by radiative decay

NASA Astrophysics Data System (ADS)

Marsman, A.; Horbatsch, M.; Hessels, E. A.

2017-12-01

The resonant line shape from driving a transition between two states, |a 〉 and |b 〉 , can be distorted due to a quantum-mechanical interference effect involving a resonance between two different states, |c 〉 and |d 〉 , if |c 〉 has a decay path to |a 〉 and |d 〉 has a decay path to |b 〉 . This interference can cause a shift of the measured resonance, despite the fact that the two resonances do not have a common initial or final state. As an example, we demonstrate that such a shift affects measurements of the atomic hydrogen 2 S1 /2 -to-2 P1 /2 Lamb-shift transition due to 3 S -to-3 P transitions if the 3 S1 /2 state has some initial population.

Primary weathering rates, water transit times, and concentration-discharge relations: A theoretical analysis for the critical zone

NASA Astrophysics Data System (ADS)

Ameli, Ali A.; Beven, Keith; Erlandsson, Martin; Creed, Irena F.; McDonnell, Jeffrey J.; Bishop, Kevin

2017-01-01

The permeability architecture of the critical zone exerts a major influence on the hydrogeochemistry of the critical zone. Water flow path dynamics drive the spatiotemporal pattern of geochemical evolution and resulting streamflow concentration-discharge (C-Q) relation, but these flow paths are complex and difficult to map quantitatively. Here we couple a new integrated flow and particle tracking transport model with a general reversible Transition State Theory style dissolution rate law to explore theoretically how C-Q relations and concentration in the critical zone respond to decline in saturated hydraulic conductivity (Ks) with soil depth. We do this for a range of flow rates and mineral reaction kinetics. Our results show that for minerals with a high ratio of equilibrium concentration (Ceq) to intrinsic weathering rate (Rmax), vertical heterogeneity in Ks enhances the gradient of weathering-derived solute concentration in the critical zone and strengthens the inverse stream C-Q relation. As CeqRmax decreases, the spatial distribution of concentration in the critical zone becomes more uniform for a wide range of flow rates, and stream C-Q relation approaches chemostatic behavior, regardless of the degree of vertical heterogeneity in Ks. These findings suggest that the transport-controlled mechanisms in the hillslope can lead to chemostatic C-Q relations in the stream while the hillslope surface reaction-controlled mechanisms are associated with an inverse stream C-Q relation. In addition, as CeqRmax decreases, the concentration in the critical zone and stream become less dependent on groundwater age (or transit time).

Anomalies in the coil-stretch transition of flexible polymers

NASA Astrophysics Data System (ADS)

Ghosal, Aishani; Cherayil, Binny J.

2018-03-01

The flow-induced coil-stretch transition of high molecular weight polymers has generally been held to be of first order. But evidence of significant slowing down in the rate at which the polymers relax to equilibrium in the vicinity of the transition suggests that the thermodynamic character of the transition may be less clear-cut. The above slowing down effect is actually characteristic of a second-order transition, and it points to the existence of a broad spectrum of conformational states in the transition region, analogous to the existence of fluctuations of all length scales at a critical point. In this paper, using a path integral approach based on a free-draining finitely extensible chain model, we calculate various polymer properties as a function of elongational flow as a way of exploring different statistical mechanical details of the coil-stretch transition. These properties include the molecular weight dependence of the flow-extension curve of the polymer, the distribution of its steady-state end-to-end distances, and the characteristic relaxation time τR of these distances. Among other findings, our calculations indicate that the coil-stretch transition is discontinuous in the N → ∞ limit, that the effective free energy of the chain is unimodal at all values of the flow, becoming broad and flat in the immediate vicinity of the transition, and that the ratio of τR to the Rouse relaxation time increases abruptly at the transition before eventually reaching a plateau value at large flow strengths. These aspects of the coil-stretch transition place it among a larger class of unconventional nominally first-order single chain transitions that include the adsorption transition of surface-tethered polymers and the escape transition of compressed polymers.

Path-integral methods for analyzing the effects of fluctuations in stochastic hybrid neural networks.

PubMed

Bressloff, Paul C

2015-01-01

We consider applications of path-integral methods to the analysis of a stochastic hybrid model representing a network of synaptically coupled spiking neuronal populations. The state of each local population is described in terms of two stochastic variables, a continuous synaptic variable and a discrete activity variable. The synaptic variables evolve according to piecewise-deterministic dynamics describing, at the population level, synapses driven by spiking activity. The dynamical equations for the synaptic currents are only valid between jumps in spiking activity, and the latter are described by a jump Markov process whose transition rates depend on the synaptic variables. We assume a separation of time scales between fast spiking dynamics with time constant [Formula: see text] and slower synaptic dynamics with time constant τ. This naturally introduces a small positive parameter [Formula: see text], which can be used to develop various asymptotic expansions of the corresponding path-integral representation of the stochastic dynamics. First, we derive a variational principle for maximum-likelihood paths of escape from a metastable state (large deviations in the small noise limit [Formula: see text]). We then show how the path integral provides an efficient method for obtaining a diffusion approximation of the hybrid system for small ϵ. The resulting Langevin equation can be used to analyze the effects of fluctuations within the basin of attraction of a metastable state, that is, ignoring the effects of large deviations. We illustrate this by using the Langevin approximation to analyze the effects of intrinsic noise on pattern formation in a spatially structured hybrid network. In particular, we show how noise enlarges the parameter regime over which patterns occur, in an analogous fashion to PDEs. Finally, we carry out a [Formula: see text]-loop expansion of the path integral, and use this to derive corrections to voltage-based mean-field equations, analogous to the modified activity-based equations generated from a neural master equation.

Effects of C5-substituent group on the hydrogen peroxide-mediated tautomerisation of protonated cytosine: a theoretical perspective

NASA Astrophysics Data System (ADS)

Jin, Lingxia; Shi, Shengnan; Zhao, Yang; Luo, Liyang; Zhao, Caibin; Lu, Jiufu; Jiang, Min

2018-02-01

The direct tautomerism (path A) and H2O2 as a catalyst (path B) have been studied in conversion of Cyt2t+ into CytN3+ isomer. The protonated 5-carboxycytosine (5-caCyt) is represented and has been further explored in the presence of H2O2 (path C). In going from a four-membered-ring transition state in the case of the direct tautomerism to the six-membered ring for H2O2, the H2O2 significantly contributes to decreasing the free energy barrier of tautomerisation. Although the carboxylic substituent of 5-carboxycytosine has certain affected on the electron distribution of the pyrimidine ring, the six-membered-ring transition state has not changed. This result illustrates that the C5-carboxylation has no significant effect on the H2O2-mediated isomerisation of Cyt2t+ to CytN3+ isomer. Meanwhile, these paths A-C have been further explored in the presence of two water molecules. Use of implicit solvent models (PCM) does not significantly alter the energetics of water-mediated paths A-C compared to those in gas phase. Furthermore, the rate constant with Wigner tunnelling correction of path A is obviously smaller than those of paths B and C. Finally, the lifetime τ99.9% of paths B and C is 10-5 s, which is implemented by the mechanism of the concerted synchronous double proton transfer.

Variational transition state theory: theoretical framework and recent developments.

PubMed

Bao, Junwei Lucas; Truhlar, Donald G

2017-12-11

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications. The theoretical methods reviewed here include multidimensional quantum mechanical tunneling, multistructural VTST (MS-VTST), multi-path VTST (MP-VTST), both reaction-path VTST (RP-VTST) and variable reaction coordinate VTST (VRC-VTST), system-specific quantum Rice-Ramsperger-Kassel theory (SS-QRRK) for predicting pressure-dependent rate constants, and VTST in the solid phase, liquid phase, and enzymes. We also provide some perspectives regarding the general applicability of VTST.

Improving Upon String Methods for Transition State Discovery.

PubMed

Chaffey-Millar, Hugh; Nikodem, Astrid; Matveev, Alexei V; Krüger, Sven; Rösch, Notker

2012-02-14

Transition state discovery via application of string methods has been researched on two fronts. The first front involves development of a new string method, named the Searching String method, while the second one aims at estimating transition states from a discretized reaction path. The Searching String method has been benchmarked against a number of previously existing string methods and the Nudged Elastic Band method. The developed methods have led to a reduction in the number of gradient calls required to optimize a transition state, as compared to existing methods. The Searching String method reported here places new beads on a reaction pathway at the midpoint between existing beads, such that the resolution of the path discretization in the region containing the transition state grows exponentially with the number of beads. This approach leads to favorable convergence behavior and generates more accurate estimates of transition states from which convergence to the final transition states occurs more readily. Several techniques for generating improved estimates of transition states from a converged string or nudged elastic band have been developed and benchmarked on 13 chemical test cases. Optimization approaches for string methods, and pitfalls therein, are discussed.

The Heavy Ion Afternoon Bulge: Structure and Formation Mechanisms

NASA Astrophysics Data System (ADS)

Fernandes, P. A.; Larsen, B.; Skoug, R. M.; Reeves, G. D.; Denton, M.; Engel, M.; Ferradas, C.; Funsten, H. O.; Henderson, M. G.; Jahn, J. M.; Morley, S.; Thomsen, M. F.

2017-12-01

Recent observations of near-equatorial inner magnetosphere plasma composition indicate the presence of an "afternoon bulge" plasma population at low L-shell. A detailed statistical survey using HOPE data characterized this afternoon bulge as an enhancement in 10 keV O+ and He+ ions extending from 1100-2200 MLT and 2 ≤ L ≤ 4 during quiet/moderate geomagnetic activity (Kp < 5). This statistical HOPE study postulated that formation of the bulge is caused by variations in Kp: 10 keV particles have access to low L-shells during geomagnetically active times and become trapped during the transition to quiet times. In this study, we expand on previous observations of the afternoon bulge by examining individual transits of this feature by the Van Allen Probes. We analyze periods with optimal spacecraft transits of the afternoon bulge region, including: May - Oct. 2013, Feb. - June 2014, and Apr. - Aug. 2015. We determine the presence and duration of the bulge during case studies representing three categories of geomagnetic activity: 1) extended quiet geomagnetic conditions; 2) sharp transitions of Kp from active to quiet conditions; and 3) rises and falls in Kp on the time scales of spacecraft orbits to days. We thoroughly characterize the energy structure of the bulge as a function of Kp. We also analyze these transits of the bulge in the context of plasma access using both drift path modeling and UBK-derived energy access maps.

A stochastic estimation procedure for intermittently-observed semi-Markov multistate models with back transitions.

PubMed

Aralis, Hilary; Brookmeyer, Ron

2017-01-01

Multistate models provide an important method for analyzing a wide range of life history processes including disease progression and patient recovery following medical intervention. Panel data consisting of the states occupied by an individual at a series of discrete time points are often used to estimate transition intensities of the underlying continuous-time process. When transition intensities depend on the time elapsed in the current state and back transitions between states are possible, this intermittent observation process presents difficulties in estimation due to intractability of the likelihood function. In this manuscript, we present an iterative stochastic expectation-maximization algorithm that relies on a simulation-based approximation to the likelihood function and implement this algorithm using rejection sampling. In a simulation study, we demonstrate the feasibility and performance of the proposed procedure. We then demonstrate application of the algorithm to a study of dementia, the Nun Study, consisting of intermittently-observed elderly subjects in one of four possible states corresponding to intact cognition, impaired cognition, dementia, and death. We show that the proposed stochastic expectation-maximization algorithm substantially reduces bias in model parameter estimates compared to an alternative approach used in the literature, minimal path estimation. We conclude that in estimating intermittently observed semi-Markov models, the proposed approach is a computationally feasible and accurate estimation procedure that leads to substantial improvements in back transition estimates.

An axisymmetric single-path model for gas transport in the conducting airways.

PubMed

Madasu, Srinath; Borhan, All; Ultman, James S

2006-02-01

In conventional one-dimensional single-path models, radially averaged concentration is calculated as a function of time and longitudinal position in the lungs, and coupled convection and diffusion are accounted for with a dispersion coefficient. The axisymmetric single-path model developed in this paper is a two-dimensional model that incorporates convective-diffusion processes in a more fundamental manner by simultaneously solving the Navier-Stokes and continuity equations with the convection-diffusion equation. A single airway path was represented by a series of straight tube segments interconnected by leaky transition regions that provide for flow loss at the airway bifurcations. As a sample application, the model equations were solved by a finite element method to predict the unsteady state dispersion of an inhaled pulse of inert gas along an airway path having dimensions consistent with Weibel's symmetric airway geometry. Assuming steady, incompressible, and laminar flow, a finite element analysis was used to solve for the axisymmetric pressure, velocity and concentration fields. The dispersion calculated from these numerical solutions exhibited good qualitative agreement with the experimental values, but quantitatively was in error by 20%-30% due to the assumption of axial symmetry and the inability of the model to capture the complex recirculatory flows near bifurcations.

Skill of ship-following large-eddy simulations in reproducing MAGIC observations across the northeast Pacific stratocumulus to cumulus transition region

DOE PAGES

McGibbon, J.; Bretherton, C. S.

2017-03-17

During the Marine ARM GPCI Investigation of Clouds (MAGIC) in October 2011 to September 2012, a container ship making periodic cruises between Los Angeles, CA, and Honolulu, HI, was instrumented with surface meteorological, aerosol and radiation instruments, a cloud radar and ceilometer, and radiosondes. Here large-eddy simulation (LES) is performed in a ship-following frame of reference for 13 four day transects from the MAGIC field campaign. The goal is to assess if LES can skillfully simulate the broad range of observed cloud characteristics and boundary layer structure across the subtropical stratocumulus to cumulus transition region sampled during different seasons andmore » meteorological conditions. Results from Leg 15A, which sampled a particularly well-defined stratocumulus to cumulus transition, demonstrate the approach. The LES reproduces the observed timing of decoupling and transition from stratocumulus to cumulus and matches the observed evolution of boundary layer structure, cloud fraction, liquid water path, and precipitation statistics remarkably well. Considering the simulations of all 13 cruises, the LES skillfully simulates the mean diurnal variation of key measured quantities, including liquid water path (LWP), cloud fraction, measures of decoupling, and cloud radar-derived precipitation. The daily mean quantities are well represented, and daily mean LWP and cloud fraction show the expected correlation with estimated inversion strength. There is a –0.6 K low bias in LES near-surface air temperature that results in a high bias of 5.6 W m –2 in sensible heat flux (SHF). Altogether, these results build confidence in the ability of LES to represent the northeast Pacific stratocumulus to trade cumulus transition region.« less

Office of Biological and Physical Research: Overview Transitioning to the Vision for Space Exploration

NASA Technical Reports Server (NTRS)

Crouch, Roger

2004-01-01

Viewgraphs on NASA's transition to its vision for space exploration is presented. The topics include: 1) Strategic Directives Guiding the Human Support Technology Program; 2) Progressive Capabilities; 3) A Journey to Inspire, Innovate, and Discover; 4) Risk Mitigation Status Technology Readiness Level (TRL) and Countermeasures Readiness Level (CRL); 5) Biological And Physical Research Enterprise Aligning With The Vision For U.S. Space Exploration; 6) Critical Path Roadmap Reference Missions; 7) Rating Risks; 8) Current Critical Path Roadmap (Draft) Rating Risks: Human Health; 9) Current Critical Path Roadmap (Draft) Rating Risks: System Performance/Efficiency; 10) Biological And Physical Research Enterprise Efforts to Align With Vision For U.S. Space Exploration; 11) Aligning with the Vision: Exploration Research Areas of Emphasis; 12) Code U Efforts To Align With The Vision For U.S. Space Exploration; 13) Types of Critical Path Roadmap Risks; and 14) ISS Human Support Systems Research, Development, and Demonstration. A summary discussing the vision for U.S. space exploration is also provided.

Saddle-node bifurcation to jammed state for quasi-one-dimensional counter-chemotactic flow.

PubMed

Fujii, Masashi; Awazu, Akinori; Nishimori, Hiraku

2010-07-01

The transition of a counter-chemotactic particle flow from a free-flow state to a jammed state in a quasi-one-dimensional path is investigated. One of the characteristic features of such a flow is that the constituent particles spontaneously form a cluster that blocks the path, called a path-blocking cluster (PBC), and causes a jammed state when the particle density is greater than a threshold value. Near the threshold value, the PBC occasionally collapses on itself to recover the free flow. In other words, the time evolution of the size of the PBC governs the flux of a counter-chemotactic flow. In this Rapid Communication, on the basis of numerical results of a stochastic cellular automata (SCA) model, we introduce a Langevin equation model for the size evolution of the PBC that reproduces the qualitative characteristics of the SCA model. The results suggest that the emergence of the jammed state in a quasi-one-dimensional counterflow is caused by a saddle-node bifurcation.

Determination of the Residence Time of Food Particles During Aseptic Sterilization

NASA Technical Reports Server (NTRS)

Carl, J. R.; Arndt, G. D.; Nguyen, T. X.

1994-01-01

The paper describes a non-invasive method to measure the time an individual particle takes to move through a length of stainless steel pipe. The food product is in two phase flow (liquids and solids) and passes through a pipe with pressures of approximately 60 psig and temperatures of 270-285 F. The proposed problem solution is based on the detection of transitory amplitude and/or phase changes in a microwave transmission path caused by the passage of the particles of interest. The particles are enhanced in some way, as will be discussed later, such that they will provide transitory changes that are distinctive enough not to be mistaken for normal variations in the received signal (caused by the non-homogeneous nature of the medium). Two detectors (transmission paths across the pipe) will be required and place at a known separation. A minimum transit time calculation is made from which the maximum velocity can be determined. This provides the minimum residence time. Also average velocity and statistical variations can be computed so that the amount of 'over-cooking' can be determined.

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

Electron elevator: Excitations across the band gap via a dynamical gap state

DOE PAGES

Lim, Anthony; Foulkes, W. M. C.; Horsfield, A. P.; ...

2016-01-27

We use time-dependent density functional theory to study self-irradiated Si. We calculate the electronic stopping power of Si in Si by evaluating the energy transferred to the electrons per unit path length by an ion of kinetic energy from 1 eV to 100 keV moving through the host. Electronic stopping is found to be significant below the threshold velocity normally identified with transitions across the band gap. A structured crossover at low velocity exists in place of a hard threshold. Lastly, an analysis of the time dependence of the transition rates using coupled linear rate equations enables one of themore » excitation mechanisms to be clearly identified: a defect state induced in the gap by the moving ion acts like an elevator and carries electrons across the band gap.« less

Electron Elevator: Excitations across the Band Gap via a Dynamical Gap State.

PubMed

Lim, A; Foulkes, W M C; Horsfield, A P; Mason, D R; Schleife, A; Draeger, E W; Correa, A A

2016-01-29

We use time-dependent density functional theory to study self-irradiated Si. We calculate the electronic stopping power of Si in Si by evaluating the energy transferred to the electrons per unit path length by an ion of kinetic energy from 1 eV to 100 keV moving through the host. Electronic stopping is found to be significant below the threshold velocity normally identified with transitions across the band gap. A structured crossover at low velocity exists in place of a hard threshold. An analysis of the time dependence of the transition rates using coupled linear rate equations enables one of the excitation mechanisms to be clearly identified: a defect state induced in the gap by the moving ion acts like an elevator and carries electrons across the band gap.

International Space Station: Transitional Platform for Moon and Mars

NASA Technical Reports Server (NTRS)

Greeniesen, Michael C.

2006-01-01

Humans on the path to Mars are employing the Space Station to better understand the Life Sciences issues during long duration space flight. In this phase the problems, for example, of bone loss, skeletal muscle atrophy and radiation will be prioritized for countermeasure development. This presentation will feature NASA's critical path to the Moon and Mars as the initial blueprint for addressing these Human Life Sciences challenges necessary to accomplish a successful Mars transit, surface exploration and return to Earth. A Moon base will be the test bed for resolving the engineering obstacles for later establishment of the Mars Crew Habitat. Current engineering concept scenarios for Moon and Mars bases plus Mars transit vehicles will receive the final focus.

Monte Carlo simulations on atropisomerism of thienotriazolodiazepines applicable to slow transition phenomena using potential energy surfaces by ab initio molecular orbital calculations.

PubMed

Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru

2014-01-01

Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.

A reversible bipolar WORM device based on AlOxNy thin film with Al nano phase embedded

NASA Astrophysics Data System (ADS)

Zhu, W.; Li, J.; Zhang, L.; Hu, X. C.

2017-03-01

An Al-rich AlOxNy thin film based reversible Write-Once-Read-Many-Times (WORM) memory device with MIS structure could transit from high resistance state (HRS, ∼1011 Ω) to low resistance state (LRS, ∼105 Ω) by sweeping voltage up to ∼20 V. The first switching could be recorded as writing process for WORM device which may relate to conductive path are formed through the thin film. The conductive path should be formed by both Al nano phase and oxygen vacancies. Among of them, Al nano phases are not easy to move, but oxygen vacancies could migrate under high E-field or at high temperature environment. Such conductive path is not sensitive to charging effect after it formed, but it could be broken by heating effect, which may relate to the migration of excess Al ions and oxygen vacancies at high temperature. After baking LRS (ON state) WORM device at 200 °C for 2 min, the conductivity will decrease to HRS which indicates conductive path is broken and device back to HRS (OFF state) again. This phenomenon could be recorded as recovery process. Both writing and recovery process related to migration of oxygen vacancies and could be repeated over 10 times in this study. It also indicates that there is no permanent breakdown occurred in MIS structured WORM device operation. We suggest that this conductive path only can be dissolved by a temperature sensitive electro-chemical action. This WORM device could maintain at LRS over 105 s with on-off ratio over 4 orders.

Mode pumping experiments on biomolecules

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

Austin, R.H.; Erramilli, S.; Xie, A.

1995-12-31

We will explore several aspects of protein dynamics and energy transfer that can be explored by using the intense, picosecond, tunable mid-IR output of the FEL. In order of appearance they are: (1) Saturation recovery and inter-level coupling of the low temperature amide-I band in acetanilide. This is a continuation of earlier experiments to test soliton models in crystalline hydrogen bonded solids. In this experiment we utilize the sub-picosecond time resolution and low repetition rate of the Stanford SCLA FEL to do both T{sub 1} and T{sub 2} relaxation measurements at 1650 cm{sup -1}. (2) Probing the influence of collectivemore » dynamics in sensory rhodopsin. In this experiment we use the FIR output of the Stanford FIREFLY FEL to determine the lifetime of collective modes in the photo-active protein sensory rhodopsin, and begin experiments on the influence of collective modes on retinal reaction dynamics. (3) Probing the transition states of enzymes. This experiment, in the initial stages, attempts to use the intense IR output of the FEL to probe and influence the reaction path of a transition state analog for the protein nucleoside hydrolase. The transition state of the inosine substrate is believed to have critical modes softened by the protein so that bond-breaking paths show absorption at approximately 800 cm{sup -1}. A form of action spectrum using FEL excitation will be used to probe this state.« less

Subcritical transition scenarios via linear and nonlinear localized optimal perturbations in plane Poiseuille flow

NASA Astrophysics Data System (ADS)

Farano, Mirko; Cherubini, Stefania; Robinet, Jean-Christophe; De Palma, Pietro

2016-12-01

Subcritical transition in plane Poiseuille flow is investigated by means of a Lagrange-multiplier direct-adjoint optimization procedure with the aim of finding localized three-dimensional perturbations optimally growing in a given time interval (target time). Space localization of these optimal perturbations (OPs) is achieved by choosing as objective function either a p-norm (with p\\gg 1) of the perturbation energy density in a linear framework; or the classical (1-norm) perturbation energy, including nonlinear effects. This work aims at analyzing the structure of linear and nonlinear localized OPs for Poiseuille flow, and comparing their transition thresholds and scenarios. The nonlinear optimization approach provides three types of solutions: a weakly nonlinear, a hairpin-like and a highly nonlinear optimal perturbation, depending on the value of the initial energy and the target time. The former shows localization only in the wall-normal direction, whereas the latter appears much more localized and breaks the spanwise symmetry found at lower target times. Both solutions show spanwise inclined vortices and large values of the streamwise component of velocity already at the initial time. On the other hand, p-norm optimal perturbations, although being strongly localized in space, keep a shape similar to linear 1-norm optimal perturbations, showing streamwise-aligned vortices characterized by low values of the streamwise velocity component. When used for initializing direct numerical simulations, in most of the cases nonlinear OPs provide the most efficient route to transition in terms of time to transition and initial energy, even when they are less localized in space than the p-norm OP. The p-norm OP follows a transition path similar to the oblique transition scenario, with slightly oscillating streaks which saturate and eventually experience secondary instability. On the other hand, the nonlinear OP rapidly forms large-amplitude bent streaks and skips the phases of streak saturation, providing a contemporary growth of all of the velocity components due to strong nonlinear coupling.

Stationary properties of maximum-entropy random walks.

PubMed

Dixit, Purushottam D

2015-10-01

Maximum-entropy (ME) inference of state probabilities using state-dependent constraints is popular in the study of complex systems. In stochastic systems, how state space topology and path-dependent constraints affect ME-inferred state probabilities remains unknown. To that end, we derive the transition probabilities and the stationary distribution of a maximum path entropy Markov process subject to state- and path-dependent constraints. A main finding is that the stationary distribution over states differs significantly from the Boltzmann distribution and reflects a competition between path multiplicity and imposed constraints. We illustrate our results with particle diffusion on a two-dimensional landscape. Connections with the path integral approach to diffusion are discussed.

Identifying transit corridors for elephant using a long time-series

NASA Astrophysics Data System (ADS)

Pittiglio, Claudia; Skidmore, Andrew K.; van Gils, Hein A. M. J.; Prins, Herbert H. T.

2012-02-01

The role of corridors in mitigating the effects of landscape fragmentation on biodiversity is controversial. Recent studies have highlighted the need for new approaches in corridor design using long-term datasets. We present a method to identify transit corridors for elephant at a population scale over a large area and an extended period of time using long-term aerial surveys. We investigated environmental and anthropogenic factors directly and indirectly related to the wet versus dry season distribution of elephant and its transit corridors. Four environmental variables predicted the presence of elephant at the landscape scale in both seasons: distance from permanent water, protected areas and settlements and vegetation structure. Path analysis revealed that altitude and monthly average NDVI, and distance from temporary water had a significant indirect effect on elephant distribution at local scale in dry and wet seasons respectively. Five transit corridors connecting Tarangire National Park and the northern as well as south-eastern wet season dispersal areas were identified and matched the wildlife migration routes described in the 1960s. The corridors are stable over the decades, providing landscape connectivity for elephant. Our approach yielded insights how advanced spatial analysis can be integrated with biological data available from long-term datasets to identify actual transit corridors and predictors of species distribution.

An early warning indicator for atmospheric blocking events using transfer operators

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

Tantet, Alexis, E-mail: a.j.j.tantet@uu.nl; Burgt, Fiona R. van der; Dijkstra, Henk A.

The existence of persistent midlatitude atmospheric flow regimes with time-scales larger than 5–10 days and indications of preferred transitions between them motivates to develop early warning indicators for such regime transitions. In this paper, we use a hemispheric barotropic model together with estimates of transfer operators on a reduced phase space to develop an early warning indicator of the zonal to blocked flow transition in this model. It is shown that the spectrum of the transfer operators can be used to study the slow dynamics of the flow as well as the non-Markovian character of the reduction. The slowest motionsmore » are thereby found to have time scales of three to six weeks and to be associated with meta-stable regimes (and their transitions) which can be detected as almost-invariant sets of the transfer operator. From the energy budget of the model, we are able to explain the meta-stability of the regimes and the existence of preferred transition paths. Even though the model is highly simplified, the skill of the early warning indicator is promising, suggesting that the transfer operator approach can be used in parallel to an operational deterministic model for stochastic prediction or to assess forecast uncertainty.« less

Radiative recombination in GaN/InGaN heterojunction bipolar transistors

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

Kao, Tsung-Ting; Lee, Yi-Che; Kim, Hee-Jin

2015-12-14

We report an electroluminescence (EL) study on npn GaN/InGaN heterojunction bipolar transistors (HBTs). Three radiative recombination paths are resolved in the HBTs, corresponding to the band-to-band transition (3.3 eV), conduction-band-to-acceptor-level transition (3.15 eV), and yellow luminescence (YL) with the emission peak at 2.2 eV. We further study possible light emission paths by operating the HBTs under different biasing conditions. The band-to-band and the conduction-band-to-acceptor-level transitions mostly arise from the intrinsic base region, while a defect-related YL band could likely originate from the quasi-neutral base region of a GaN/InGaN HBT. The I{sub B}-dependent EL intensities for these three recombination paths are discussed. The resultsmore » also show the radiative emission under the forward-active transistor mode operation is more effective than that using a diode-based emitter due to the enhanced excess electron concentration in the base region as increasing the collector current increases.« less

Impacts of solar-absorbing aerosol layers on the transition of stratocumulus to trade cumulus clouds

DOE PAGES

Zhou, Xiaoli; Ackerman, Andrew S.; Fridlind, Ann M.; ...

2017-10-26

Here, the effects of an initially overlying layer of solar-absorbing aerosol on the transition of stratocumulus to trade cumulus clouds are examined using large-eddy simulations. For lightly drizzling cloud the transition is generally hastened, resulting mainly from increased cloud droplet number concentration ( N c) induced by entrained aerosol. The increased N c slows sedimentation of cloud droplets and shortens their relaxation time for diffusional growth, both of which accelerate entrainment of overlying air and thereby stratocumulus breakup. However, the decrease in albedo from cloud breakup is more than offset by redistributing cloud water over a greater number of droplets,more » such that the diurnal-average shortwave forcing at the top of the atmosphere is negative. The negative radiative forcing is enhanced by sizable longwave contributions, which result from the greater cloud breakup and a reduced boundary layer height associated with aerosol heating. A perturbation of moisture instead of aerosol aloft leads to a greater liquid water path and a more gradual transition. Adding absorbing aerosol to that atmosphere results in substantial reductions in liquid water path (LWP) and cloud cover that lead to positive shortwave and negative longwave forcings on average canceling each other. Only for heavily drizzling clouds is the breakup delayed, as inhibition of precipitation overcomes cloud water loss from enhanced entrainment. Considering these simulations as an imperfect proxy for biomass burning plumes influencing Namibian stratocumulus, we expect regional indirect plus semi-direct forcings to be substantially negative to negligible at the top of the atmosphere, with its magnitude sensitive to background and perturbation properties.« less

Impacts of solar-absorbing aerosol layers on the transition of stratocumulus to trade cumulus clouds

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

Zhou, Xiaoli; Ackerman, Andrew S.; Fridlind, Ann M.

Here, the effects of an initially overlying layer of solar-absorbing aerosol on the transition of stratocumulus to trade cumulus clouds are examined using large-eddy simulations. For lightly drizzling cloud the transition is generally hastened, resulting mainly from increased cloud droplet number concentration ( N c) induced by entrained aerosol. The increased N c slows sedimentation of cloud droplets and shortens their relaxation time for diffusional growth, both of which accelerate entrainment of overlying air and thereby stratocumulus breakup. However, the decrease in albedo from cloud breakup is more than offset by redistributing cloud water over a greater number of droplets,more » such that the diurnal-average shortwave forcing at the top of the atmosphere is negative. The negative radiative forcing is enhanced by sizable longwave contributions, which result from the greater cloud breakup and a reduced boundary layer height associated with aerosol heating. A perturbation of moisture instead of aerosol aloft leads to a greater liquid water path and a more gradual transition. Adding absorbing aerosol to that atmosphere results in substantial reductions in liquid water path (LWP) and cloud cover that lead to positive shortwave and negative longwave forcings on average canceling each other. Only for heavily drizzling clouds is the breakup delayed, as inhibition of precipitation overcomes cloud water loss from enhanced entrainment. Considering these simulations as an imperfect proxy for biomass burning plumes influencing Namibian stratocumulus, we expect regional indirect plus semi-direct forcings to be substantially negative to negligible at the top of the atmosphere, with its magnitude sensitive to background and perturbation properties.« less

Impacts of solar-absorbing aerosol layers on the transition of stratocumulus to trade cumulus clouds

NASA Astrophysics Data System (ADS)

Zhou, Xiaoli; Ackerman, Andrew S.; Fridlind, Ann M.; Wood, Robert; Kollias, Pavlos

2017-10-01

The effects of an initially overlying layer of solar-absorbing aerosol on the transition of stratocumulus to trade cumulus clouds are examined using large-eddy simulations. For lightly drizzling cloud the transition is generally hastened, resulting mainly from increased cloud droplet number concentration (Nc) induced by entrained aerosol. The increased Nc slows sedimentation of cloud droplets and shortens their relaxation time for diffusional growth, both of which accelerate entrainment of overlying air and thereby stratocumulus breakup. However, the decrease in albedo from cloud breakup is more than offset by redistributing cloud water over a greater number of droplets, such that the diurnal-average shortwave forcing at the top of the atmosphere is negative. The negative radiative forcing is enhanced by sizable longwave contributions, which result from the greater cloud breakup and a reduced boundary layer height associated with aerosol heating. A perturbation of moisture instead of aerosol aloft leads to a greater liquid water path and a more gradual transition. Adding absorbing aerosol to that atmosphere results in substantial reductions in liquid water path (LWP) and cloud cover that lead to positive shortwave and negative longwave forcings on average canceling each other. Only for heavily drizzling clouds is the breakup delayed, as inhibition of precipitation overcomes cloud water loss from enhanced entrainment. Considering these simulations as an imperfect proxy for biomass burning plumes influencing Namibian stratocumulus, we expect regional indirect plus semi-direct forcings to be substantially negative to negligible at the top of the atmosphere, with its magnitude sensitive to background and perturbation properties.

Impacts of Solar-Absorbing Aerosol Layers on the Transition of Stratocumulus to Trade Cumulus Clouds

NASA Technical Reports Server (NTRS)

Zhou, Xiaoli; Ackerman, Andrew S.; Fridlind, Ann M.; Wood, Robert; Kollias, Pavlos

2017-01-01

The effects of an initially overlying layer of solar-absorbing aerosol on the transition of stratocumulus to trade cumulus clouds are examined using large-eddy simulations. For lightly drizzling cloud the transition is generally hastened, resulting mainly from increased cloud droplet number concentration (Nc) induced by entrained aerosol. The increased Nc slows sedimentation of cloud droplets and shortens their relaxation time for diffusional growth, both of which accelerate entrainment of overlying air and thereby stratocumulus breakup. However, the decrease in albedo from cloud breakup is more than offset by redistributing cloud water over a greater number of droplets, such that the diurnal-average shortwave forcing at the top of the atmosphere is negative. The negative radiative forcing is enhanced by sizable longwave contributions, which result from the greater cloud breakup and a reduced boundary layer height associated with aerosol heating. A perturbation of moisture instead of aerosol aloft leads to a greater liquid water path and a more gradual transition. Adding absorbing aerosol to that atmosphere results in substantial reductions in liquid water path (LWP) and cloud cover that lead to positive short-wave and negative longwave forcings on average canceling each other. Only for heavily drizzling clouds is the breakup delayed, as inhibition of precipitation overcomes cloud water loss from enhanced entrainment. Considering these simulations as an imperfect proxy for biomass burning plumes influencing Namibian stratocumulus, we expect regional indirect plus semi-direct forcings to be substantially negative to negligible at the top of the atmosphere, with its magnitude sensitive to background and perturbation properties.

Quantum optimal control of isomerization dynamics of a one-dimensional reaction-path model dominated by a competing dissociation channel

NASA Astrophysics Data System (ADS)

Kurosaki, Yuzuru; Artamonov, Maxim; Ho, Tak-San; Rabitz, Herschel

2009-07-01

Quantum wave packet optimal control simulations with intense laser pulses have been carried out for studying molecular isomerization dynamics of a one-dimensional (1D) reaction-path model involving a dominant competing dissociation channel. The 1D intrinsic reaction coordinate model mimics the ozone open→cyclic ring isomerization along the minimum energy path that successively connects the ozone cyclic ring minimum, the transition state (TS), the open (global) minimum, and the dissociative O2+O asymptote on the O3 ground-state A1' potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O2+O dissociation channel lie at ˜0.05, ˜0.086, and ˜0.037 hartree above the open isomer, respectively. The molecular orientation of the modeled ozone is held constant with respect to the laser-field polarization and several optimal fields are found that all produce nearly perfect isomerization. The optimal control fields are characterized by distinctive high temporal peaks as well as low frequency components, thereby enabling abrupt transfer of the time-dependent wave packet over the TS from the open minimum to the targeted ring minimum. The quick transition of the ozone wave packet avoids detrimental leakage into the competing O2+O channel. It is possible to obtain weaker optimal laser fields, resulting in slower transfer of the wave packets over the TS, when a reduced level of isomerization is satisfactory.

Electronic excited state paths of Stone-Wales rearrangement in pyrene: roles of conical intersections.

PubMed

Yamazaki, Kaoru; Niitsu, Naoyuki; Nakamura, Kosuke; Kanno, Manabu; Kono, Hirohiko

2012-11-26

We investigated the reaction paths of Stone-Wales rearrangement (SWR), i.e., π/2 rotation of two carbon atoms with respect to the midpoint of the bond, in graphene and carbon nanotube quantum chemically. Our particular attention is focused on the roles of electronic excitations and conical intersections (CIs) in the reaction mechanism. We used pyrene as a model system. The reaction paths were determined by constructing potential energy surfaces at the MS-CASPT2//SA-CASSCF level of theory. We found that there are no CIs involved in SWR when both of C-C bond cleavage and formation occur simultaneously (concerted mechanism). In contrast, for the reaction path with stepwise cleavage and formation of C-C bonds, C-C bond breaking and making processes proceed through two CIs. When SWR starts from the ground (S(0)) state, the concerted and stepwise paths have an equivalent reaction barrier ΔE(‡) (9.5-9.6 eV). For the reaction path starting from excited states, only the stepwise mechanism is energetically preferable. This path contains a nonadabatic transition between the S(1) and S(0) states via a CI associated with the first stage of C-C bond cleavage and has ΔE(‡) as large as in the S(0) paths. We confirmed that the main active molecular orbitals and electron configurations for the low-lying electronic states of larger nanocarbons are the same as those in pyrene. This result suggests the importance of the nonadiabatic transitions through CIs in the photochemical reactions in large nanocarbons.

The Mathematics of Mixing Things Up

NASA Astrophysics Data System (ADS)

Diaconis, Persi

2011-08-01

How long should a Markov chain Monte Carlo algorithm be run? Using examples from statistical physics (Ehrenfest urn, Ising model, hard discs) as well as card shuffling, this tutorial paper gives an overview of a body of mathematical results that can give useful answers to practitioners (viz: seven shuffles suffice for practical purposes). It points to new techniques (path coupling, geometric inequalities, and Harris recurrence). The discovery of phase transitions in mixing times (the cutoff phenomenon) is emphasized.

Phase transitions and adiabatic preparation of a fractional Chern insulator in a boson cold-atom model

NASA Astrophysics Data System (ADS)

Motruk, Johannes; Pollmann, Frank

2017-10-01

We investigate the fate of hardcore bosons in a Harper-Hofstadter model which was experimentally realized by Aidelsburger et al. [Nat. Phys. 11, 162 (2015), 10.1038/nphys3171] at half-filling of the lowest band. We discuss the stability of an emergent fractional Chern insulator (FCI) state in a finite region of the phase diagram that is separated from a superfluid state by a first-order transition when tuning the band topology following the protocol used in the experiment. Since crossing a first-order transition is unfavorable for adiabatically preparing the FCI state, we extend the model to stabilize a featureless insulating state. The transition between this phase and the topological state proves to be continuous, providing a path in parameter space along which an FCI state could be adiabatically prepared. To further corroborate this statement, we perform time-dependent DMRG calculations which demonstrate that the FCI state may indeed be reached by adiabatically tuning a simple product state.

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

Impulsive noise suppression in color images based on the geodesic digital paths

NASA Astrophysics Data System (ADS)

Smolka, Bogdan; Cyganek, Boguslaw

2015-02-01

In the paper a novel filtering design based on the concept of exploration of the pixel neighborhood by digital paths is presented. The paths start from the boundary of a filtering window and reach its center. The cost of transitions between adjacent pixels is defined in the hybrid spatial-color space. Then, an optimal path of minimum total cost, leading from pixels of the window's boundary to its center is determined. The cost of an optimal path serves as a degree of similarity of the central pixel to the samples from the local processing window. If a pixel is an outlier, then all the paths starting from the window's boundary will have high costs and the minimum one will also be high. The filter output is calculated as a weighted mean of the central pixel and an estimate constructed using the information on the minimum cost assigned to each image pixel. So, first the costs of optimal paths are used to build a smoothed image and in the second step the minimum cost of the central pixel is utilized for construction of the weights of a soft-switching scheme. The experiments performed on a set of standard color images, revealed that the efficiency of the proposed algorithm is superior to the state-of-the-art filtering techniques in terms of the objective restoration quality measures, especially for high noise contamination ratios. The proposed filter, due to its low computational complexity, can be applied for real time image denoising and also for the enhancement of video streams.

Setting the foundation for your future: transitioning from an undergraduate student to research chemist

USDA-ARS?s Scientific Manuscript database

Understanding your goals in life will assist you identifying the right career path. As we transition from an undergraduate student into our professional career there are an array of skills we will require over the years. This leads to, how do we stand out from the crowd? Here I discuss how I transit...

Unzip instabilities: Straight to oscillatory transitions in the cutting of thin polymer sheets

NASA Astrophysics Data System (ADS)

Reis, P. M.; Kumar, A.; Shattuck, M. D.; Roman, B.

2008-06-01

We report an experimental investigation of the cutting of a thin brittle polymer sheet with a blunt tool. It was recently shown that the fracture path becomes oscillatory when the tool is much wider than the sheet thickness. Here we uncover two novel transitions from straight to oscillatory fracture by varying either the tilt angle of the tool or the speed of cutting, respectively. We denote these by angle and speed unzip instabilities and analyze them by quantifying both the dynamics of the crack tip and the final shapes of the fracture paths. Moreover, for the speed unzip instability, the straight crack lip obtained at low speeds exhibits out-of-plane buckling undulations (as opposed to being flat above the instability threshold) suggesting a transition from ductile to brittle fracture.

Low carbon transition and sustainable development path of tourism industry

NASA Astrophysics Data System (ADS)

Zhu, Hongbing; Zhang, Jing; Zhao, Lei; Jin, Shenglang

2017-05-01

The low carbon transition is as much a transformative technology shift as it represents a response to global environment challenges. The low carbon paradigm presents a new direction of change for tourism industry. However, the lack of theoretical frameworks on low carbon transformation in tourism industry context provides a significant knowledge gap. This paper firstly investigates the relationships between low carbon and sustainable development, followed by exploring the existing challenges of tourism sustainable development. At last, this paper presents a sustainable development path framework for low carbon transition of tourism industry, which include accelerating deployment of renewable energy, energy-saving green building construction, improving green growth investment, and adopting a sustainable consumption and production system, in order to promote energy and water efficiency, waste management, GHG emissions mitigation and eventually enhance its sustainability.

A one-way shooting algorithm for transition path sampling of asymmetric barriers

NASA Astrophysics Data System (ADS)

Brotzakis, Z. Faidon; Bolhuis, Peter G.

2016-10-01

We present a novel transition path sampling shooting algorithm for the efficient sampling of complex (biomolecular) activated processes with asymmetric free energy barriers. The method employs a fictitious potential that biases the shooting point toward the transition state. The method is similar in spirit to the aimless shooting technique by Peters and Trout [J. Chem. Phys. 125, 054108 (2006)], but is targeted for use with the one-way shooting approach, which has been shown to be more effective than two-way shooting algorithms in systems dominated by diffusive dynamics. We illustrate the method on a 2D Langevin toy model, the association of two peptides and the initial step in dissociation of a β-lactoglobulin dimer. In all cases we show a significant increase in efficiency.

Dynamic heterogeneity in the folding/unfolding transitions of FiP35

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

Mori, Toshifumi, E-mail: mori@ims.ac.jp; Saito, Shinji, E-mail: shinji@ims.ac.jp

Molecular dynamics simulations have become an important tool in studying protein dynamics over the last few decades. Atomistic simulations on the order of micro- to milliseconds are becoming feasible and are used to study the state-of-the-art experiments in atomistic detail. Yet, analyzing the high-dimensional-long-temporal trajectory data is still a challenging task and sometimes leads to contradictory results depending on the analyses. To reveal the dynamic aspect of the trajectory, here we propose a simple approach which uses a time correlation function matrix and apply to the folding/unfolding trajectory of FiP35 WW domain [Shaw et al., Science 330, 341 (2010)]. Themore » approach successfully characterizes the slowest mode corresponding to the folding/unfolding transitions and determines the free energy barrier indicating that FiP35 is not an incipient downhill folder. The transition dynamics analysis further reveals that the folding/unfolding transition is highly heterogeneous, e.g., the transition path time varies by ∼100 fold. We identify two misfolded states and show that the dynamic heterogeneity in the folding/unfolding transitions originates from the trajectory being trapped in the misfolded and half-folded intermediate states rather than the diffusion driven by a thermal noise. The current results help reconcile the conflicting interpretations of the folding mechanism and highlight the complexity in the folding dynamics. This further motivates the need to understand the transition dynamics beyond a simple free energy picture using simulations and single-molecule experiments.« less

A statistical mechanics approach to computing rare transitions in multi-stable turbulent geophysical flows

NASA Astrophysics Data System (ADS)

Laurie, J.; Bouchet, F.

2012-04-01

Many turbulent flows undergo sporadic random transitions, after long periods of apparent statistical stationarity. For instance, paths of the Kuroshio [1], the Earth's magnetic field reversal, atmospheric flows [2], MHD experiments [3], 2D turbulence experiments [4,5], 3D flows [6] show this kind of behavior. The understanding of this phenomena is extremely difficult due to the complexity, the large number of degrees of freedom, and the non-equilibrium nature of these turbulent flows. It is however a key issue for many geophysical problems. A straightforward study of these transitions, through a direct numerical simulation of the governing equations, is nearly always impracticable. This is mainly a complexity problem, due to the large number of degrees of freedom involved for genuine turbulent flows, and the extremely long time between two transitions. In this talk, we consider two-dimensional and geostrophic turbulent models, with stochastic forces. We consider regimes where two or more attractors coexist. As an alternative to direct numerical simulation, we propose a non-equilibrium statistical mechanics approach to the computation of this phenomenon. Our strategy is based on large deviation theory [7], derived from a path integral representation of the stochastic process. Among the trajectories connecting two non-equilibrium attractors, we determine the most probable one. Moreover, we also determine the transition rates, and in which cases this most probable trajectory is a typical one. Interestingly, we prove that in the class of models we consider, a mechanism exists for diffusion over sets of connected attractors. For the type of stochastic forces that allows this diffusion, the transition between attractors is not a rare event. It is then very difficult to characterize the flow as bistable. However for another class of stochastic forces, this diffusion mechanism is prevented, and genuine bistability or multi-stability is observed. We discuss how these results are probably connected to the long debated existence of multi-stability in the atmosphere and oceans.

Development of FB-MultiPier dynamic vessel-collision analysis models, phase 2.

DOT National Transportation Integrated Search

2014-07-01

Massive waterway vessels such as barges regularly transit navigable waterways in the U.S. During passages that fall within : the vicinity of bridge structures, vessels may (under extreme circumstances) deviate from the intended vessel transit path. A...

The Regime Shift Associated with the 2004–2008 US Housing Market Bubble

PubMed Central

Cheong, Siew Ann

2016-01-01

The Subprime Bubble preceding the Subprime Crisis of 2008 was fueled by risky lending practices, manifesting in the form of a large abrupt increase in the proportion of subprime mortgages issued in the US. This event also coincided with critical slowing down signals associated with instability, which served as evidence of a regime shift or phase transition in the US housing market. Here, we show that the US housing market underwent a regime shift between alternate stable states consistent with the observed critical slowing down signals. We modeled this regime shift on a universal transition path and validated the model by estimating when the bubble burst. Additionally, this model reveals loose monetary policy to be a plausible cause of the phase transition, implying that the bubble might have been deflatable by a timely tightening of monetary policy. PMID:27583633

2010 Program of Study: Swirling and Swimming in Turbulence

DTIC Science & Technology

2011-06-01

total transit time for half the particle path is then T = −12 log a− 1 + 3 2 log 2− b −1 . (10) For small a, the first term dominates the travel time... the half -saturation density, which provides a limitation to the amount of prey that can be eaten at large P , i.e. Z depends linearly on P until the ...implies that, for example, a new generation of Z00 is produced by all interactions between two Z00, half of the interactions between Z00 and Z01, and 1 in

Inversion symmetry breaking induced triply degenerate points in orderly arranged PtSeTe family materials

NASA Astrophysics Data System (ADS)

Xiao, R. C.; Cheung, C. H.; Gong, P. L.; Lu, W. J.; Si, J. G.; Sun, Y. P.

2018-06-01

k paths exactly with symmetry allow to find triply degenerate points (TDPs) in band structures. The paths that host the type-II Dirac points in PtSe2 family materials also have the spatial symmetry. However, due to Kramers degeneracy (the systems have both inversion symmetry and time reversal symmetry), the crossing points in them are Dirac ones. In this work, based on symmetry analysis, first-principles calculations, and method, we predict that PtSe2 family materials should undergo topological transitions if the inversion symmetry is broken, i.e. the Dirac fermions in PtSe2 family materials split into TDPs in PtSeTe family materials (PtSSe, PtSeTe, and PdSeTe) with orderly arranged S/Se (Se/Te). It is different from the case in high-energy physics that breaking inversion symmetry I leads to the splitting of Dirac fermion into Weyl fermions. We also address a possible method to achieve the orderly arranged in PtSeTe family materials in experiments. Our study provides a real example that Dirac points transform into TDPs, and is helpful to investigate the topological transition between Dirac fermions and TDP fermions.

Atomic clouds as spectrally selective and tunable delay lines for single photons from quantum dots

NASA Astrophysics Data System (ADS)

Wildmann, Johannes S.; Trotta, Rinaldo; Martín-Sánchez, Javier; Zallo, Eugenio; O'Steen, Mark; Schmidt, Oliver G.; Rastelli, Armando

2015-12-01

We demonstrate a compact, spectrally selective, and tunable delay line for single photons emitted by quantum dots. This is achieved by fine-tuning the wavelength of the optical transitions of such "artificial atoms" into a spectral window in which a cloud of natural atoms behaves as a slow-light medium. By employing the ground-state fine-structure-split exciton confined in an InGaAs/GaAs quantum dot as a source of single photons at different frequencies and the hyperfine-structure-split D1 transition of Cs-vapors as a tunable delay medium, we achieve a differential delay of up 2.4 ns on a 7.5-cm-long path for photons that are only 60 μ eV (14.5 GHz) apart. To quantitatively explain the experimental data, we develop a theoretical model that accounts for both the inhomogeneous broadening of the quantum-dot emission lines and the Doppler broadening of the atomic lines. The concept we proposed here may be used to implement time-reordering operations aimed at erasing the "which-path" information that deteriorates entangled-photon emission from excitons with finite fine-structure splitting.

Understanding eye movements in face recognition using hidden Markov models.

PubMed

Chuk, Tim; Chan, Antoni B; Hsiao, Janet H

2014-09-16

We use a hidden Markov model (HMM) based approach to analyze eye movement data in face recognition. HMMs are statistical models that are specialized in handling time-series data. We conducted a face recognition task with Asian participants, and model each participant's eye movement pattern with an HMM, which summarized the participant's scan paths in face recognition with both regions of interest and the transition probabilities among them. By clustering these HMMs, we showed that participants' eye movements could be categorized into holistic or analytic patterns, demonstrating significant individual differences even within the same culture. Participants with the analytic pattern had longer response times, but did not differ significantly in recognition accuracy from those with the holistic pattern. We also found that correct and wrong recognitions were associated with distinctive eye movement patterns; the difference between the two patterns lies in the transitions rather than locations of the fixations alone. © 2014 ARVO.

Experimental tests of truncated diffusion in fault damage zones

NASA Astrophysics Data System (ADS)

Suzuki, Anna; Hashida, Toshiyuki; Li, Kewen; Horne, Roland N.

2016-11-01

Fault zones affect the flow paths of fluids in groundwater aquifers and geological reservoirs. Fault-related fracture damage decreases to background levels with increasing distance from the fault core according to a power law. This study investigated mass transport in such a fault-related structure using nonlocal models. A column flow experiment is conducted to create a permeability distribution that varies with distance from a main conduit. The experimental tracer response curve is preasymptotic and implies subdiffusive transport, which is slower than the normal Fickian diffusion. If the surrounding area is a finite domain, an upper truncated behavior in tracer response (i.e., exponential decline at late times) is observed. The tempered anomalous diffusion (TAD) model captures the transition from subdiffusive to Fickian transport, which is characterized by a smooth transition from power-law to an exponential decline in the late-time breakthrough curves.

Integration of geospatial multi-mode transportation Systems in Kuala Lumpur

NASA Astrophysics Data System (ADS)

Ismail, M. A.; Said, M. N.

2014-06-01

Public transportation serves people with mobility and accessibility to workplaces, health facilities, community resources, and recreational areas across the country. Development in the application of Geographical Information Systems (GIS) to transportation problems represents one of the most important areas of GIS-technology today. To show the importance of GIS network analysis, this paper highlights the determination of the optimal path between two or more destinations based on multi-mode concepts. The abstract connector is introduced in this research as an approach to integrate urban public transportation in Kuala Lumpur, Malaysia including facilities such as Light Rapid Transit (LRT), Keretapi Tanah Melayu (KTM) Komuter, Express Rail Link (ERL), KL Monorail, road driving as well as pedestrian modes into a single intelligent data model. To assist such analysis, ArcGIS's Network Analyst functions are used whereby the final output includes the total distance, total travelled time, directional maps produced to find the quickest, shortest paths, and closest facilities based on either time or distance impedance for multi-mode route analysis.

Open quantum random walks: Bistability on pure states and ballistically induced diffusion

NASA Astrophysics Data System (ADS)

Bauer, Michel; Bernard, Denis; Tilloy, Antoine

2013-12-01

Open quantum random walks (OQRWs) deal with quantum random motions on a line for systems with internal and orbital degrees of freedom. The internal system behaves as a quantum random gyroscope coding for the direction of the orbital moves. We reveal the existence of a transition, depending on OQRW moduli, in the internal system behaviors from simple oscillations to random flips between two unstable pure states. This induces a transition in the orbital motions from the usual diffusion to ballistically induced diffusion with a large mean free path and large effective diffusion constant at large times. We also show that mixed states of the internal system are converted into random pure states during the process. We touch upon possible experimental realizations.

Can quantum transition state theory be defined as an exact t = 0+ limit?

NASA Astrophysics Data System (ADS)

Jang, Seogjoo; Voth, Gregory A.

2016-02-01

The definition of the classical transition state theory (TST) as a t → 0+ limit of the flux-side time correlation function relies on the assumption that simultaneous measurement of population and flux is a well defined physical process. However, the noncommutativity of the two measurements in quantum mechanics makes the extension of such a concept to the quantum regime impossible. For this reason, quantum TST (QTST) has been generally accepted as any kind of quantum rate theory reproducing the TST in the classical limit, and there has been a broad consensus that no unique QTST retaining all the properties of TST can be defined. Contrary to this widely held view, Hele and Althorpe (HA) [J. Chem. Phys. 138, 084108 (2013)] recently suggested that a true QTST can be defined as the exact t → 0+ limit of a certain kind of quantum flux-side time correlation function and that it is equivalent to the ring polymer molecular dynamics (RPMD) TST. This work seeks to question and clarify certain assumptions underlying these suggestions and their implications. First, the time correlation function used by HA as a starting expression is not related to the kinetic rate constant by virtue of linear response theory, which is the first important step in relating a t = 0+ limit to a physically measurable rate. Second, a theoretical analysis calls into question a key step in HA's proof which appears not to rely on an exact quantum mechanical identity. The correction of this makes the true t = 0+ limit of HA's QTST different from the RPMD-TST rate expression, but rather equal to the well-known path integral quantum transition state theory rate expression for the case of centroid dividing surface. An alternative quantum rate expression is then formulated starting from the linear response theory and by applying a recently developed formalism of real time dynamics of imaginary time path integrals [S. Jang, A. V. Sinitskiy, and G. A. Voth, J. Chem. Phys. 140, 154103 (2014)]. It is shown that the t → 0+ limit of the new rate expression vanishes in the exact quantum limit.

Effects of dynamical paths on the energy gap and the corrections to the free energy in path integrals of mean-field quantum spin systems

NASA Astrophysics Data System (ADS)

Koh, Yang Wei

2018-03-01

In current studies of mean-field quantum spin systems, much attention is placed on the calculation of the ground-state energy and the excitation gap, especially the latter, which plays an important role in quantum annealing. In pure systems, the finite gap can be obtained by various existing methods such as the Holstein-Primakoff transform, while the tunneling splitting at first-order phase transitions has also been studied in detail using instantons in many previous works. In disordered systems, however, it remains challenging to compute the gap of large-size systems with specific realization of disorder. Hitherto, only quantum Monte Carlo techniques are practical for such studies. Recently, Knysh [Nature Comm. 7, 12370 (2016), 10.1038/ncomms12370] proposed a method where the exponentially large dimensionality of such systems is condensed onto a random potential of much lower dimension, enabling efficient study of such systems. Here we propose a slightly different approach, building upon the method of static approximation of the partition function widely used for analyzing mean-field models. Quantum effects giving rise to the excitation gap and nonextensive corrections to the free energy are accounted for by incorporating dynamical paths into the path integral. The time-dependence of the trace of the time-ordered exponential of the effective Hamiltonian is calculated by solving a differential equation perturbatively, yielding a finite-size series expansion of the path integral. Formulae for the first excited-state energy are proposed to aid in computing the gap. We illustrate our approach using the infinite-range ferromagnetic Ising model and the Hopfield model, both in the presence of a transverse field.

Getting the tail to wag the dog: Incorporating groundwater transport into catchment solute transport models using rank StorAge Selection (rSAS) functions

NASA Astrophysics Data System (ADS)

Harman, C. J.

2015-12-01

Surface water hydrologic models are increasingly used to analyze the transport of solutes through the landscape, such as nitrate. However, many of these models cannot adequately capture the effect of groundwater flow paths, which can have long travel times and accumulate legacy contaminants, releasing them to streams over decades. If these long lag times are not accounted for, the short-term efficacy of management activities to reduce nitrogen loads may be overestimated. Models that adopt a simple 'well-mixed' assumption, leading to an exponential transit time distribution at steady state, cannot adequately capture the broadly skewed nature of groundwater transit times in typical watersheds. Here I will demonstrate how StorAge Selection functions can be used to capture the long lag times of groundwater in a typical subwatershed-based hydrologic model framework typical of models like SWAT, HSPF, HBV, PRMS and others. These functions can be selected and calibrated to reproduce historical data where available, but can also be fitted to the results of a steady-state groundwater transport model like MODFLOW/MODPATH, allowing those results to directly inform the parameterization of an unsteady surface water model. The long tails of the transit time distribution predicted by the groundwater model can then be completely captured by the surface water model. Examples of this application in the Chesapeake Bay watersheds and elsewhere will be given.

Transition Specialists Partner with Students to Turn Dreams into Reality

ERIC Educational Resources Information Center

Flannery, Ann

2013-01-01

Ann Flannery is one of two transition specialists who serve youth and families statewide through the Post-Secondary Transition Program of the Idaho Educational Services for the Deaf and the Blind. In this article she writes that too often her office was seeing graduates coming back to school after failing to find a path to success. They returned…

The Academic Spin-Offs as an Engine of Economic Transition in Eastern Europe. A Path-Dependent Approach

ERIC Educational Resources Information Center

Tchalakov, Ivan; Mitev, Tihomir; Petrov, Venelin

2010-01-01

The paper questions some of the premises in studying academic spin-offs in developed countries, claiming that when taken as characteristics of "academic spin-offs per se," they are of little help in understanding the phenomenon in the Eastern European countries during the transitional and post-transitional periods after 1989. It argues…

A Quantitative Comparative Analysis of Ninth Grade Academies and Graduation Rates in Texas High Schools

ERIC Educational Resources Information Center

Lyons, Guy Kevin

2014-01-01

Students face many challenges in the transition to high school. From pressures of high-stakes testing for graduation to transitioning to the high school environment, many diversions can delay or even stop a student's path to graduation. Ninth-grade students are at a pivotal point in their educational careers, and a successful transition to high…

Energy barrier of bcc-fcc phase transition via the Bain path in Yukawa system

NASA Astrophysics Data System (ADS)

Kiyokawa, Shuji

2018-05-01

In the Yukawa system with the dimensionless screening parameter κ>1.5 , when bcc-fcc transition occurs via Bain path, we show that spontaneous transitions do not occur even if the system temperature reaches the transition point of bcc-fcc because it is necessary to increase once the free energy in the process of transition from bcc to fcc through Bain deformation. Here, we refer the temporary increment of the free energy during Bain deformation as Bain barrier. Since there are the Bain barriers at the transitions between bcc and fcc phases, these phases may coexist as metastable state in the wide region (not a coexistence line) of κ and the coupling constant Γ. We study the excess energy of the system and the free energy difference between bcc and fcc phases by the Monte Carlo method, where the simulation box is divided into a large number of elements with small volume and a particle in the box is restricted be placed in one of these elements. By this method, we can tabulate the values of the interparticle potential and can calculate the internal energy fast and precisely.

Sorry John--try again next year.

PubMed Central

Rowlands, B J

1978-01-01

The new legislation affecting foreign medical graduates has placed several obstacles in the path of potential visitors and immigrants to the United States. Now that there is no longer a shortage of doctors in the USA the need for these new laws is clear, but their implementation has been hasty and has allowed no time for planned transition. If further modifications are made, which may well happen, every effort should be made to disseminate information about new requirements as widely and rapidly as possible. PMID:698665

Critical Behavior of Spatial Evolutionary Game with Altruistic to Spiteful Preferences on Two-Dimensional Lattices

NASA Astrophysics Data System (ADS)

Yang, Bo; Li, Xiao-Teng; Chen, Wei; Liu, Jian; Chen, Xiao-Song

2016-10-01

Self-questioning mechanism which is similar to single spin-flip of Ising model in statistical physics is introduced into spatial evolutionary game model. We propose a game model with altruistic to spiteful preferences via weighted sums of own and opponent's payoffs. This game model can be transformed into Ising model with an external field. Both interaction between spins and the external field are determined by the elements of payoff matrix and the preference parameter. In the case of perfect rationality at zero social temperature, this game model has three different phases which are entirely cooperative phase, entirely non-cooperative phase and mixed phase. In the investigations of the game model with Monte Carlo simulation, two paths of payoff and preference parameters are taken. In one path, the system undergoes a discontinuous transition from cooperative phase to non-cooperative phase with the change of preference parameter. In another path, two continuous transitions appear one after another when system changes from cooperative phase to non-cooperative phase with the prefenrence parameter. The critical exponents v, β, and γ of two continuous phase transitions are estimated by the finite-size scaling analysis. Both continuous phase transitions have the same critical exponents and they belong to the same universality class as the two-dimensional Ising model. Supported by the National Natural Science Foundation of China under Grant Nos. 11121403 and 11504384

A Non-Abelian Geometric Phase for Spin Systems

NASA Astrophysics Data System (ADS)

H M, Bharath; Boguslawski, Matthew; Barrios, Maryrose; Chapman, Michael

Berry's geometric phase has been used to characterize topological phase transitions. Recent works have addressed the question of whether generalizations of Berry's phase to mixed states can be used to characterize topological phase transitions. Berry's phase is essentially the geometric information stored in the overall phase of a quantum system. Here, we show that geometric information is also stored in the higher order spin moments of a quantum spin system. In particular, we show that when the spin vector of a quantum spin system with a spin 1 or higher is transported along a closed path inside the Bloch ball, the tensor of second moments picks up a geometric phase in the form of an SO(3) operator. Geometrically interpreting this phase is tantamount to defining a steradian angle for closed paths inside the Bloch ball. Typically the steradian angle is defined by projecting the path onto the surface of the Bloch ball. However, paths that pass through the center cannot be projected onto the surface. We show that the steradian angles of all paths, including those that pass through the center can be defined by projecting them onto a real projective plane, instead of a sphere. This steradian angle is equal to the geometric phase picked up by a spin system.

On the ion-pair dissociation mechanisms in the small NaCl·(H2 O)6 cluster: A perspective from reaction path search calculations.

PubMed

Takayanagi, Toshiyuki; Nakatomi, Taiki; Yonetani, Yoshiteru

2018-04-20

We performed reaction path search calculations for the NaCl·(H 2 O) 6 cluster using the global reaction route mapping (GRRM) code to understand the atomic-level mechanisms of the NaCl → Na +  + Cl - ionic dissociation induced by water solvents. Low-lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the NaCl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7-3.7 Å and that the NaCl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus' theory.

PubMed

Tiwari, Ambuj; Ensing, Bernd

2016-12-22

Outer sphere electron transfer between two ions in aqueous solution is a rare event on the time scale of first principles molecular dynamics simulations. We have used transition path sampling to generate an ensemble of reactive trajectories of the self-exchange reaction between a pair of Ru 2+ and Ru 3+ ions in water. To distinguish between the reactant and product states, we use as an order parameter the position of the maximally localised Wannier center associated with the transferring electron. This allows us to align the trajectories with respect to the moment of barrier crossing and compute statistical averages over the path ensemble. We compare our order parameter with two typical reaction coordinates used in applications of Marcus theory of electron transfer: the vertical gap energy and the solvent electrostatic potential at the ions.

Paths and wakes of deformable nearly spheroidal rising bubbles close to the transition to path instability

NASA Astrophysics Data System (ADS)

Cano-Lozano, José Carlos; Martínez-Bazán, Carlos; Magnaudet, Jacques; Tchoufag, Joël

2016-09-01

We report on a series of results provided by three-dimensional numerical simulations of nearly spheroidal bubbles freely rising and deforming in a still liquid in the regime close to the transition to path instability. These results improve upon those of recent computational studies [Cano-Lozano et al., Int. J. Multiphase Flow 51, 11 (2013), 10.1016/j.ijmultiphaseflow.2012.11.005; Phys. Fluids 28, 014102 (2016), 10.1063/1.4939703] in which the neutral curve associated with this transition was obtained by considering realistic but frozen bubble shapes. Depending on the dimensionless parameters that characterize the system, various paths geometries are observed by letting an initially spherical bubble starting from rest rise under the effect of buoyancy and adjust its shape to the surrounding flow. These include the well-documented rectilinear axisymmetric, planar zigzagging, and spiraling (or helical) regimes. A flattened spiraling regime that most often eventually turns into either a planar zigzagging or a helical regime is also frequently observed. Finally, a chaotic regime in which the bubble experiences small horizontal displacements (typically one order of magnitude smaller than in the other regimes) is found to take place in a region of the parameter space where no standing eddy exists at the back of the bubble. The discovery of this regime provides evidence that path instability does not always result from a wake instability as previously believed. In each regime, we examine the characteristics of the path, bubble shape, and vortical structure in the wake, as well as their couplings. In particular, we observe that, depending on the fluctuations of the rise velocity, two different vortex shedding modes exist in the zigzagging regime, confirming earlier findings with falling spheres. The simulations also reveal that significant bubble deformations may take place along zigzagging or spiraling paths and that, under certain circumstances, they dramatically alter the wake structure. The instability thresholds that can be inferred from the computations compare favorably with experimental data provided by various sets of recent experiments guaranteeing that the bubble surface is free of surfactants.

Error reduction study employing a pseudo-random binary sequence for use in acoustic pyrometry of gases

NASA Astrophysics Data System (ADS)

Ewan, B. C. R.; Ireland, S. N.

2000-12-01

Acoustic pyrometry uses the temperature dependence of sound speed in materials to measure temperature. This is normally achieved by measuring the transit time for a sound signal over a known path length and applying the material relation between temperature and velocity to extract an "average" temperature. Sources of error associated with the measurement of mean transit time are discussed in implementing the technique in gases, one of the principal causes being background noise in typical industrial environments. A number of transmitted signal and processing strategies which can be used in the area are examined and the expected error in mean transit time associated with each technique is quantified. Transmitted signals included pulses, pure frequencies, chirps, and pseudorandom binary sequences (prbs), while processing involves edge detection and correlation. Errors arise through the misinterpretation of the positions of edge arrival or correlation peaks due to instantaneous deviations associated with background noise and these become more severe as signal to noise amplitude ratios decrease. Population errors in the mean transit time are estimated for the different measurement strategies and it is concluded that PRBS combined with correlation can provide the lowest errors when operating in high noise environments. The operation of an instrument based on PRBS transmitted signals is described and test results under controlled noise conditions are presented. These confirm the value of the strategy and demonstrate that measurements can be made with signal to noise amplitude ratios down to 0.5.

Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

PubMed

Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

2018-04-10

Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of reaction rates and an improved understanding of activated states.

Transitional Patterns of Adolescent Females in Non-Traditional Career Paths.

ERIC Educational Resources Information Center

Ciccocioppo, Anna-Lisa; Stewin, Leonard L.; Madill, Helen M.; Montgomerie, T. Craig; Tovell, Dorothy R.; Armour, Margaret-Ann; Fitzsimmons, George W.

2002-01-01

Examines the factors that affected the career decision-making of adolescent females and young women in undergraduate science, engineering, and technology programs. Qualitative analysis was used to uncover seven themes: transition from high school, educational influences, family influences, academic issues, coursework management, gender issues, and…

Change in Parenting Democracy during the Transition to Adolescence: The Roles of Young Adolescents’ Noncompliance and Mothers’ Perceived Influence

PubMed Central

Morrissey, Rebecca A.; Gondoli, Dawn M.

2012-01-01

SYNOPSIS Objective This study assessed the direct relation between young adolescents’ regulated noncompliance and mothers’ democratic childrearing practices as well as the potential mediating role of mothers’ perceived influence during the transition to adolescence. Design Three years of self-reported adolescent noncompliance, perceived influence, and parenting democracy were gathered from 166 mothers and their firstborn children (55% female), ages 9 – 11 years at time 1. Results Longitudinal path analysis indicated a total effect between adolescents’ regulated noncompliance and higher maternal democracy. In addition, the total effect was mediated by mothers’ perceived influence, such that adolescents’ regulated noncompliance at time 1 was associated with greater perceptions of influence at time 2, which, in turn, was associated with greater maternal democracy at time 3. Conclusions Mothers with young adolescents who resist in a relatively mature, regulated manner tend to have more positive perceptions of their influence on their emerging adolescents’ behavior. In turn, mothers expecting to maintain their influence despite normative adolescent resistance are more likely to use democratic parenting strategies, granting their adolescents more input in decisions. PMID:22844228

A scrutiny of the premise of the Rice-Ramsperger-Kassel-Marcus theory in isomerization reaction of an Ar7-type molecule

NASA Astrophysics Data System (ADS)

Takatsuka, Kazuo; Seko, Chihiro

1996-12-01

The validity of the physical premise of the Rice-Ramsperger-Kassel-Marcus (RRKM) theory is investigated in terms of the classical dynamics of isomerization reaction in Ar7-like molecules (clusters). The passage times of classical trajectories through the potential basins of isomers in the structural transitions are examined. In the high energy region corresponding to the so-called liquidlike phase, remarkable uniformity of the average passage times has been found. That is, the average passage time is characterized only by a basin through which a trajectory is currently passing and, hence, does not depend on the next visiting basins. This behavior is out of accord with the ordinary chemical law in that the ``reaction rates'' do not seem to depend on the height of the individual potential barriers. We ascribe this seemingly strange uniformity to the strong mixing (chaos) lying behind the rate process. That is, as soon as a classical path enters a basin, it gets involved into a chaotic zone in which many paths having different channels are entangled among each other, and effectively (in the statistical sense) loses its memory about which basin it came from and where it should visit next time. This model is verified by confirming that the populations of the lifetime of transition from one basin to others are expressed in exponential functions, which should have very similar exponents to each other in each passing-through basin. The inverse of the exponent is essentially proportional to the average passage time, and consequently brings about the uniformity. These populations set a foundation for the multichannel generalization of the RRKM theory. Two cases of the non-RRKM behaviors have been studied. One is a nonstatistical behavior in the low energy region such as the so-called coexistence phase. The other is the short-time behavior. It is well established [M. Berblinger and C. Schlier, J. Chem. Phys. 101, 4750 (1994)] that in a relatively simple and small system such as H+3, the so-called direct paths, which lead to dissociation before the phase-space mixing is completed, increase the probability of short-time passage. In contrast, we have found in our Ar7-like molecules that trajectories of short passage time are fewer than expected by the statistical theory. It is conceived that somewhat a long time in the initial stage of the isomerization is spent by a trajectory to find its ways out to the next basins.

Saliency Detection via Absorbing Markov Chain With Learnt Transition Probability.

PubMed

Lihe Zhang; Jianwu Ai; Bowen Jiang; Huchuan Lu; Xiukui Li

2018-02-01

In this paper, we propose a bottom-up saliency model based on absorbing Markov chain (AMC). First, a sparsely connected graph is constructed to capture the local context information of each node. All image boundary nodes and other nodes are, respectively, treated as the absorbing nodes and transient nodes in the absorbing Markov chain. Then, the expected number of times from each transient node to all other transient nodes can be used to represent the saliency value of this node. The absorbed time depends on the weights on the path and their spatial coordinates, which are completely encoded in the transition probability matrix. Considering the importance of this matrix, we adopt different hierarchies of deep features extracted from fully convolutional networks and learn a transition probability matrix, which is called learnt transition probability matrix. Although the performance is significantly promoted, salient objects are not uniformly highlighted very well. To solve this problem, an angular embedding technique is investigated to refine the saliency results. Based on pairwise local orderings, which are produced by the saliency maps of AMC and boundary maps, we rearrange the global orderings (saliency value) of all nodes. Extensive experiments demonstrate that the proposed algorithm outperforms the state-of-the-art methods on six publicly available benchmark data sets.

Iodine-frequency-stabilized laser diode and displacement-measuring interferometer based on sinusoidal phase modulation

NASA Astrophysics Data System (ADS)

Duong, Quang Anh; Vu, Thanh Tung; Higuchi, Masato; Wei, Dong; Aketagawa, Masato

2018-06-01

We propose a sinusoidal phase modulation method to achieve both the frequency stabilization of an external-cavity laser diode (ECLD) to an 127I2 saturated absorption transition near 633 nm and displacement measurement using a Mach–Zehnder interferometer. First, the frequency of the ECLD is stabilized to the b 21 hyperfine component of the P(33) 6-3 transition of 127I2 by combining sinusoidal phase modulation by an electro-optic modulator and frequency modulation spectroscopy by chopping the pump beam using an acousto-optic modulator. Even though a small modulation index of m  =  3.768 rad is utilized, a relative frequency stability of 10‑11 order is obtained over a sampling time of 400 s. Secondly, the frequency-stabilized ECLD is applied as a light source to a Mach–Zehnder interferometer. From the two consecutive modulation harmonics (second and third orders) involved in the interferometer signal, the displacement of the moving mirror is determined for four optical path differences (L 0  =  100, 200, 500, and 1000 mm). The measured modulation indexes for the four optical path differences coincide with the designated value (3.768 rad) within 0.5%. Compared with the sinusoidal frequency modulation Michelson interferometer (Vu et al 2016 Meas. Sci. Technol. 27 105201) which was demonstrated by some of the same authors of this paper, the phase modulation Mach–Zhender interferometer could fix the modulation index to a constant value for the four optical path differences. In this report, we discuss the measurement principle, experimental system, and results.

Theoretical studies for excited-state tautomerization in the 7-azaindole-(CH3OH)n (n = 1 and 2) complexes in the gas phase.

PubMed

Fang, Hua; Kim, Yongho

2011-12-01

The excited-state tautomerization of 7-azaindole (7AI) complexes bonded with either one or two methanol molecule(s) was studied by systematic quantum mechanical calculations in the gas phases. Electronic structures and energies for the reactant, transition state (TS), and product were computed at the complete active space self-consistent field (CASSCF) levels with the second-order multireference perturbation theory (MRPT2) to consider the dynamic electron correlation. The time-dependent density functional theory (TDDFT) was also used for comparison. The excited-state double proton transfer (ESDPT) in 7AI-CH(3)OH occurs in a concerted but asynchronous mechanism. Similarly, such paths are also found in the two transition states during the excited-state triple proton transfer (ESTPT) of the 7AI-(CH(3)OH)(2) complex. In the first TS, the pyrrole ring proton first migrated to methanol, while in the second the methanol proton moved first to the pyridine ring. The CASSCF level with the MRPT2 correction showed that the former path was much preferable to the latter, and the ESDPT is much slower than the ESTPT. Additionally, the vibrational-mode enhanced tautomerization in the 7AI-(CH(3)OH)(2) complex was also studied. We found that the excitation of the low-frequency mode shortens the reaction path to increase the tautomerization rate. Overall, most TDDFT methods used in this study predicted different TS structures and barriers from the CASSCF methods with MRPT2 corrections. © 2011 American Chemical Society

Bifurcations on Potential Energy Surfaces of Organic Reactions

PubMed Central

Ess, Daniel H.; Wheeler, Steven E.; Iafe, Robert G.; Xu, Lai; Çelebi-Ölçüm, Nihan; Houk, K. N.

2009-01-01

A single transition state may lead to multiple intermediates or products if there is a post-transition state reaction path bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects control selectivity rather than transition state energetics. This minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions. PMID:18767086

Analysis of energy relaxation kinetics for control of the electron energy distributions in capacitively coupled RF discharges

NASA Astrophysics Data System (ADS)

Lee, Jung Yeol; Verboncoeur, John P.; Lee, Hae June

2018-04-01

The transition of electron energy probability functions (EEPFs) through the change of heating mode is an important issue in plasma science. A well-known example is that the increase of gas pressure, which was analyzed in terms of the ratio of the energy relaxation mean free path to the electrode gap distance, changes the EEPF from bi-Maxwellian to Maxwellian or Druyvesteyn. In this study, a new aspect of the temporal decay of kinetic energy during the energy relaxation time is theoretically analyzed and compared with a particle-in-cell Monte Carlo collision simulation of capacitively coupled plasmas. A fully kinetic description of electron transport and collisions shows drastic changes of EEPFs with the variation of the driving frequency due to the heating mode transition.

Precision spectroscopy of the 2S-4P transition in atomic hydrogen

NASA Astrophysics Data System (ADS)

Maisenbacher, Lothar; Beyer, Axel; Matveev, Arthur; Grinin, Alexey; Pohl, Randolf; Khabarova, Ksenia; Kolachevsky, Nikolai; Hänsch, Theodor W.; Udem, Thomas

2017-04-01

Precision measurements of atomic hydrogen have long been successfully used to extract fundamental constants and to test bound-state QED. However, both these applications are limited by measurements of hydrogen lines other than the very precisely known 1S-2S transition. Moreover, the proton r.m.s.charge radius rp extracted from electronic hydrogen measurements currently disagrees by 4 σ with the much more precise value extracted from muonic hydrogen spectroscopy. We have measured the 2S-4P transition in atomic hydrogen using a cryogenic beam of hydrogen atoms optically excited to the initial 2S state. The first order Doppler shift of the one-photon 2S-4P transition is suppressed by actively stabilized counter-propagating laser beams and time-of-flight resolved detection. Quantum interference between excitation paths can lead to significant line distortions in our system. We use an experimentally verified, simple line shape model to take these distortions into account. With this, we can extract a new value for rp and the Rydberg constant R∞ with comparable accuracy as the combined previous H world data.

Temporal dynamics in dominant runoff sources and flow paths in the Andean Páramo

NASA Astrophysics Data System (ADS)

Correa, Alicia; Windhorst, David; Tetzlaff, Doerthe; Crespo, Patricio; Célleri, Rolando; Feyen, Jan; Breuer, Lutz

2017-07-01

The relative importance of catchment's water provenance and flow paths varies in space and time, complicating the conceptualization of the rainfall-runoff responses. We assessed the temporal dynamics in source areas, flow paths, and age by End Member Mixing Analysis (EMMA), hydrograph separation, and Inverse Transit Time Proxies (ITTPs) estimation within a headwater catchment in the Ecuadorian Andes. Twenty-two solutes, stable isotopes, pH, and electrical conductivity from a stream and 12 potential sources were analyzed. Four end-members were required to satisfactorily represent the hydrological system, i.e., rainfall, spring water, and water from the bottom layers of Histosols and Andosols. Water from Histosols in and near the riparian zone was the highest source contributor to runoff throughout the year (39% for the drier season, 45% for the wetter season), highlighting the importance of the water that is stored in the riparian zone. Spring water contributions to streamflow tripled during the drier season, as evidenced by geochemical signatures that are consistent with deeper flow paths rather than shallow interflow through Andosols. Rainfall exhibited low seasonal variation in this contribution. Hydrograph separation revealed that 94% and 84% is preevent water in the drier and wetter seasons, respectively. From low-flow to high-flow conditions, all the sources increased their contribution except spring water. The relative age of stream water decreased during wetter periods, when the contributing area of the riparian zone expands. The multimethod and multitracer approach enabled to closely study the interchanging importance of flow processes and water source dynamics from an interannual perspective.

Aircraft automatic-flight-control system with inversion of the model in the feed-forward path using a Newton-Raphson technique for the inversion

NASA Technical Reports Server (NTRS)

Smith, G. A.; Meyer, G.; Nordstrom, M.

1986-01-01

A new automatic flight control system concept suitable for aircraft with highly nonlinear aerodynamic and propulsion characteristics and which must operate over a wide flight envelope was investigated. This exact model follower inverts a complete nonlinear model of the aircraft as part of the feed-forward path. The inversion is accomplished by a Newton-Raphson trim of the model at each digital computer cycle time of 0.05 seconds. The combination of the inverse model and the actual aircraft in the feed-forward path alloys the translational and rotational regulators in the feedback path to be easily designed by linear methods. An explanation of the model inversion procedure is presented. An extensive set of simulation data for essentially the full flight envelope for a vertical attitude takeoff and landing aircraft (VATOL) is presented. These data demonstrate the successful, smooth, and precise control that can be achieved with this concept. The trajectory includes conventional flight from 200 to 900 ft/sec with path accelerations and decelerations, altitude changes of over 6000 ft and 2g and 3g turns. Vertical attitude maneuvering as a tail sitter along all axes is demonstrated. A transition trajectory from 200 ft/sec in conventional flight to stationary hover in the vertical attitude includes satisfactory operation through lift-cure slope reversal as attitude goes from horizontal to vertical at constant altitude. A vertical attitude takeoff from stationary hover to conventional flight is also demonstrated.

Genome-scale modeling of the evolutionary path to C4 photosynthesis

NASA Astrophysics Data System (ADS)

Myers, Christopher R.; Bogart, Eli

In C4 photosynthesis, plants maintain a high carbon dioxide level in specialized bundle sheath cells surrounding leaf veins and restrict CO2 assimilation to those cells, favoring CO2 over O2 in competition for Rubisco active sites. In C3 plants, which do not possess such a carbon concentrating mechanism, CO2 fixation is reduced due to this competition. Despite the complexity of the C4 system, it has evolved convergently from more than 60 independent origins in diverse families of plants around the world over the last 30 million years. We study the evolution of the C4 system in a genome-scale model of plant metabolism that describes interacting mesophyll and bundle sheath cells and enforces key nonlinear kinetic relationships. Adapting the zero-temperature string method for simulating transition paths in physics and chemistry, we find the highest-fitness paths connecting C3 and C4 positions in the model's high-dimensional parameter space, and show that they reproduce known aspects of the C3-C4 transition while making additional predictions about metabolic changes along the path. We explore the relationship between evolutionary history and C4 biochemical subtype, and the effects of atmospheric carbon dioxide levels.

MEPSA: minimum energy pathway analysis for energy landscapes.

PubMed

Marcos-Alcalde, Iñigo; Setoain, Javier; Mendieta-Moreno, Jesús I; Mendieta, Jesús; Gómez-Puertas, Paulino

2015-12-01

From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: pagomez@cbm.csic.es. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Weinberg propagator of a free massive particle with an arbitrary spin from the BFV-BRST path integral

NASA Astrophysics Data System (ADS)

Zima, V. G.; Fedoruk, S. O.

1999-11-01

The transition amplitude is obtained for a free massive particle of arbitrary spin by calculating the path integral in the index-spinor formulation within the BFV-BRST approach. No renormalizations of the path integral measure were applied. The calculation has given the Weinberg propagator written in the index-free form by the use of an index spinor. The choice of boundary conditions on the index spinor determines the holomorphic or antiholomorphic representation for the canonical description of particle/antiparticle spin.

Nucleation and hysteresis of vapor-liquid phase transitions in confined spaces: effects of fluid-wall interaction.

PubMed

Men, Yumei; Yan, Qingzhao; Jiang, Guangfeng; Zhang, Xianren; Wang, Wenchuan

2009-05-01

In this work, we propose a method to stabilize a nucleus in the framework of lattice density-functional theory (LDFT) by imposing a suitable constraint. Using this method, the shape of critical nucleus and height of the nucleation barrier can be determined without using a predefined nucleus as input. As an application of this method, we study the nucleation behavior of vapor-liquid transition in nanosquare pores with infinite length and relate the observed hysteresis loop on an adsorption isotherm to the nucleation mechanism. According to the dependence of hysteresis and the nucleation mechanism on the fluid-wall interaction, w , in this work, we have classified w into three regions ( w>0.9 , 0.1< or =w< or =0.9 , and w<0.1 ), which are denoted as strongly, moderately, and weakly attractive fluid-wall interaction, respectively. The dependence of hysteresis on the fluid-wall interaction is interpreted by the different nucleation mechanisms. Our constrained LDFT calculations also show that the different transition paths may induce different nucleation behaviors. The transition path dependence should be considered if morphological transition of nuclei exists during a nucleation process.

A path integral approach to the full Dicke model with dipole-dipole interaction

NASA Astrophysics Data System (ADS)

Aparicio Alcalde, M.; Stephany, J.; Svaiter, N. F.

2011-12-01

We consider the full Dicke spin-boson model composed by a single bosonic mode and an ensemble of N identical two-level atoms with different couplings for the resonant and anti-resonant interaction terms, and incorporate a dipole-dipole interaction between the atoms. Assuming that the system is in thermal equilibrium with a reservoir at temperature β-1, we compute the free energy in the thermodynamic limit N → ∞ in the saddle-point approximation to the path integral and determine the critical temperature for the super-radiant phase transition. In the zero temperature limit, we recover the critical coupling of the quantum phase transition, presented in the literature.

Advective and Mixing Time Scales for Transport of Denmark Strait Overflow Water from the Labrador Sea to the Western Subtropical Atlantic Ocean Determined from 129I, CFC and Hydrographic Time Series Observations

NASA Astrophysics Data System (ADS)

Smethie, W. M., Jr.; Smith, J.; Curry, R. G.; Yashayaev, I.; Azetsu-Scott, K.

2016-02-01

129I released to the North Sea from two nuclear fuel reprocessing plants is transported through the Nordic Seas and the Arctic Ocean and is entering the deep North Atlantic, predominantly in dense Denmark Strait Overflow Water (DSOW). CFCs enter the surface ocean and also become incorporated in DSOW. Measurements of temperature, salinity, CFCs and 129I have been made at least annually along WOCE/CLIVAR line AR7W in the Labrador Sea from the mid 1990s to present, along Line W extending from the continental slope southeast of Cape Cod toward Bermuda from 2003 to 2014, and along a single occupation of a line extending from Bermuda southeast across the Bermuda Rise in 2010. The measurements in the Labrador Sea were used as input to DSOW flowing from there to the subtropical western Atlantic Ocean. We compared the temporal changes along Line W to the temporal changes along the AR7W line and applied the boundary current model of Waugh and Hall (J. Phys. Oceanogr. 35,1538-1552, 2005) to the Line W and Bermuda Rise line observations to determine the transit time of DSOW transported to Line W in the Deep Western Boundary Current (DWBC) and transported to the southeastern flank of Bermuda via interior flow paths. The lateral mixing time scale along these two flow paths was also estimated with this model. CFC-11 and 129I increase monotonically in the DSOW in the Labrador Sea and salinity oscillates on a 5-year cycle. The boundary current model reproduces all of these trends. The transit time and lateral mixing time constant for DSOW transported to Line W are 7 years (mean flow velocity of 2.1 cm/sec) and 3-6 years, respectively, and for DSOW transported to the southeast flank of Bermuda are 6-10 years and 2-5 years.

MD modeling of screw dislocation influence upon initiation and mechanism of BCC-HCP polymorphous transition in iron

NASA Astrophysics Data System (ADS)

Dremov, V. V.; Ionov, G. V.; Sapozhnikov, F. A.; Smirnov, N. A.; Karavaev, A. V.; Vorobyova, M. A.; Ryzhkov, M. V.

2015-09-01

The present work is devoted to classical molecular dynamics investigation into microscopic mechanisms of the bcc-hcp transition in iron. The interatomic potential of EAM type used in the calculations was tested for the capability to reproduce ab initio data on energy evolution along the bcc-hcp transformation path (Burgers deformation + shuffe) and then used in the large-scale MD simulations. The large-scale simulations included constant volume deformation along the Burgers path to study the origin and nature of the plasticity, hydrostatic volume compression of defect free samples above the bcc to hcp transition threshold to observe the formation of new phase embryos, and the volume compression of samples containing screw dislocations to study the effect of the dislocations on the probability of the new phase critical embryo formation. The volume compression demonstrated high level of metastability. The transition starts at pressure much higher than the equilibrium one. Dislocations strongly affect the probability of the critical embryo formation and significantly reduce the onset pressure of transition. The dislocations affect also the resulting structure of the samples upon the transition. The formation of layered structure is typical for the samples containing the dislocations. The results of the simulations were compared with the in-situ experimental data on the mechanism of the bcc-hcp transition in iron.

Quantum transport in graphene in presence of strain-induced pseudo-Landau levels

NASA Astrophysics Data System (ADS)

Settnes, Mikkel; Leconte, Nicolas; Barrios-Vargas, Jose E.; Jauho, Antti-Pekka; Roche, Stephan

2016-09-01

We report on mesoscopic transport fingerprints in disordered graphene caused by strain-field induced pseudomagnetic Landau levels (pLLs). Efficient numerical real space calculations of the Kubo formula are performed for an ordered network of nanobubbles in graphene, creating pseudomagnetic fields up to several hundreds of Tesla, values inaccessible by real magnetic fields. Strain-induced pLLs yield enhanced scattering effects across the energy spectrum resulting in lower mean free path and enhanced localization effects. In the vicinity of the zeroth order pLL, we demonstrate an anomalous transport regime, where the mean free paths increases with disorder. We attribute this puzzling behavior to the low-energy sub-lattice polarization induced by the zeroth order pLL, which is unique to pseudomagnetic fields preserving time-reversal symmetry. These results, combined with the experimental feasibility of reversible deformation fields, open the way to tailor a metal-insulator transition driven by pseudomagnetic fields.

Emerging Adults With Type 1 Diabetes: A Comparison to Peers Without Diabetes

PubMed Central

Helgeson, Vicki S.; Reynolds, Kerry A.; Becker, Dorothy J.; Siminerio, Linda M.; Escobar, Oscar

2013-01-01

Objective This longitudinal study compared emerging adults with and without type 1 diabetes on life path decisions, health behaviors, and psychological well-being during the transition out of high school. Methods Administered questionnaires during the senior year of high school and 1 year later to 117 emerging adults with diabetes and 122 emerging adults without diabetes. Comparisons were conducted with respect to health status, sex, and school status. Results Those with and without diabetes chose similar life paths and engaged in similar levels of risky behaviors, but disturbed sleep increased for males with diabetes only. Having diabetes was not associated with depressive symptoms, loneliness, or bulimic symptoms, but was associated with lower life satisfaction and lower life purpose over time. Conclusions Emerging adults with and without diabetes fare similarly on most dimensions studied during the first year out of high school. PMID:23475831

From the physics of interacting polymers to optimizing routes on the London Underground

PubMed Central

Yeung, Chi Ho; Saad, David; Wong, K. Y. Michael

2013-01-01

Optimizing paths on networks is crucial for many applications, ranging from subway traffic to Internet communication. Because global path optimization that takes account of all path choices simultaneously is computationally hard, most existing routing algorithms optimize paths individually, thus providing suboptimal solutions. We use the physics of interacting polymers and disordered systems to analyze macroscopic properties of generic path optimization problems and derive a simple, principled, generic, and distributed routing algorithm capable of considering all individual path choices simultaneously. We demonstrate the efficacy of the algorithm by applying it to: (i) random graphs resembling Internet overlay networks, (ii) travel on the London Underground network based on Oyster card data, and (iii) the global airport network. Analytically derived macroscopic properties give rise to insightful new routing phenomena, including phase transitions and scaling laws, that facilitate better understanding of the appropriate operational regimes and their limitations, which are difficult to obtain otherwise. PMID:23898198

From the physics of interacting polymers to optimizing routes on the London Underground.

PubMed

Yeung, Chi Ho; Saad, David; Wong, K Y Michael

2013-08-20

Optimizing paths on networks is crucial for many applications, ranging from subway traffic to Internet communication. Because global path optimization that takes account of all path choices simultaneously is computationally hard, most existing routing algorithms optimize paths individually, thus providing suboptimal solutions. We use the physics of interacting polymers and disordered systems to analyze macroscopic properties of generic path optimization problems and derive a simple, principled, generic, and distributed routing algorithm capable of considering all individual path choices simultaneously. We demonstrate the efficacy of the algorithm by applying it to: (i) random graphs resembling Internet overlay networks, (ii) travel on the London Underground network based on Oyster card data, and (iii) the global airport network. Analytically derived macroscopic properties give rise to insightful new routing phenomena, including phase transitions and scaling laws, that facilitate better understanding of the appropriate operational regimes and their limitations, which are difficult to obtain otherwise.

Measurements in a Transitional Boundary Layer Under Low-Pressure Turbine Airfoil Conditions

NASA Technical Reports Server (NTRS)

Simon, Terrence W.; Qiu, Songgang; Yuan, Kebiao; Ashpis, David (Technical Monitor); Simon, Fred (Technical Monitor)

2000-01-01

This report presents the results of an experimental study of transition from laminar to turbulent flow in boundary layers or in shear layers over separation zones on a convex-curved surface which simulates the suction surface of a low-pressure turbine airfoil. Flows with various free-stream turbulence intensity (FSTI) values (0.5%, 2.5% and 10%), and various Reynolds numbers (50,000, 100,000 200,000 and 300,000) are investigated. Reynold numbers in the present study are based on suction surface length and passage exit mean velocity. Flow separation followed by transition within the separated flow region is observed for the lower-Re cases at each of the FSTI levels. At the highest Reynolds numbers and at elevated FSn, transition of the attached boundary layer begins before separation, and the separation zone is small. Transition proceeds in the shear layer over the separation bubble. For both the transitional boundary layer and the transitional shear layer, mean velocity, turbulence intensity and intermittency (the fraction of the time the flow is turbulent) distributions are presented. The present data are compared to published distribution models for bypass transition, intermittency distribution through transition, transition start position, and transition length. A model developed for transition of separated flows is shown to adequately predict the location of the beginning of transition, for these cases, and a model developed for transitional boundary layer flows seems to adequately predict the path of intermittency through transition when the transition start and end are known. These results are useful for the design of low-pressure turbine stages which are known to operate under conditions replicated by these tests.

An Alternative Humans to Mars Approach: Reducing Mission Mass with Multiple Mars Flyby Trajectories and Minimal Capability Investments

NASA Technical Reports Server (NTRS)

Whitley, Ryan J.; Jedrey, Richard; Landau, Damon; Ocampo, Cesar

2015-01-01

Mars flyby trajectories and Earth return trajectories have the potential to enable lower- cost and sustainable human exploration of Mars. Flyby and return trajectories are true minimum energy paths with low to zero post-Earth departure maneuvers. By emplacing the large crew vehicles required for human transit on these paths, the total fuel cost can be reduced. The traditional full-up repeating Earth-Mars-Earth cycler concept requires significant infrastructure, but a Mars only flyby approach minimizes mission mass and maximizes opportunities to build-up missions in a stepwise manner. In this paper multiple strategies for sending a crew of 4 to Mars orbit and back are examined. With pre-emplaced assets in Mars orbit, a transit habitat and a minimally functional Mars taxi, a complete Mars mission can be accomplished in 3 SLS launches and 2 Mars Flyby's, including Orion. While some years are better than others, ample opportunities exist within a given 15-year Earth-Mars alignment cycle. Building up a mission cadence over time, this approach can translate to Mars surface access. Risk reduction, which is always a concern for human missions, is mitigated by the use of flybys with Earth return (some of which are true free returns) capability.

Detailed Jaramillo field reversals recorded in lake sediments from Armenia - Lower mantle influence on the magnetic field revisited

NASA Astrophysics Data System (ADS)

Kirscher, U.; Winklhofer, M.; Hackl, M.; Bachtadse, V.

2018-02-01

While it is well established that the Earth's magnetic field is generated by a self sustaining dynamo that reversed its polarity at irregular intervals in the geological past, the very mechanisms causing field reversals remain obscure. Paleomagnetic reconstructions of polarity transitions have been essential for physically constraining the underlying mechanisms in terms of time scale, but thus far remain ambiguous with regard to the transitional field geometry. Here we present new paleomagnetic records from a rapidly deposited lacustrine sediment sequence with extraordinarily stable paleomagnetic signals, which has captured in unprecedented detail the bottom (reverse to normal: R-N) and top (normal to reverse: N-R) transitions of the Jaramillo subchron (at 1.072 Ma and at 0.988 Ma). The obtained virtual geomagnetic pole (VGP) path indicates an oscillatory transitional field behavior with four abrupt transequatorial precursory jumps across the Pacific. The distribution of VGP positions indicates regions of preferred occurrence. Our results are in agreement with previously proposed bands of transitional VGP occurrence over the Americas and Australia/northwest Pacific. Additionally, our VGP positions seem to avoid large low shear velocity provinces (LLSVPs) above the core mantle boundary (CMB). Thus, our data supports the idea that the transitional field geometry is controlled by heat flux heterogeneities at the CMB linked to LLSVPs.

Efficient collective influence maximization in cascading processes with first-order transitions

PubMed Central

Pei, Sen; Teng, Xian; Shaman, Jeffrey; Morone, Flaviano; Makse, Hernán A.

2017-01-01

In many social and biological networks, the collective dynamics of the entire system can be shaped by a small set of influential units through a global cascading process, manifested by an abrupt first-order transition in dynamical behaviors. Despite its importance in applications, efficient identification of multiple influential spreaders in cascading processes still remains a challenging task for large-scale networks. Here we address this issue by exploring the collective influence in general threshold models of cascading process. Our analysis reveals that the importance of spreaders is fixed by the subcritical paths along which cascades propagate: the number of subcritical paths attached to each spreader determines its contribution to global cascades. The concept of subcritical path allows us to introduce a scalable algorithm for massively large-scale networks. Results in both synthetic random graphs and real networks show that the proposed method can achieve larger collective influence given the same number of seeds compared with other scalable heuristic approaches. PMID:28349988

Efficient collective influence maximization in cascading processes with first-order transitions

NASA Astrophysics Data System (ADS)

Pei, Sen; Teng, Xian; Shaman, Jeffrey; Morone, Flaviano; Makse, Hernán A.

2017-03-01

In many social and biological networks, the collective dynamics of the entire system can be shaped by a small set of influential units through a global cascading process, manifested by an abrupt first-order transition in dynamical behaviors. Despite its importance in applications, efficient identification of multiple influential spreaders in cascading processes still remains a challenging task for large-scale networks. Here we address this issue by exploring the collective influence in general threshold models of cascading process. Our analysis reveals that the importance of spreaders is fixed by the subcritical paths along which cascades propagate: the number of subcritical paths attached to each spreader determines its contribution to global cascades. The concept of subcritical path allows us to introduce a scalable algorithm for massively large-scale networks. Results in both synthetic random graphs and real networks show that the proposed method can achieve larger collective influence given the same number of seeds compared with other scalable heuristic approaches.

Unlabored system motion by specially conditioned electromagnetic fields in higher dimensional realms

NASA Astrophysics Data System (ADS)

David Froning, H.; Meholic, Gregory V.

2010-01-01

This third of three papers explores the possibility of swift, stress-less system transitions between slower-than-light and faster-than-light speeds with negligible net expenditure of system energetics. The previous papers derived a realm of higher dimensionality than 4-D spacetime that enabled such unlabored motion; and showed that fields that could propel and guide systems on unlabored paths in the higher dimensional realm must be fields that have been conditioned to SU(2) (or higher) Lie group symmetry. This paper shows that the system's surrounding vacuum dielectric ɛμ, within the higher dimensional realm's is a vector (not scalar) quantity with fixed magnitude ɛ0μ0 and changing direction within the realm with changing system speed. Thus, ɛμ generated by the system's EM field must remain tuned to vacuum ɛ0μ0 in both magnitude and direction during swift, unlabored system transitions between slower and faster than light speeds. As a result, the system's changing path and speed is such that the magnitude of the higher dimensional realm's ɛ0μ0 is not disturbed. And it is shown that a system's flight trajectories associated with its swift, unlabored transitions between zero and infinite speed can be represented by curved paths traced-out within the higher dimensional realm.

Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape

PubMed Central

Yu, Hao; Dee, Derek R.; Liu, Xia; Brigley, Angela M.; Sosova, Iveta; Woodside, Michael T.

2015-01-01

The timescale for the microscopic dynamics of proteins during conformational transitions is set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and aggregation in many diseases, it has proven challenging to measure D for these processes because of their heterogeneity. We used single-molecule force spectroscopy to overcome these challenges and determine D for misfolding of the prion protein PrP. Observing directly the misfolding of individual dimers into minimal aggregates, we reconstructed the energy landscape governing nonnative structure formation. Remarkably, rather than displaying multiple pathways, as typically expected for aggregation, PrP dimers were funneled into a thermodynamically stable misfolded state along a single pathway containing several intermediates, one of which blocked native folding. Using Kramers’ rate theory, D was found to be 1,000-fold slower for misfolding than for native folding, reflecting local roughening of the misfolding landscape, likely due to increased internal friction. The slow diffusion also led to much longer transit times for barrier crossing, allowing transition paths to be observed directly for the first time to our knowledge. These results open a new window onto the microscopic mechanisms governing protein misfolding. PMID:26109573

Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape.

PubMed

Yu, Hao; Dee, Derek R; Liu, Xia; Brigley, Angela M; Sosova, Iveta; Woodside, Michael T

2015-07-07

The timescale for the microscopic dynamics of proteins during conformational transitions is set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and aggregation in many diseases, it has proven challenging to measure D for these processes because of their heterogeneity. We used single-molecule force spectroscopy to overcome these challenges and determine D for misfolding of the prion protein PrP. Observing directly the misfolding of individual dimers into minimal aggregates, we reconstructed the energy landscape governing nonnative structure formation. Remarkably, rather than displaying multiple pathways, as typically expected for aggregation, PrP dimers were funneled into a thermodynamically stable misfolded state along a single pathway containing several intermediates, one of which blocked native folding. Using Kramers' rate theory, D was found to be 1,000-fold slower for misfolding than for native folding, reflecting local roughening of the misfolding landscape, likely due to increased internal friction. The slow diffusion also led to much longer transit times for barrier crossing, allowing transition paths to be observed directly for the first time to our knowledge. These results open a new window onto the microscopic mechanisms governing protein misfolding.

The Senior Year: Culminating Experiences and Transitions

ERIC Educational Resources Information Center

Hunter, Mary Stuart, Ed.; Keup, Jennifer R., Ed.; Kinzie, Jillian, Ed.; Maietta, Heather, Ed.

2012-01-01

Increasing pressures on colleges and universities to ensure degree completion and job placement as measures of success make it imperative that the path to graduation is clear and that seniors receive the support needed to earn a degree and make a successful transition to life beyond college. This new edited collection describes today's college…

Attachment, Well-Being, and College Senior Concerns about the Transition out of College

ERIC Educational Resources Information Center

Lane, Joel A.

2016-01-01

This study examined the relationships among attachment, psychological well-being (PWB), life satisfaction, and concerns about the transition out of college among a sample of college seniors. A path analysis was conducted predicting that PWB and life satisfaction would mediate the relationships between attachment and 3 types of graduation…

Youth Transition to Employment in Vietnam: A Vulnerable Path

ERIC Educational Resources Information Center

Tran, Thi Tuyet

2018-01-01

Literature suggests that educational attainment is one of the significant factors affecting youth transition to work. The process of capital accumulation through education is suggested as the key marker of social inclusion and exclusion. This paper compares the educational attainment among youth in Vietnam with their status in employment. It uses…

Technologies and Species Transitions: Polanyi, on a Path to Posthumanity?

ERIC Educational Resources Information Center

Doede, Robert

2011-01-01

Polanyi and Transhumanism both place technologies in pivotal roles in bringing about "Homo sapiens"' species transitions. The question is asked whether Polanyi's emphasis on the role of technology in "Homo sapiens"' rise out of mute beasthood indicates that he might have been inclined to embrace the Transhumanist vision of "Homo sapiens"'…

A Strategic Enrollment Management Approach to Studying High School Student Transition to a Two-Year College

ERIC Educational Resources Information Center

Wang, Yan; Ye, Feifei; Pilarzyk, Tom

2014-01-01

This study used a strategic enrollment management (SEM) approach to studying high school students' transition to a two-year college and their initial college success. Path analyses suggested two important findings: (a) clear career choices among students, family influence, academic preparedness, and college recruitment efforts predicted earlier…

Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.

PubMed

Banerjee, Rahul; Cukier, Robert I

2014-03-20

Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformers. In the MD trajectory, only four of the eight backbone dihedrals exhibit bistable behavior. Defining a conformer as the string XXXX with X = "+" or "-" denoting, respectively, positive or negative values of a given dihedral angle and obtaining the populations of these conformers shows that only four conformers are highly populated, implying a strong correlation among these dihedrals. Clustering in dihedral space to construct the MSM finds the same four bistable dihedral angles. These state populations are very similar to those found directly from the MD trajectory. TPT is used to obtain pathways, parametrized by committor values, in dihedral state space that are followed in transitioning from closed to open states. Pathway costs are estimated by introducing a kinetics-based procedure that orders pathways from least (shortest) to greater cost paths. The least costly pathways in dihedral space are found to only involve the same XXXX set of dihedral angles, and the conformers accessed in the closed to open transition pathways are identified. For these major pathways, a correlation between reaction path progress (committors) and the end-to-end distance is identified. A dihedral space principal component analysis of the MD trajectory shows that the first three modes capture most of the overall fluctuation, and pick out the same four dihedrals having essentially all the weight in those modes. A MSM based on root-mean-square backbone clustering was also carried out, with good agreement found with dihedral clustering for the static information, but with results that differ significantly for the pathway analysis.

Proceedings of the First Landscape State-and-Transition Simulation Modeling Conference, June 14–16, 2011, Portland, Oregon

Treesearch

Becky K. Kerns; Ayn J. Shlisky; Colin J. Daniel

2012-01-01

The first ever Landscape State-and-Transition Simulation Modeling Conference was held from June 14–16, 2011, in Portland Oregon. The conference brought together over 70 users of state-and-transition simulation modeling tools—the Vegetation Dynamics Development Tool (VDDT), the Tool for Exploratory Landscape Analysis (TELSA) and the Path Landscape Model. The goal of the...

Weak values, 'negative probability', and the uncertainty principle

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

Sokolovski, D.

2007-10-15

A quantum transition can be seen as a result of interference between various pathways (e.g., Feynman paths), which can be labeled by a variable f. An attempt to determine the value of f without destroying the coherence between the pathways produces a weak value of f. We show f to be an average obtained with an amplitude distribution which can, in general, take negative values, which, in accordance with the uncertainty principle, need not contain information about the actual range of f which contributes to the transition. It is also demonstrated that the moments of such alternating distributions have amore » number of unusual properties which may lead to a misinterpretation of the weak-measurement results. We provide a detailed analysis of weak measurements with and without post-selection. Examples include the double-slit diffraction experiment, weak von Neumann and von Neumann-like measurements, traversal time for an elastic collision, phase time, and local angular momentum.« less

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Wang, Ting; Plecháč, Petr

2017-12-01

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

Transitions to improved confinement regimes induced by changes in heating in zero-dimensional models for tokamak plasmas

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

Zhu, H.; Chapman, S. C.; Max Planck Institute for the Physics of Complex Systems, Dresden

2014-06-15

It is shown that rapid substantial changes in heating rate can induce transitions to improved energy confinement regimes in zero-dimensional models for tokamak plasma phenomenology. We examine for the first time the effect of step changes in heating rate in the models of Kim and Diamond [Phys. Rev. Lett. 90, 185006 (2003)] and Malkov and Diamond [Phys. Plasmas 16, 012504 (2009)], which nonlinearly couple the evolving temperature gradient, micro-turbulence, and a mesoscale flow; and in the extension of Zhu et al. [Phys. Plasmas 20, 042302 (2013)], which couples to a second mesoscale flow component. The temperature gradient rises, as doesmore » the confinement time defined by analogy with the fusion context, while micro-turbulence is suppressed. This outcome is robust against variation of heating rise time and against introduction of an additional variable into the model. It is also demonstrated that oscillating changes in heating rate can drive the level of micro-turbulence through a period-doubling path to chaos, where the amplitude of the oscillatory component of the heating rate is the control parameter.« less

Exact transition probabilities in a 6-state Landau–Zener system with path interference

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

Sinitsyn, Nikolai A.

2015-04-23

In this paper, we identify a nontrivial multistate Landau–Zener (LZ) model for which transition probabilities between any pair of diabatic states can be determined analytically and exactly. In the semiclassical picture, this model features the possibility of interference of different trajectories that connect the same initial and final states. Hence, transition probabilities are generally not described by the incoherent successive application of the LZ formula. Finally, we discuss reasons for integrability of this system and provide numerical tests of the suggested expression for the transition probability matrix.

Spring operated accelerator and constant force spring mechanism therefor

NASA Technical Reports Server (NTRS)

Shillinger, G. L., Jr. (Inventor)

1977-01-01

A spring assembly consisting of an elongate piece of flat spring material formed into a spiral configuration and a free running spool in circumscribing relation to which this spring is disposed was developed. The spring has a distal end that is externally accessible so that when the distal end is drawn along a path, the spring unwinds against a restoring force present in the portion of the spring that resides in a transition region between a relatively straight condition on the path and a fully wound condition on the spool. When the distal end is released, the distal end is accelerated toward the spool by the force existing at the transition region which force is proportional to the cross-sectional area of the spring.

Study of the De-Icing Properties of the ASDE-3 Rotodome.

DTIC Science & Technology

1982-04-01

Heat Transfer Coefficients ........................... 3 -18 3.2.3 Prediction of De-Icing Capability ...... 3 -23 3.2.4 Calculation of Mean DIA & PATH...kVA 3 -31 N NUL =ti: :6 i ::p :: %:::::28 -R) [ eN 23,100t Averaged for Laminar & Turbulent Regimes. SAssuming a transition from Laminar to. Turbulent...Calculation of Mean Dia .& Path Length for Roof Mean Path Length for Roof: y 4r 4x 9 3.82 ft 3 x 7 1 2(92 3.8221/2 1 = 2(92 - 3.822 = 8.15 ft x 2 16.3 ft 16.3

Exploring the role of mixing between subsurface flow paths on transit time distributions using a Lagrangian model

NASA Astrophysics Data System (ADS)

Zehe, Erwin; Jackisch, Conrad; Rodriguez, Nicolas; Klaus, Julian

2017-04-01

Only a minute amount of global fresh water is stored in the unsaturated zone. Yet this tiny compartment controls soil microbial activity and associated trace gas emissions, transport and transformations of contaminants, plant productivity, runoff generation and groundwater recharge. To date, the processes controlling renewal and age of different fractions of the soil water stock are far from being understood. Current theories and process concepts were largely inferred either from over-simplified laboratory experiments, or non-exhaustive point observations and tracer data in the field. Tracer data provide key but yet integrated information about the distribution of travel times of the tracer molecules to a certain depth or on their travel depth distribution within a given time. We hence are able to observe the "effect" of soil structure i.e. partitioning of infiltrating water between fast preferential and slow flow paths and imperfect subsequent mixing between these flow paths in the subsurface and the related plant water uptake. However, we are not able to study the "cause" - because technologies for in-situ observations of flow, flow path topology and exchange processes at relevant interfaces have up to now not been at hand. In the present study we will make use of a Lagrangian model for subsurface water dynamics to explore how subsurface heterogeneity and mixing among different storage fractions affects residence time distribution in the unsaturated zone in a forward approach. Soil water is represented by particles of constant mass, which travel according to the Itô form of the Fokker Planck equation. The model concept builds on established soil physics by estimating the drift velocity and the diffusion term based on the soil water characteristics. The model has been shown to simulate capillary driven soil moisture dynamics in good accordance with a) the Richards equation and b) observed soil moisture data in different soil. The particle model may furthermore account for preferential non equilibrium infiltration in a straightforward manner by treating event water as different type of particle, which travel initially in a macropore/ coarse pore fraction and experience a slow diffusive mixing with the pre-event water particles within a characteristic mixing time. In the present study we will particularly use the last approach in combination with artificial tracer data and stable isotopes to explore how different assumptions on mixing between different flow paths affect the travel time and residence time distributions of water particles in different fractions of the pore space.

Time optimal paths for high speed maneuvering

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

Reister, D.B.; Lenhart, S.M.

1993-01-01

Recent theoretical results have completely solved the problem of determining the minimum length path for a vehicle with a minimum turning radius moving from an initial configuration to a final configuration. Time optimal paths for a constant speed vehicle are a subset of the minimum length paths. This paper uses the Pontryagin maximum principle to find time optimal paths for a constant speed vehicle. The time optimal paths consist of sequences of axes of circles and straight lines. The maximum principle introduces concepts (dual variables, bang-bang solutions, singular solutions, and transversality conditions) that provide important insight into the nature ofmore » the time optimal paths. We explore the properties of the optimal paths and present some experimental results for a mobile robot following an optimal path.« less

It's My Life! Career Paths for Young Women in Transition. Coordinator's Handbook.

ERIC Educational Resources Information Center

Florio, Carol; And Others

This document is the coordinator's handbook for a four-day workshop for young women in transition from high school to two-year colleges. The program covers career information, self-awareness and skills assessment (with special regard for mathematics), the many roles of women, and decision making and planning. It includes large- and small-group…

Suicidal or Self-Harming Ideation in Military Personnel Transitioning to Civilian Life

ERIC Educational Resources Information Center

Mansfield, Alyssa J.; Bender, Randall H.; Hourani, Laurel L.; Larson, Gerald E.

2011-01-01

Suicides have markedly increased among military personnel in recent years. We used path analysis to examine factors associated with suicidal/self-harming ideation among male Navy and Marine Corps personnel transitioning to civilian life. Roughly 7% of men (Sailors = 5.3%, Marines = 9.0%) reported ideation during the previous 30 days. Results…

Approaches to incorporating climate change effects in state and transition simulation models of vegetation

Treesearch

Becky K. Kerns; Miles A. Hemstrom; David Conklin; Gabriel I. Yospin; Bart Johnson; Dominique Bachelet; Scott Bridgham

2012-01-01

Understanding landscape vegetation dynamics often involves the use of scientifically-based modeling tools that are capable of testing alternative management scenarios given complex ecological, management, and social conditions. State-and-transition simulation model (STSM) frameworks and software such as PATH and VDDT are commonly used tools that simulate how landscapes...

Lost in Transition: Building a Better Path from School to College and Careers

ERIC Educational Resources Information Center

Bottoms, Gene; Young, Marna

2008-01-01

In 2005 and 2006, the "High Schools That Work" ("HSTW") program of the Southern Regional Education Board (SREB) and the College and Career Transitions Initiative of the League for Innovation in the Community College (League) facilitated a series of 15 state-level forums aimed at identifying ways to foster collaboration between secondary and…

Architecting Technology Transition Pathways: Insights from the Military Tactical Network Upgrade

DTIC Science & Technology

2015-05-08

effective transition path design...1. Introduction  Today’s engineering systems are increasingly complex and interdependent. As part of this trend, the luxury of green‐field design...operations can’t take effect until all or most of the airframes have the new equipment. Since the cost‐burden will be unequally born by airlines

Is History Destiny? Resources, Transitions and Child Education Attainments in Canada. Final Report

ERIC Educational Resources Information Center

Hoddinott, John; Lethbridge, Lynn; Phipps, Shelley

2002-01-01

This paper examines three inter-related issues: whether past levels of resources, context and opportunity structures carry long-term consequences for subsequent child attainments and behaviours; whether shocks, or transition events, alter the path of these outcomes in a positive or negative fashion; and what role can be played by policy…

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

PubMed Central

2015-01-01

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled. PMID:25516726

Theory of Disk-to-Vesicle Transformation

NASA Astrophysics Data System (ADS)

Li, Jianfeng; Shi, An-Chang

2009-03-01

Self-assembled membranes from amphiphilic molecules, such as lipids and block copolymers, can assume a variety of morphologies dictated by energy minimization of system. The membrane energy is characterized by a bending modulus (κ), a Gaussian modulus (κG), and the line tension (γ) of the edge. Two basic morphologies of membranes are flat disks that minimize the bending energy at the cost of the edge energy, and enclosed vesicles that minimize the edge energy at the cost of bending energy. In our work, the transition from disk to vesicle is studied theoretically using the string method, which is designed to find the minimum energy path (MEP) or the most probable transition path between two local minima of an energy landscape. Previous studies of disk-to-vesicle transition usually approximate the transitional states by a series of spherical cups, and found that the spherical cups do not correspond to stable or meta-stable states of the system. Our calculation demonstrates that the intermediate shapes along the MEP are very different from spherical cups. Furthermore, some of these transitional states can be meta-stable. The disk-to-vesicle transition pathways are governed by two scaled parameters, κG/κ and γR0/4κ, where R0 is the radius of the disk. In particular, a meta-stable intermediate state is predicted, which may correspond to the open morphologies observed in experiments and simulations.

Computational study of the melting-freezing transition in the quantum hard-sphere system for intermediate densities. II. Structural features.

PubMed

Sesé, Luis M; Bailey, Lorna E

2007-04-28

The structural features of the quantum hard-sphere system in the region of the fluid-face-centered-cubic-solid transition, for reduced number densities 0.45

Analytical techniques of pilot scanning behavior and their application

NASA Technical Reports Server (NTRS)

Harris, R. L., Sr.; Glover, B. J.; Spady, A. A., Jr.

1986-01-01

The state of the art of oculometric data analysis techniques and their applications in certain research areas such as pilot workload, information transfer provided by various display formats, crew role in automated systems, and pilot training are documented. These analytical techniques produce the following data: real-time viewing of the pilot's scanning behavior, average dwell times, dwell percentages, instrument transition paths, dwell histograms, and entropy rate measures. These types of data are discussed, and overviews of the experimental setup, data analysis techniques, and software are presented. A glossary of terms frequently used in pilot scanning behavior and a bibliography of reports on related research sponsored by NASA Langley Research Center are also presented.

Momentum space view of the ultrafast dynamics of surface photocurrents on topological insulators

NASA Astrophysics Data System (ADS)

Kuroda, K.; Reimann, J.; Güdde, J.; Höfer, U.

2017-02-01

The Dirac-cone surface states of topological insulators are characterized by a chiral spin texture in k-space with the electron spin locked to its parallel momentum. Mid-infrared pump pulses can induce spin-polarized photocurrents in such a topological surface state by optical transitions between the occupied and unoccupied part of the Dirac cone. We monitor the ultrafast dynamics of the corresponding asymmetric electron population in momentum space directly by time- and angle-resolved two-photon photoemission (2PPE). The elastic scattering times of 2.5 ps deduced for Sb2Te3 corresponds to a mean-fee path of 0.75 μm in real space.

Determining the Edges of the Path of Totality on August 21, 2017

NASA Astrophysics Data System (ADS)

Dunham, David W.; Maley, Paul D.; Kok, Jan; Bruenjes, Fred

2018-01-01

The International Occultation Timing Association (IOTA) attempted a citizen-science project to determine the locations of the edges of the path of totality, similar to what was done visually in New York City during the 1925 eclipse. With ubiquitous smart phones, we asked observers to record the eclipse, preferably with clip-on 8x telephoto lenses. The limits are not sharp since the solar intensity drops off gradually at the path edges. We hoped to determine how accurately the path edges could be determined, and the width of their “fuzziness”. But it was not possible to find any astronomers who weren’t also going to the center, who might otherwise help organize some path edge observations. In 1925, people were less concerned about the possibility of suffering eye damage from quick glimpses at the eclipse. In 2017, several were concerned about damage to their cell phones, although our tests showed this was not a problem for the two minutes desired. The only successes were at Minden, Nebraska where high school students set up 15 stations across the southern limit and recorded the eclipse with iPads, and near Wheatland, Wyoming, where Jan Kok set up 21 pre-pointed smart phones with 8x lenses that he was able to program, to record the eclipse during the critical two minutes. We found that the dynamic range of the smart phone recordings could not distinguish between the corona, and the Baily’s beads around the contacts, so useful times of the duration of “totality” could not be determined. A few IOTA observers recorded Baily’s beads telescopically at a few locations near the eclipse limits. An especially good color recording of Baily’s beads was made by Fred Bruenjes from only 1.3 km inside the southern limit. We hope that similar recordings with accurate time stamping can be obtained at a few locations near both limits of future eclipses. Even better might be recordings of the flash spectrum near both limits, to measure the transition from absorption lines in the photosphere to emission lines of the chomosphere.

Effect of bedrock permeability on stream base flow mean transit time scaling relations: 1. A multiscale catchment intercomparison

NASA Astrophysics Data System (ADS)

Hale, V. Cody; McDonnell, Jeffrey J.

2016-02-01

The effect of bedrock permeability and underlying catchment boundaries on stream base flow mean transit time (MTT) and MTT scaling relationships in headwater catchments is poorly understood. Here we examine the effect of bedrock permeability on MTT and MTT scaling relations by comparing 15 nested research catchments in western Oregon; half within the HJ Andrews Experimental Forest and half at the site of the Alsea Watershed Study. The two sites share remarkably similar vegetation, topography, and climate and differ only in bedrock permeability (one poorly permeable volcanic rock and the other more permeable sandstone). We found longer MTTs in the catchments with more permeable fractured and weathered sandstone bedrock than in the catchments with tight, volcanic bedrock (on average, 6.2 versus 1.8 years, respectively). At the permeable bedrock site, 67% of the variance in MTT across catchments scales was explained by drainage area, with no significant correlation to topographic characteristics. The poorly permeable site had opposite scaling relations, where MTT showed no correlation to drainage area but the ratio of median flow path length to median flow path gradient explained 91% of the variance in MTT across seven catchment scales. Despite these differences, hydrometric analyses, including flow duration and recession analysis, and storm response analysis, show that the two sites share relatively indistinguishable hydrodynamic behavior. These results show that similar catchment forms and hydrologic regimes hide different subsurface routing, storage, and scaling behavior—a major issue if only hydrometric data are used to define hydrological similarity for assessing land use or climate change response.

The Avahan Transition: Effects of Transition Readiness on Program Institutionalization and Sustained Outcomes

PubMed Central

Singh, Suneeta; Singh, Kriti; Chhabra, Vibha; Bennett, Sara

2016-01-01

Background With declines in development assistance for health and growing interest in country ownership, donors are increasingly faced with the task of transitioning health programs to local actors towards a path to sustainability. Yet there is little available guidance on how to measure and evaluate the success of a transition and its subsequent effects. This study assesses the transition of the Avahan HIV/AIDS prevention program in India to investigate how preparations for transition affected continuation of program activities post-transition. Methods Two rounds of two surveys were conducted and supplemented by data from government and Avahan Computerized Management Information Systems (CMIS). Exploratory factor analysis was used to develop two measures: 1) transition readiness pre-transition, and 2) institutionalization (i.e. integration of initial program systems into organizational procedures and behaviors) post-transition. A fixed effects model was built to examine changes in key program delivery outcomes over time. An ordinary least square regression was used to assess the relationship between transition readiness and sustainability of service outcomes both directly, and indirectly through institutionalization. Results Transition readiness data revealed 3 factors (capacity, alignment and communication), on a 15-item scale with adequate internal consistency (alpha 0.73). Institutionalization was modeled as a unidimensional construct, and a 12-item scale demonstrated moderate internal consistency (alpha 0.60). Coverage of key populations and condom distribution were sustained compared to pre-transition levels (p<0.01). Transition readiness, but not institutionalization, predicted sustained outcomes post-transition. Transition readiness did not necessarily lead to institutionalization of key program elements one year after transition. Conclusion Greater preparedness prior to transition is important to achieve better service delivery outcomes post-transition. This paper illustrates a methodology to measure transition readiness pre-transition to identify less ready organizations or program components in advance, improving the likelihood of service sustainability. Further research is needed around the conceptualization and development of measures of institutionalization and its effects on long-term program sustainability. PMID:27434542

Optimization of the transition path of the head hardening with using the genetic algorithms

NASA Astrophysics Data System (ADS)

Wróbel, Joanna; Kulawik, Adam

2016-06-01

An automated method of choice of the transition path of the head hardening in heat treatment process for the plane steel element is proposed in this communication. This method determines the points on the path of moving heat source using the genetic algorithms. The fitness function of the used algorithm is determined on the basis of effective stresses and yield point depending on the phase composition. The path of the hardening tool and also the area of the heat affected zone is determined on the basis of obtained points. A numerical model of thermal phenomena, phase transformations in the solid state and mechanical phenomena for the hardening process is implemented in order to verify the presented method. A finite element method (FEM) was used for solving the heat transfer equation and getting required temperature fields. The moving heat source is modeled with a Gaussian distribution and the water cooling is also included. The macroscopic model based on the analysis of the CCT and CHT diagrams of the medium-carbon steel is used to determine the phase transformations in the solid state. A finite element method is also used for solving the equilibrium equations giving us the stress field. The thermal and structural strains are taken into account in the constitutive relations.

Crustal structure of the Kaapvaal craton and its significance for early crustal evolution

NASA Astrophysics Data System (ADS)

James, David E.; Niu, Fenglin; Rokosky, Juliana

2003-12-01

High-quality seismic data obtained from a dense broadband array near Kimberley, South Africa, exhibit crustal reverberations of remarkable clarity that provide well-resolved constraints on the structure of the lowermost crust and Moho. Receiver function analysis of Moho conversions and crustal multiples beneath the Kimberley array shows that the crust is 35 km thick with an average Poisson's ratio of 0.25. The density contrast across the Moho is ˜15%, indicating a crustal density about 2.86 gm/cc just above the Moho, appropriate for felsic to intermediate rock compositions. Analysis of waveform broadening of the crustal reverberation phases suggests that the Moho transition can be no more than 0.5 km thick and the total variation in crustal thickness over the 2400 km 2 footprint of the array no more than 1 km. Waveform and travel time analysis of a large earthquake triggered by deep gold mining operations (the Welkom mine event) some 200 km away from the array yield an average crustal thickness of 35 km along the propagation path between the Kimberley array and the event. P- and S-wave velocities for the lowermost crust are modeled to be 6.75 and 3.90 km/s, respectively, with uppermost mantle velocities of 8.2 and 4.79 km/s, respectively. Seismograms from the Welkom event exhibit theoretically predicted but rarely observed crustal reverberation phases that involve reflection or conversion at the Moho. Correlation between observed and synthetic waveforms and phase amplitudes of the Moho reverberations suggests that the crust along the propagation path between source and receiver is highly uniform in both thickness and average seismic velocity and that the Moho transition zone is everywhere less than about 2 km thick. While the extremely flat Moho, sharp transition zone and low crustal densities beneath the region of study may date from the time of crustal formation, a more geologically plausible interpretation involves extensive crustal melting and ductile flow during the major craton-wide Ventersdorp tectonomagmatic event near the end of Archean time.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

An asymptotic preserving unified gas kinetic scheme for gray radiative transfer equations

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

Sun, Wenjun, E-mail: sun_wenjun@iapcm.ac.cn; Jiang, Song, E-mail: jiang@iapcm.ac.cn; Xu, Kun, E-mail: makxu@ust.hk

The solutions of radiative transport equations can cover both optical thin and optical thick regimes due to the large variation of photon's mean-free path and its interaction with the material. In the small mean free path limit, the nonlinear time-dependent radiative transfer equations can converge to an equilibrium diffusion equation due to the intensive interaction between radiation and material. In the optical thin limit, the photon free transport mechanism will emerge. In this paper, we are going to develop an accurate and robust asymptotic preserving unified gas kinetic scheme (AP-UGKS) for the gray radiative transfer equations, where the radiation transportmore » equation is coupled with the material thermal energy equation. The current work is based on the UGKS framework for the rarefied gas dynamics [14], and is an extension of a recent work [12] from a one-dimensional linear radiation transport equation to a nonlinear two-dimensional gray radiative system. The newly developed scheme has the asymptotic preserving (AP) property in the optically thick regime in the capturing of diffusive solution without using a cell size being smaller than the photon's mean free path and time step being less than the photon collision time. Besides the diffusion limit, the scheme can capture the exact solution in the optical thin regime as well. The current scheme is a finite volume method. Due to the direct modeling for the time evolution solution of the interface radiative intensity, a smooth transition of the transport physics from optical thin to optical thick can be accurately recovered. Many numerical examples are included to validate the current approach.« less

Astr 101 Students' Attitudes Towards Essays On Transits, Eclipses And Occultations

NASA Astrophysics Data System (ADS)

D'Cruz, Noella L.

2012-05-01

Joliet Junior College, Joliet, IL offers a one semester introductory astronomy course each semester. We teach over 110 primarily non-science major students each semester. We use proven active learning strategies such lecture tutorials, think-pair-share questions and small group discussions to help these students develop and retain a good understanding of astrophysical concepts. Occasionally, we offer projects that allow students to explore course topics beyond the classroom. We hope that such projects will increase students' interest in astronomy. We also hope that these assignments will help students to improve their critical thinking and writing skills. In Spring 12, we are offering three short individual essay assignments in our face-to-face sections. The essays focus on transits, eclipses and occultations to highlight the 2012 transit of Venus. For the first essay, students will find images of transit and occultation events using the Astronomy Picture of the Day website and describe their chosen events. In addition, students will predict how variations in certain physical and orbital parameters would alter their particular events. The second essay involves transits, eclipses and occultations observed by spacecraft. Students will describe their transit event, their spacecraft's mission, orbital path, how the orbital path was achieved, etc. The third essay deals with transiting exoplanets. Students will choose at least two exoplanets from an exoplanet database, one of which has been discovered through the transit method. This essay will enable students to learn about detecting exoplanets and how they compare with our solar system. Details of the essay assignments and students' reactions to them will be presented at the meeting.

Dynamic phase transitions of the Blume-Emery-Griffiths model under an oscillating external magnetic field by the path probability method

NASA Astrophysics Data System (ADS)

Ertaş, Mehmet; Keskin, Mustafa

2015-03-01

By using the path probability method (PPM) with point distribution, we study the dynamic phase transitions (DPTs) in the Blume-Emery-Griffiths (BEG) model under an oscillating external magnetic field. The phases in the model are obtained by solving the dynamic equations for the average order parameters and a disordered phase, ordered phase and four mixed phases are found. We also investigate the thermal behavior of the dynamic order parameters to analyze the nature dynamic transitions as well as to obtain the DPT temperatures. The dynamic phase diagrams are presented in three different planes in which exhibit the dynamic tricritical point, double critical end point, critical end point, quadrupole point, triple point as well as the reentrant behavior, strongly depending on the values of the system parameters. We compare and discuss the dynamic phase diagrams with dynamic phase diagrams that were obtained within the Glauber-type stochastic dynamics based on the mean-field theory.

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

Chen, Hang, E-mail: hangchen@mit.edu; Thill, Peter; Cao, Jianshu

In biochemical systems, intrinsic noise may drive the system switch from one stable state to another. We investigate how kinetic switching between stable states in a bistable network is influenced by dynamic disorder, i.e., fluctuations in the rate coefficients. Using the geometric minimum action method, we first investigate the optimal transition paths and the corresponding minimum actions based on a genetic toggle switch model in which reaction coefficients draw from a discrete probability distribution. For the continuous probability distribution of the rate coefficient, we then consider two models of dynamic disorder in which reaction coefficients undergo different stochastic processes withmore » the same stationary distribution. In one, the kinetic parameters follow a discrete Markov process and in the other they follow continuous Langevin dynamics. We find that regulation of the parameters modulating the dynamic disorder, as has been demonstrated to occur through allosteric control in bistable networks in the immune system, can be crucial in shaping the statistics of optimal transition paths, transition probabilities, and the stationary probability distribution of the network.« less

Markov State Models of gene regulatory networks.

PubMed

Chu, Brian K; Tse, Margaret J; Sato, Royce R; Read, Elizabeth L

2017-02-06

Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking. The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models. Application of transition path theory to the constructed Markov State Model decomposes global dynamics into a set of dominant transition paths and associated relative probabilities for stochastic state-switching. In this proof-of-concept study, we found that the Markov State Model provides a general framework for analyzing and visualizing stochastic multistability and state-transitions in gene networks. Our results suggest that this framework-adopted from the field of atomistic Molecular Dynamics-can be a useful tool for quantitative Systems Biology at the network scale.

Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.

PubMed

Templeton, Clark; Chen, Szu-Hua; Fathizadeh, Arman; Elber, Ron

2017-10-21

The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system.

Occurrence and transport of pharmaceuticals in a karst groundwater system affected by domestic wastewater treatment plants.

PubMed

Einsiedl, Florian; Radke, Michael; Maloszewski, Piotr

2010-09-20

The occurrence of two pharmaceuticals, ibuprofen and diclofenac, in a vulnerable karst groundwater system was investigated. The hydrogeology of the karst system was identified by collecting (3)H samples in groundwater over 27years and by performing tracer tests. The isotopes and tracer data were interpreted by mathematical modeling to estimate the mean transit time of water and to characterize the hydrogeological flow paths in the groundwater system. By this approach, a mean (3)H transit time of 4.6 years for the fissured-porous karst aquifer was determined, whereas the fast flowing water in the conduit system showed a mean transit time of days. Both pharmaceuticals which infiltrated along sinkholes and small streams into the karst system were detected in concentrations of up to approximately 1 microg/L in effluent water of the wastewater treatment plants. Diclofenac was present in most samples collected from four springs discharging the karst groundwater to the rivers Altmühl and Anlauter in concentrations between 3.6 and 15.4 ng/L. In contrast, ibuprofen was rarely detected in groundwater. The results of this study suggest that both pharmaceuticals move into the fractured system of the karst system and go into storage. Thus dilution processes are the dominant control on the concentrations of both pharmaceuticals in the fractured system, whereas biodegradation is likely less important. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Investigating the age distribution of fracture discharge using multiple environmental tracers, Bedrichov Tunnel, Czech Republic

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

Gardner, W. Payton; Hokr, Milan; Shao, Hua

We investigated the transit time distribution (TTD) of discharge collected from fractures in the Bedrichov Tunnel, Czech Republic, using lumped parameter models and multiple environmental tracers. We then utilize time series of δ 18O, δ 2H and 3H along with CFC measurements from individual fractures in the Bedrichov Tunnel of the Czech Republic to investigate the TTD, and the uncertainty in estimated mean travel time in several fracture networks of varying length and discharge. We also compare several TTDs, including the dispersion distribution, the exponential distribution, and a developed TTD which includes the effects of matrix diffusion. The effect ofmore » seasonal recharge is explored by comparing several seasonal weighting functions to derive the historical recharge concentration. We identify best fit mean ages for each TTD by minimizing the error-weighted, multi-tracer χ2 residual for each seasonal weighting function. We use this methodology to test the ability of each TTD and seasonal input function to fit the observed tracer concentrations, and the effect of choosing different TTD and seasonal recharge functions on the mean age estimation. We find that the estimated mean transit time is a function of both the assumed TTD and seasonal weighting function. Best fits as measured by the χ2 value were achieved for the dispersion model using the seasonal input function developed here for two of the three modeled sites, while at the third site, equally good fits were achieved with the exponential model and the dispersion model and our seasonal input function. The average mean transit time for all TTDs and seasonal input functions converged to similar values at each location. The sensitivity of the estimated mean transit time to the seasonal weighting function was equal to that of the TTD. These results indicated that understanding seasonality of recharge is at least as important as the uncertainty in the flow path distribution in fracture networks and that unique identification of the TTD and mean transit time is difficult given the uncertainty in the recharge function. But, the mean transit time appears to be relatively robust to the structural model uncertainty. The results presented here should be applicable to other studies using environmental tracers to constrain flow and transport properties in fractured rock systems.« less

Investigating the age distribution of fracture discharge using multiple environmental tracers, Bedrichov Tunnel, Czech Republic

DOE PAGES

Gardner, W. Payton; Hokr, Milan; Shao, Hua; ...

2016-10-19

We investigated the transit time distribution (TTD) of discharge collected from fractures in the Bedrichov Tunnel, Czech Republic, using lumped parameter models and multiple environmental tracers. We then utilize time series of δ 18O, δ 2H and 3H along with CFC measurements from individual fractures in the Bedrichov Tunnel of the Czech Republic to investigate the TTD, and the uncertainty in estimated mean travel time in several fracture networks of varying length and discharge. We also compare several TTDs, including the dispersion distribution, the exponential distribution, and a developed TTD which includes the effects of matrix diffusion. The effect ofmore » seasonal recharge is explored by comparing several seasonal weighting functions to derive the historical recharge concentration. We identify best fit mean ages for each TTD by minimizing the error-weighted, multi-tracer χ2 residual for each seasonal weighting function. We use this methodology to test the ability of each TTD and seasonal input function to fit the observed tracer concentrations, and the effect of choosing different TTD and seasonal recharge functions on the mean age estimation. We find that the estimated mean transit time is a function of both the assumed TTD and seasonal weighting function. Best fits as measured by the χ2 value were achieved for the dispersion model using the seasonal input function developed here for two of the three modeled sites, while at the third site, equally good fits were achieved with the exponential model and the dispersion model and our seasonal input function. The average mean transit time for all TTDs and seasonal input functions converged to similar values at each location. The sensitivity of the estimated mean transit time to the seasonal weighting function was equal to that of the TTD. These results indicated that understanding seasonality of recharge is at least as important as the uncertainty in the flow path distribution in fracture networks and that unique identification of the TTD and mean transit time is difficult given the uncertainty in the recharge function. But, the mean transit time appears to be relatively robust to the structural model uncertainty. The results presented here should be applicable to other studies using environmental tracers to constrain flow and transport properties in fractured rock systems.« less

Paths to Success in Young Adulthood from Mental Health and Life Transitions in Emerging Adulthood

ERIC Educational Resources Information Center

Howard, Andrea L.; Galambos, Nancy L.; Krahn, Harvey J.

2010-01-01

This study followed a school-based sample (N = 920) to explore how trajectories of depressive symptoms and expressed anger from age 18 to 25, along with important life transitions, predicted life and career satisfaction at age 32. A two-group (women and men) bivariate growth model revealed that higher depressive symptoms at age 18 predicted lower…

Preliminary assignments of 2 ν 3 - ν 4 hot band of 12 CH 4 in the 2 μm transparency window from long-path FTS spectra

NASA Astrophysics Data System (ADS)

Nikitin, A. V.; Daumont, L.; Thomas, X.; Régalia, L.; Rey, M.; Tyuterev, Vl. G.; Brown, L. R.

2011-07-01

New measurements and assignments for the rovibrational transitions of the hot band 2 v3- v4 of 12CH 4 are reported from 4600 to 4880 cm -1 and refer to lower part of the 2 μm methane transparency window. Three long-path spectra were recorded with a Fourier transform spectrometer (FTS) in Reims using an L = 1603 m absorption path length at 1, 7, 34 h Pa for the natural samples of CH 4; a spectrum of enriched 13CH 4 was also used. Assignments were made for 196 lines of 2 v3(F 2,E)- v4. These transitions had an integrated intensity of 5 × 10 -24 cm/molecule at 296 K and improved the overall description of absorption in the 2.1 μm region. The empirical upper state levels of these assignments belong to Tetradecad (4800-6200 cm -1). The new analysis provided much better accuracies of badly blended positions of 2 v3(F 2)-ground state manifolds at 1.66 μm.

Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers.

PubMed

Nivaskumar, Mangayarkarasi; Bouvier, Guillaume; Campos, Manuel; Nadeau, Nathalie; Yu, Xiong; Egelman, Edward H; Nilges, Michael; Francetic, Olivera

2014-05-06

The closely related bacterial type II secretion (T2S) and type IV pilus (T4P) systems are sophisticated machines that assemble dynamic fibers promoting protein transport, motility, or adhesion. Despite their essential role in virulence, the molecular mechanisms underlying helical fiber assembly remain unknown. Here, we use electron microscopy and flexible modeling to study conformational changes of PulG pili assembled by the Klebsiella oxytoca T2SS. Neural network analysis of 3,900 pilus models suggested a transition path toward low-energy conformations driven by progressive increase in fiber helical twist. Detailed predictions of interprotomer contacts along this path were tested by site-directed mutagenesis, pilus assembly, and protein secretion analyses. We demonstrate that electrostatic interactions between adjacent protomers (P-P+1) in the membrane drive pseudopilin docking, while P-P+3 and P-P+4 contacts determine downstream fiber stabilization steps. These results support a model of a spool-like assembly mechanism for fibers of the T2SS-T4P superfamily. Copyright © 2014 Elsevier Ltd. All rights reserved.

Distinct docking and stabilization steps of the pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers

PubMed Central

Nivaskumar, Mangayarkarasi; Bouvier, Guillaume; Campos, Manuel; Nadeau, Nathalie; Yu, Xiong; Egelman, Edward H.; Nilges, Michael; Francetic, Olivera

2014-01-01

SUMMARY The closely related bacterial type II secretion (T2S) and type IV pilus (T4P) systems are sophisticated machines that assemble dynamic fibers promoting protein transport, motility or adhesion. Despite their essential role in virulence, the molecular mechanisms underlying helical fiber assembly remain unknown. Here we use electron microscopy and flexible modeling to study conformational changes of PulG pili assembled by the Klebsiella oxytoca T2SS. Neural network analysis of 3900 pilus models suggested a transition path towards low-energy conformations driven by progressive increase in fiber helical twist. Detailed predictions of inter-protomer contacts along this path were tested by site-directed mutagenesis, pilus assembly and protein secretion analyses. We demonstrate that electrostatic interactions between adjacent protomers (P-P+1) in the membrane drive pseudopilin docking, while P-P+3 and P-P+4 contacts determine downstream fiber stabilization steps. These results support a new model of a spool-like assembly mechanism for fibers of the T2SS-T4P superfamily. PMID:24685147

Traveling salesman problem with a center.

PubMed

Lipowski, Adam; Lipowska, Dorota

2005-06-01

We study a traveling salesman problem where the path is optimized with a cost function that includes its length L as well as a certain measure C of its distance from the geometrical center of the graph. Using simulated annealing (SA) we show that such a problem has a transition point that separates two phases differing in the scaling behavior of L and C, in efficiency of SA, and in the shape of minimal paths.

Development of Complexity Science and Technology Tools for NextGen Airspace Research and Applications

NASA Technical Reports Server (NTRS)

Holmes, Bruce J.; Sawhill, Bruce K.; Herriot, James; Seehart, Ken; Zellweger, Dres; Shay, Rick

2012-01-01

The objective of this research by NextGen AeroSciences, LLC is twofold: 1) to deliver an initial "toolbox" of algorithms, agent-based structures, and method descriptions for introducing trajectory agency as a methodology for simulating and analyzing airspace states, including bulk properties of large numbers of heterogeneous 4D aircraft trajectories in a test airspace -- while maintaining or increasing system safety; and 2) to use these tools in a test airspace to identify possible phase transition structure to predict when an airspace will approach the limits of its capacity. These 4D trajectories continuously replan their paths in the presence of noise and uncertainty while optimizing performance measures and performing conflict detection and resolution. In this approach, trajectories are represented as extended objects endowed with pseudopotential, maintaining time and fuel-efficient paths by bending just enough to accommodate separation while remaining inside of performance envelopes. This trajectory-centric approach differs from previous aircraft-centric distributed approaches to deconfliction. The results of this project are the following: 1) we delivered a toolbox of algorithms, agent-based structures and method descriptions as pseudocode; and 2) we corroborated the existence of phase transition structure in simulation with the addition of "early warning" detected prior to "full" airspace. This research suggests that airspace "fullness" can be anticipated and remedied before the airspace becomes unsafe.

A dynamic parking charge optimal control model under perspective of commuters' evolutionary game behavior

NASA Astrophysics Data System (ADS)

Lin, XuXun; Yuan, PengCheng

2018-01-01

In this research we consider commuters' dynamic learning effect by modeling the trip mode choice behavior from a new perspective of dynamic evolutionary game theory. We explore the behavior pattern of different types of commuters and study the evolution path and equilibrium properties under different traffic conditions. We further establish a dynamic parking charge optimal control (referred to as DPCOC) model to alter commuters' trip mode choice while minimizing the total social cost. Numerical tests show. (1) Under fixed parking fee policy, the evolutionary results are completely decided by the travel time and the only method for public transit induction is to increase the parking charge price. (2) Compared with fixed parking fee policy, DPCOC policy proposed in this research has several advantages. Firstly, it can effectively turn the evolutionary path and evolutionary stable strategy to a better situation while minimizing the total social cost. Secondly, it can reduce the sensitivity of trip mode choice behavior to traffic congestion and improve the ability to resist interferences and emergencies. Thirdly, it is able to control the private car proportion to a stable state and make the trip behavior more predictable for the transportation management department. The research results can provide theoretical basis and decision-making references for commuters' mode choice prediction, dynamic setting of urban parking charge prices and public transit induction.

SDO/AIA AND HINODE/EIS OBSERVATIONS OF INTERACTION BETWEEN AN EUV WAVE AND ACTIVE REGION LOOPS

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

Yang, Liheng; Zhang, Jun; Li, Ting

2013-09-20

We present detailed analysis of an extreme-ultraviolet (EUV) wave and its interaction with active region (AR) loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly and the Hinode EUV Imaging Spectrometer (EIS). This wave was initiated from AR 11261 on 2011 August 4 and propagated at velocities of 430-910 km s{sup –1}. It was observed to traverse another AR and cross over a filament channel on its path. The EUV wave perturbed neighboring AR loops and excited a disturbance that propagated toward the footpoints of these loops. EIS observations of AR loops revealed that at the time of the wavemore » transit, the original redshift increased by about 3 km s{sup –1}, while the original blueshift decreased slightly. After the wave transit, these changes were reversed. When the EUV wave arrived at the boundary of a polar coronal hole, two reflected waves were successively produced and part of them propagated above the solar limb. The first reflected wave above the solar limb encountered a large-scale loop system on its path, and a secondary wave rapidly emerged 144 Mm ahead of it at a higher speed. These findings can be explained in the framework of a fast-mode magnetosonic wave interpretation for EUV waves, in which observed EUV waves are generated by expanding coronal mass ejections.« less

Characterizing the Global Impact of P2P Overlays on the AS-Level Underlay

NASA Astrophysics Data System (ADS)

Rasti, Amir Hassan; Rejaie, Reza; Willinger, Walter

This paper examines the problem of characterizing and assessing the global impact of the load imposed by a Peer-to-Peer (P2P) overlay on the AS-level underlay. In particular, we capture Gnutella snapshots for four consecutive years, obtain the corresponding AS-level topology snapshots of the Internet and infer the AS-paths associated with each overlay connection. Assuming a simple model of overlay traffic, we analyze the observed load imposed by these Gnutella snapshots on the AS-level underlay using metrics that characterize the load seen on individual AS-paths and by the transit ASes, illustrate the churn among the top transit ASes during this 4-year period, and describe the propagation of traffic within the AS-level hierarchy.

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

DOE PAGES

Kale, Seyit; Sode, Olaseni; Weare, Jonathan; ...

2014-11-07

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum undermore » DFT by several fold. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.« less

A quantum chemical study for the multichannel reaction PH 2 + PH 2

NASA Astrophysics Data System (ADS)

Pimentel, André S.; Viana, Rommel B.

2007-04-01

The PH 2 + PH 2 multichannel reaction path was proposed in this study. The transition state that connects the reactants to cis-P 2H 2 isomer was found for the first time ever. This process is not allowed to occur at ordinary conditions because of its high energy barrier, 70 kcal mol -1. The PH 2 + PH 2 disproportionation to form the triplet PH 3 radical is an exothermic and spontaneous reaction. The PH 2 + PH 2 reaction may also form the P 2H 4 molecule in the absence of surfaces.

Sustaining the Clinical and Translational Research Workforce: Training and Empowering the Next Generation of Investigators.

PubMed

Yin, Helen L; Gabrilove, Janice; Jackson, Rebecca; Sweeney, Carol; Fair, Alecia M; Toto, Robert

2015-07-01

There is mounting concern that clinician-scientists are a vanishing species and that the pipeline for clinical and translational research (CTR) investigators is in jeopardy. For the majority of current junior CTR investigators, the career path involves first obtaining a National Institutes of Health (NIH)-funded K-type career development award, particularly K08 and K23, and subsequently an NIH R01. This transition, popularly referred to as K2R, is a major hurdle with a low success rate and gaps in funding. In this Perspective, the authors identify factors that facilitate K2R transition and important aspects of increasing and sustaining the pipeline of CTR investigators. They also highlight significant differences in success rates of women and those underrepresented in biomedical research. Early career exposure to research methodology, protected time, multidisciplinary mentoring, and institutional "culture shift" are important for fostering and rewarding team science. Mentoring is the single most important contributor to K2R success, and emerging evidence suggests that formal mentor training and team mentoring are effective. Leadership training can empower junior investigators to thrive as independent CTR investigators. Future research should focus on delineating the difference between essential and supplemental factors to achieve this transition, and mentoring methods that foster success, including those that promote K2R transition of women and those underrepresented in biomedical research. The Clinical and Translational Science Awards National Consortium is well positioned to test existing models aimed at shortening the time frame, increasing the rate of K2R transition, and identifying strategies that improve success.

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

Reister, D.B.; Lenhart, S.M.

Recent theoretical results have completely solved the problem of determining the minimum length path for a vehicle with a minimum turning radius moving from an initial configuration to a final configuration. Time optimal paths for a constant speed vehicle are a subset of the minimum length paths. This paper uses the Pontryagin maximum principle to find time optimal paths for a constant speed vehicle. The time optimal paths consist of sequences of axes of circles and straight lines. The maximum principle introduces concepts (dual variables, bang-bang solutions, singular solutions, and transversality conditions) that provide important insight into the nature ofmore » the time optimal paths. We explore the properties of the optimal paths and present some experimental results for a mobile robot following an optimal path.« less

EMERGENCE OF GRANULAR-SIZED MAGNETIC BUBBLES THROUGH THE SOLAR ATMOSPHERE. III. THE PATH TO THE TRANSITION REGION

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

Ortiz, Ada; Hansteen, Viggo H.; Pontieu, Bart De

2016-07-10

We study, for the first time, the ascent of granular-sized magnetic bubbles from the solar photosphere through the chromosphere into the transition region and above. Such events occurred in a flux emerging region in NOAA 11850 on 2013 September 25. During that time, the first co-observing campaign between the Swedish 1-m Solar Telescope (SST) and the Interface Region Imaging Spectrograph (IRIS) spacecraft was carried out. Simultaneous observations of the chromospheric H α 656.28 nm and Ca ii 854.2 nm lines, plus the photospheric Fe i 630.25 nm line, were made with the CRISP spectropolarimeter at the Spitzer Space Telescope (more » SST ) reaching a spatial resolution of 0.″14. At the same time, IRIS was performing a four-step dense raster of the emerging flux region, taking slit jaw images at 133 (C ii, transition region), 140 (Si iv, transition region), 279.6 (Mg ii k, core, upper chromosphere), and 283.2 nm (Mg ii k, wing, photosphere). Spectroscopy of several lines was performed by the IRIS spectrograph in the far- and near-ultraviolet, of which we have used the Si iv 140.3 and the Mg ii k 279.6 nm lines. Coronal images from the Atmospheric Imaging Assembly of the Solar Dynamics Observatory were used to investigate the possible coronal signatures of the flux emergence events. The photospheric and chromospheric properties of small-scale emerging magnetic bubbles have been described in detail in Ortiz et al. Here we are able to follow such structures up to the transition region. We describe the properties, including temporal delays, of the observed flux emergence in all layers. We believe this may be an important mechanism of transporting energy and magnetic flux from subsurface layers to the transition region and corona.« less

SDO Transit, September 2015

NASA Image and Video Library

2015-09-13

On Sept. 13, 2015, as NASA's Solar Dynamics Observatory, or SDO, kept up its constant watch on the sun, its view was photobombed not once, but twice. Just as the moon came into SDO's field of view on a path to cross the sun, Earth entered the picture, blocking SDO's view completely. When SDO's orbit finally emerged from behind Earth, the moon was just completing its journey across the sun's face. Though SDO sees dozens of Earth eclipses and several lunar transits each year, this is the first time ever that the two have coincided. SDO's orbit usually gives us unobstructed views of the sun, but Earth's revolution around the sun means that SDO's orbit passes behind Earth twice each year, for two to three weeks at a time. During these phases, Earth blocks SDO's view of the sun for anywhere from a few minutes to over an hour once each day. Earth's outline looks fuzzy, while the moon's is crystal-clear. This is because-while the planet itself completely blocks the sun's light-Earth's atmosphere is an incomplete barrier, blocking different amounts of light at different altitudes. However, the moon has no atmosphere, so during the transit we can see the crisp edges of the moon's horizon. http://photojournal.jpl.nasa.gov/catalog/PIA19949

Exploration of the Transition from the Hydrodynamic-like to the Strongly Kinetic Regime in Shock-Driven Implosions

DOE PAGES

Rosenberg, M. J.; Rinderknecht, H. G.; Hoffman, N. M.; ...

2014-05-05

Clear evidence of the transition from hydrodynamiclike to strongly kinetic shock-driven implosions is, for the first time, revealed and quantitatively assessed. Implosions with a range of initial equimolar D 3He gas densities show that as the density is decreased, hydrodynamic simulations strongly diverge from and increasingly over-predict the observed nuclear yields, from a factor of ~2 at 3.1 mg/cm 3 to a factor of 100 at 0.14 mg/cm 3. (The corresponding Knudsen number, the ratio of ion mean-free path to minimum shell radius, varied from 0.3 to 9; similarly, the ratio of fusion burn duration to ion diffusion time, anothermore » figure of merit of kinetic effects, varied from 0.3 to 14.) This result is shown to be unrelated to the effects of hydrodynamic mix. As a first step to garner insight into this transition, a reduced ion kinetic (RIK) model that includes gradient-diffusion and loss-term approximations to several transport processes was implemented within the framework of a one-dimensional radiation-transport code. After empirical calibration, the RIK simulations reproduce the observed yield trends, largely as a result of ion diffusion and the depletion of the reacting tail ions.« less

Environmental, behavioral, and psychological predictors of transit ridership: Evidence from a community intervention

PubMed Central

Brown, Barbara B.; Werner, Carol M.; Smith, Ken R.; Tribby, Calvin P.; Miller, Harvey J.; Jensen, Wyatt A.; Tharp, Doug

2016-01-01

Understanding who takes advantage of new transit (public transportation) interventions is important for personal and environmental health. We examine transit ridership for residents living near a new light rail construction as part of “complete street,” pedestrian-friendly improvements. Adult residents (n=536) completed surveys and wore accelerometer and GPS units that tracked ridership before and after new transit service started. Transit riders were more physically active. Those from environments rated as more walkable were likely to be continuing transit riders. Place attachment, but not perceived physical incivilities on the path to transit, was associated with those who continued to ride or became new riders of transit. This effect was mediated through pro-city attitudes, which emphasize how the new service makes residents eager to explore areas around transit. Thus, place attachment, along with physical and health conditions, may be important predictors and promoters of transit use. PMID:27672237

Laboratory experiments on subduction-induced circulation in the wedge and the evolution of mantle diapirs

NASA Astrophysics Data System (ADS)

Sylvia, R. T.; Kincaid, C. R.; Behn, M. D.; Zhang, N.

2014-12-01

Circulation in subduction zones involves large-scale, forced-convection by the motion of the down-going slab and small scale, buoyant diapirs of hydrated mantle or subducted sediments. Models of subduction-diapir interaction often neglect large-scale flow patterns induced by rollback, back-arc extension and slab morphology. We present results from laboratory experiments relating these parameters to styles of 4-D wedge circulation and diapir ascent. A glucose fluid is used to represent the mantle. Subducting lithosphere is modeled with continuous rubber belts moving with prescribed velocities, capable of reproducing a large range in downdip relative rollback plate rates. Differential steepening of distinct plate segments simulates the evolution of slab gaps. Back-arc extension is produced using Mylar sheeting in contact with fluid beneath the overriding plate that moves relative to the slab rollback rate. Diapirs are introduced at the slab-wedge interface in two modes: 1) distributions of low density rigid spheres and 2) injection of low viscosity, low density fluid to the base of the wedge. Results from 30 experiments with imposed along-trench (y) distributions of buoyancy, show near-vertical ascent paths only in cases with simple downdip subduction and ratios (W*) of diapir rise velocity to downdip plate rate of W*>1. For W* = 0.2-1, diapir ascent paths are complex, with large (400 km) lateral offsets between source and surfacing locations. Rollback and back-arc extension enhance these offsets, occasionally aligning diapirs from different along-trench locations into trench-normal, age-progressive linear chains beneath the overriding plate. Diapirs from different y-locations may surface beneath the same volcanic center, despite following ascent paths of very different lengths and transit times. In cases with slab gaps, diapirs from the outside edge of the steep plate move 1000 km parallel to the trench before surfacing above the shallow dipping plate. "Dead zones" resulting from lateral and vertical shear in the wedge above the slab gap, produce slow transit times. These 4-D ascent pathways are being incorporated into numerical models on the thermal and melting evolution of diapirs. Models show subduction-induced circulation significantly alters diapir ascent beneath arcs.

Mach stem formation in outdoor measurements of acoustic shocks.

PubMed

Leete, Kevin M; Gee, Kent L; Neilsen, Tracianne B; Truscott, Tadd T

2015-12-01

Mach stem formation during outdoor acoustic shock propagation is investigated using spherical oxyacetylene balloons exploded above pavement. The location of the transition point from regular to irregular reflection and the path of the triple point are experimentally resolved using microphone arrays and a high-speed camera. The transition point falls between recent analytical work for weak irregular reflections and an empirical relationship derived from large explosions.

Evidence from lava flows for complex polarity transitions: The new composite Steens Mountain reversal record

USGS Publications Warehouse

Jarboe, Nicholas A.; Coe, Robert S.; Glen, Jonathan M. G.

2011-01-01

Geomagnetic polarity transitions may be significantly more complex than are currently depicted in many sedimentary and lava-flow records. By splicing together paleomagnetic results from earlier studies at Steens Mountain with those from three newly studied sections of Oregon Plateau flood basalts at Catlow Peak and Poker Jim Ridge 70–90 km to the southeast and west, respectively, we provide support for this interpretation with the most detailed account of a magnetic field reversal yet observed in volcanic rocks. Forty-five new distinguishable transitional (T) directions together with 30 earlier ones reveal a much more complex and detailed record of the 16.7 Ma reversed (R)-to-normal (N) polarity transition that marks the end of Chron C5Cr. Compared to the earlier R-T-N-T-N reversal record, the new record can be described as R-T-N-T-N-T-R-T-N. The composite record confirms earlier features, adds new west and up directions and an entire large N-T-R-T segment to the path, and fills in directions on the path between earlier directional jumps. Persistent virtual geomagnetic pole (VGP) clusters and separate VGPs have a preference for previously described longitudinal bands from transition study compilations, which suggests the presence of features at the core–mantle boundary that influence the flow of core fluid and distribution of magnetic flux. Overall the record is consistent with the generalization that VGP paths vary greatly from reversal to reversal and depend on the location of the observer. Rates of secular variation confirm that the flows comprising these sections were erupted rapidly, with maximum rates estimated to be 85–120 m ka−1 at Catlow and 130–195 m ka−1 at Poker Jim South. Paleomagnetic poles from other studies are combined with 32 non-transitional poles found here to give a clockwise rotation of the Oregon Plateau of 11.4°± 5.6° with respect to the younger Columbia River Basalt Group flows to the north and 14.5°± 4.6° with respect to cratonic North America (95 per cent confidence interval).

Minimum free-energy paths for the self-organization of polymer brushes.

PubMed

Gleria, Ignacio; Mocskos, Esteban; Tagliazucchi, Mario

2017-03-22

A methodology to calculate minimum free-energy paths based on the combination of a molecular theory and the improved string method is introduced and applied to study the self-organization of polymer brushes under poor solvent conditions. Polymer brushes in a poor solvent cannot undergo macroscopic phase separation due to the physical constraint imposed by the grafting points; therefore, they microphase separate forming aggregates. Under some conditions, the theory predicts that the homogeneous brush and the aggregates can exist as two different minima of the free energy. The theoretical methodology introduced in this work allows us to predict the minimum free-energy path connecting these two minima as well as the morphology of the system along the path. It is shown that the transition between the homogeneous brush and the aggregates may involve a free-energy barrier or be barrierless depending on the relative stability of the two morphologies and the chain length and grafting density of the polymer. In the case where a free-energy barrier exists, one of the morphologies is a metastable structure and, therefore, the properties of the brush as the quality of the solvent is cycled are expected to display hysteresis. The theory is also applied to study the adhesion/deadhesion transition between two opposing surfaces modified by identical polymer brushes and it is shown that this process may also require surpassing a free-energy barrier.

A path integral approach to the Hodgkin-Huxley model

NASA Astrophysics Data System (ADS)

Baravalle, Roman; Rosso, Osvaldo A.; Montani, Fernando

2017-11-01

To understand how single neurons process sensory information, it is necessary to develop suitable stochastic models to describe the response variability of the recorded spike trains. Spikes in a given neuron are produced by the synergistic action of sodium and potassium of the voltage-dependent channels that open or close the gates. Hodgkin and Huxley (HH) equations describe the ionic mechanisms underlying the initiation and propagation of action potentials, through a set of nonlinear ordinary differential equations that approximate the electrical characteristics of the excitable cell. Path integral provides an adequate approach to compute quantities such as transition probabilities, and any stochastic system can be expressed in terms of this methodology. We use the technique of path integrals to determine the analytical solution driven by a non-Gaussian colored noise when considering the HH equations as a stochastic system. The different neuronal dynamics are investigated by estimating the path integral solutions driven by a non-Gaussian colored noise q. More specifically we take into account the correlational structures of the complex neuronal signals not just by estimating the transition probability associated to the Gaussian approach of the stochastic HH equations, but instead considering much more subtle processes accounting for the non-Gaussian noise that could be induced by the surrounding neural network and by feedforward correlations. This allows us to investigate the underlying dynamics of the neural system when different scenarios of noise correlations are considered.

Marine Radioactivity Studies in the Suez Canal, Part I: Hydrodynamics and Transit Times

NASA Astrophysics Data System (ADS)

Abril, J. M.; Abdel-Aal, M. M.

2000-04-01

This paper describes work carried out under the IAEA Project EGY/07/002 to study the dispersion of radioactive material in the Suez Canal. This effort is linked with the increased public concern about radiation safety through this important trade route. To follow the fate of radioactive wastes along this waterway, we had to solve the hydrodynamics of the water, governed mainly by tides, atmospheric forcing and the drift currents produced by horizontal salinity gradients and by differences in mean sea level (MSL) at the two entrances of the Canal. The hydrodynamics has been studied using both 1-D and 2-D modelling approaches, and a reasonable calibration has been possible from the data set prepared with the collaboration of the Suez Canal Authority. Dispersion of conservative pollutants has been preliminarily studied by using a 1-D-Gaussian approach. Thus, we are computing the path of the plumes and the time evolution of concentrations for different scenarios of discharges and under different seasonal conditions. The transit times can vary enormously during the year, ranging from a few days to several months, depending on the differences in MSL at the two entrances of the Canal.

Metal-Insulator Transition in Nanoparticle Solids: Insights from Kinetic Monte Carlo Simulations

DOE PAGES

Qu, Luman; Vörös, Márton; Zimanyi, Gergely T.

2017-08-01

Progress has been rapid in increasing the efficiency of energy conversion in nanoparticles. However, extraction of the photo-generated charge carriers remains challenging. Encouragingly, the charge mobility has been improved recently by driving nanoparticle (NP) films across the metal-insulator transition (MIT). To simulate MIT in NP films, we developed a hierarchical Kinetic Monte Carlo transport model. Electrons transfer between neighboring NPs via activated hopping when the NP energies differ by more than an overlap energy, but transfer by a non-activated quantum delocalization, if the NP energies are closer than the overlap energy. As the overlap energy increases, emerging percolating clusters supportmore » a metallic transport across the entire film. We simulated the evolution of the temperature-dependent electron mobility. We analyzed our data in terms of two candidate models of the MIT: (a) as a Quantum Critical Transition, signaled by an effective gap going to zero; and (b) as a Quantum Percolation Transition, where a sample-spanning metallic percolation path is formed as the fraction of the hopping bonds in the transport paths is going to zero. We found that the Quantum Percolation Transition theory provides a better description of the MIT. We also observed an anomalously low gap region next to the MIT. We discuss the relevance of our results in the light of recent experimental measurements.« less

Metal-Insulator Transition in Nanoparticle Solids: Insights from Kinetic Monte Carlo Simulations

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

Qu, Luman; Vörös, Márton; Zimanyi, Gergely T.

Progress has been rapid in increasing the efficiency of energy conversion in nanoparticles. However, extraction of the photo-generated charge carriers remains challenging. Encouragingly, the charge mobility has been improved recently by driving nanoparticle (NP) films across the metal-insulator transition (MIT). To simulate MIT in NP films, we developed a hierarchical Kinetic Monte Carlo transport model. Electrons transfer between neighboring NPs via activated hopping when the NP energies differ by more than an overlap energy, but transfer by a non-activated quantum delocalization, if the NP energies are closer than the overlap energy. As the overlap energy increases, emerging percolating clusters supportmore » a metallic transport across the entire film. We simulated the evolution of the temperature-dependent electron mobility. We analyzed our data in terms of two candidate models of the MIT: (a) as a Quantum Critical Transition, signaled by an effective gap going to zero; and (b) as a Quantum Percolation Transition, where a sample-spanning metallic percolation path is formed as the fraction of the hopping bonds in the transport paths is going to zero. We found that the Quantum Percolation Transition theory provides a better description of the MIT. We also observed an anomalously low gap region next to the MIT. We discuss the relevance of our results in the light of recent experimental measurements.« less

Potential Energy Landscape of the Liquid-Liquid Phase Transition in Water and the transformation between Low-Density and High-Density Amorphous Ice

NASA Astrophysics Data System (ADS)

Giovambattista, N.; Sciortino, F.; Starr, F. W.; Poole, P. H.

The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics for describing supercooled liquids and glasses. We use the PEL formalism and computer simulations to study the transformation between low-density (LDL) and high-density liquid (HDL) water, and between low-density (LDA) and high-density amorphous ice (HDA). We employ the ST2 water model that exhibits a LDL-HDL first-order phase transition and a sharp LDA-HDA transformation, as observed in experiments. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that LDL configurations are located in the same megabasin as LDA, and that HDL configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid and the amorphous ice differ. We also study the liquid-to-ice-VII first-order phase transition. The PEL properties across this transition are qualitatively similar to the changes found during the LDA-HDA transformation, supporting the interpretation that the LDA-HDA transformation is a first-order-like phase transition between out-of-equilibrium states.

Careers beyond academia

NASA Astrophysics Data System (ADS)

Karouzos, Marios

2018-01-01

We asked the same five questions to eleven astronomers who now work in different fields in order to understand their career paths, their motivations to leave astronomy and the skills that helped them in their transition.

Identifying Source Water and Flow Paths in a Semi-Arid Watershed

NASA Astrophysics Data System (ADS)

Gulvin, C. J.; Miller, S. N.

2016-12-01

Processes controlling water delivery to perennial streams in the semi-arid mountain west are poorly understood, yet necessary to characterize water distribution across the landscape and better protect and manage diminishing water resources. Stream water chemistry profiling and hydrograph separation using stable isotopes can help identify source waters. Weekly stream water samples tested for stable water isotope fractionations, and major cations and anions at seven sites collocated with continuously recording stream depth gauges within a small watershed in southeastern Wyoming is a necessary first-step to identifying seasonally changing source water and flow paths. Sample results will help establish appropriate end members for a mixing analysis, as well as, characterize flow path heterogeneity, transit time distributions, and landscape selectively features. Hourly stream sampling during late-summer thunderstorms and rapid spring melt will help demonstrate if and how stream discharge change is affected by the two different events. Soil water and water extracted from tree xylem will help resolve how water is partitioned in the first 10m of the subsurface. In the face of land use change and a growing demand for water in the area, understanding how the water in small mountain streams is sustained is crucial for the future of agriculture, municipal water supplies, and countless ecosystem services.

Constraints on the lithosphere in and surrounding the Arctic basin from combined ambient noise and earthquake tomography

NASA Astrophysics Data System (ADS)

Krogh, J.; Dalton, C. A.; Ma, Z.

2017-12-01

Rayleigh wave dispersion extracted from ambient seismic noise has been widely used to image crustal and uppermost mantle structure in continents, but there have been relatively few studies within ocean basins. Here, we extract Rayleigh wave dispersion from ambient noise across the Arctic basin and surrounding continents. Continuous time series were collected from 427 broadband stations for the time period 1990-2016. Following the method described by Ma and Dalton (2017), we cross-correlated the noise records for 57,782 pairs of stations and measured phase arrival times for the frequency range 5-30 mHz. After data selection, which utilized criteria for path length, signal-to-noise ratio, and waveform quality, between 670 and 20,284 paths remained. Phase-velocity maps for the study region were determined from only the ambient noise Rayleigh waves and from a combined data set of ambient noise and earthquakes. Resolution tests and hit count maps illustrate the enhanced path coverage and resolution that is afforded by combining the two data sets. The maps show a clear association with tectonic features, including: fast velocities associated with the Siberian, Baltic, and North American cratons; very slow velocities associated with Iceland and the Alaska-Aleutian subduction zone; and an abrupt transition between the low-velocity North American Cordillera and fast-velocity craton that corresponds nearly perfectly with surface topography. The ultra-slow spreading Gakkel Ridge has only a weak seismic signature, although the dependence of seismic velocity on seafloor age is apparent in the maps. These results will be used to investigate the variations in temperature, composition, and melt and volatile content in the Arctic lithosphere and asthenosphere.

Exploring the full catalytic cycle of rhodium(i)–BINAP-catalysed isomerisation of allylic amines: a graph theory approach for path optimisation† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00401j Click here for additional data file.

PubMed Central

Yoshimura, Takayoshi; Taketsugu, Tetsuya; Sawamura, Masaya

2017-01-01

We explored the reaction mechanism of the cationic rhodium(i)–BINAP complex catalysed isomerisation of allylic amines using the artificial force induced reaction method with the global reaction route mapping strategy, which enabled us to search for various reaction paths without assumption of transition states. The entire reaction network was reproduced in the form of a graph, and reasonable paths were selected from the complicated network using Prim’s algorithm. As a result, a new dissociative reaction mechanism was proposed. Our comprehensive reaction path search provided rationales for the E/Z and S/R selectivities of the stereoselective reaction. PMID:28970877

The Steens Basalt of the Oregon Plateau: A geomagnetic polarity reversal and the age of the Columbia River basalt group

NASA Astrophysics Data System (ADS)

Jarboe, Nicholas A.

The Steens Basalt of the Oregon Plateau covers about 53,000 km2 of southeastern Oregon and northwestern Nevada. Three localities where volcanic sections contain transitional lavas of the Steens reversal have been studied. At Steens Mountain, previous studies showed a complex reversal path consisting of 30 transitional directional groups. At the three new localities, forty-five new transitional directional groups are discovered, show an increase in the complexity of the reversal path, and reinforce the clumping of some directions. Fifteen 40Ar/39Ar ages were determined from lavas on or near the Oregon Plateau. The lavas are shown to have erupted before, after, or during the Steens reversal in the R0, N 0, or N1 of the CRBG. Using a Bayesian statistical analysis of the mean age of the Steens reversal lavas and three other ages at the Catlow section, the best and preferred age of the Steens reversal is 16.73 +0.13/-0.08 Ma (95% confidence). Correlation of this age to a sea floor spreading time scale allows the floating magnetostratigraphy of the CRBG to be placed into the geomagnetic polarity time scale and shows that the R0 corresponds to the C5Cr chron with the Steens reversal at the top of the C5Cr chron. Twenty six paleomagnetic poles from Steens Mountain are combined with 108 non-transitional poles found in this thesis to give a clockwise rotation of the Oregon Plateau of 11.4° +/- 5.6° with respect to the younger CRBG flows to the north and 14.5° +/- 4.6° with respect to cratonic North America. Using secular variation considerations, eruption rates can be calculated at two of the sections which contain the Steens reversal: 85--120 m/ka at Catlow and 130--195 m/ka at Poker Jim South. Similarly, durations of eruptions have been determined at the four sections that do not contain the Steens reversal: ˜2.5 ka for 260 m at the Pueblo Mountains, 0.5 to 1.5 ka for 190 m at Summit Springs, 1--3 ka for 170 m at North Mickey, and ˜3 ka for 160 m at Guano Rim.

Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems

NASA Astrophysics Data System (ADS)

Meng, Luming; Sheong, Fu Kit; Zeng, Xiangze; Zhu, Lizhe; Huang, Xuhui

2017-07-01

Constructing Markov state models from large-scale molecular dynamics simulation trajectories is a promising approach to dissect the kinetic mechanisms of complex chemical and biological processes. Combined with transition path theory, Markov state models can be applied to identify all pathways connecting any conformational states of interest. However, the identified pathways can be too complex to comprehend, especially for multi-body processes where numerous parallel pathways with comparable flux probability often coexist. Here, we have developed a path lumping method to group these parallel pathways into metastable path channels for analysis. We define the similarity between two pathways as the intercrossing flux between them and then apply the spectral clustering algorithm to lump these pathways into groups. We demonstrate the power of our method by applying it to two systems: a 2D-potential consisting of four metastable energy channels and the hydrophobic collapse process of two hydrophobic molecules. In both cases, our algorithm successfully reveals the metastable path channels. We expect this path lumping algorithm to be a promising tool for revealing unprecedented insights into the kinetic mechanisms of complex multi-body processes.

Quantifying the underlying landscape and paths of cancer

PubMed Central

Li, Chunhe; Wang, Jin

2014-01-01

Cancer is a disease regulated by the underlying gene networks. The emergence of normal and cancer states as well as the transformation between them can be thought of as a result of the gene network interactions and associated changes. We developed a global potential landscape and path framework to quantify cancer and associated processes. We constructed a cancer gene regulatory network based on the experimental evidences and uncovered the underlying landscape. The resulting tristable landscape characterizes important biological states: normal, cancer and apoptosis. The landscape topography in terms of barrier heights between stable state attractors quantifies the global stability of the cancer network system. We propose two mechanisms of cancerization: one is by the changes of landscape topography through the changes in regulation strengths of the gene networks. The other is by the fluctuations that help the system to go over the critical barrier at fixed landscape topography. The kinetic paths from least action principle quantify the transition processes among normal state, cancer state and apoptosis state. The kinetic rates provide the quantification of transition speeds among normal, cancer and apoptosis attractors. By the global sensitivity analysis of the gene network parameters on the landscape topography, we uncovered some key gene regulations determining the transitions between cancer and normal states. This can be used to guide the design of new anti-cancer tactics, through cocktail strategy of targeting multiple key regulation links simultaneously, for preventing cancer occurrence or transforming the early cancer state back to normal state. PMID:25232051

Structural phase transition at high temperatures in solid molecular hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Cui, T.; Takada, Y.; Cui, Q.; Ma, Y.; Zou, G.

2001-07-01

We study the effect of temperature up to 1000 K on the structure of dense molecular para-hydrogen (p-H2) and ortho-deuterium (o-D2), using the path-integral Monte Carlo method. We find a structural phase transition from orientationally disordered hexagonal close packed (hcp) to an orthorhombic structure of Cmca symmetry before melting. The transition is basically induced by thermal fluctuations, but quantum fluctuations of protons (deuterons) are important in determining the transition temperature through effectively hardening the intermolecular interaction. We estimate the phase line between hcp and Cmca phases as well as the melting line of the Cmca solid.

Solar Transportation, on the critical path to 100% Renewables

NASA Astrophysics Data System (ADS)

Swenson, R.; Furman, B.

2016-12-01

The path from hydrocarbons and climate change to 100% renewable energy requires a complete transformation of human mobility systems—from oil to solar electricity, and away from personal cars to shared transit. Electric (and autonomous) personal vehicles cannot scale rapidly enough to address CO2 increase and resource depletion. While atmospheric science can characterize the challenge, design science aimed at order of magnitude improvements in energy and resource consumption is needed to achieve carbon free transit that can scale rapidly for urban mobility. An NGO and University engineering team collaboration has led to a multi-disciplinary international program creating prototypes and test tracks to demonstrate the efficacy and economics of solar-powered, automated, non-stop origin-to-destination, elevated on-demand transit systems. With their aptitude for innovation, students in the Solar Skyways challenge have convened from several countries in order to propel development and overcome resistance from the automotive industry incumbency. Innovation has been occurring in lesser developed countries as well as in the industrialized world. An online curriculum has been developed and will be presented to encourage international participation and rapid acceleration for sustainable zero-net-carbon transportation.

Metal-insulator transition in AlxGa1-xAs/GaAs heterostructures with large spacer width

NASA Astrophysics Data System (ADS)

Gold, A.

1991-10-01

Analytical results are presented for the mobility of a two-dimensional electron gas in a heterostructure with a thick spacer layer α. Due to multiple-scattering effects a metal-insulator transition occurs at a critical electron density Nc=N1/2i/(4π1/2α) (Ni is the impurity density). The transport mean free path l(t) (calculated in Born approximation) at the metal-insulator transition is l(t)c=2α. A localization criterion in terms of the renormalized single-particle mean free path l(sr) is presented: kFcl(sr)c=(1/2)1/2 (kFc is the Fermi wave number at the critical density). I compare the theoretical results with recent experimental results found in AlxGa1-xAs/GaAs heterostructures with large spacer width: 1200<α<2800 Å. Remote impurity doping and homogeneous background doping are considered. The only fitting parameter used for the theoretical results is the background doping density NB=6×1013 cm-3. My theory is in fair agreement with the experimental results.

Real-time network security situation visualization and threat assessment based on semi-Markov process

NASA Astrophysics Data System (ADS)

Chen, Junhua

2013-03-01

To cope with a large amount of data in current sensed environments, decision aid tools should provide their understanding of situations in a time-efficient manner, so there is an increasing need for real-time network security situation awareness and threat assessment. In this study, the state transition model of vulnerability in the network based on semi-Markov process is proposed at first. Once events are triggered by an attacker's action or system response, the current states of the vulnerabilities are known. Then we calculate the transition probabilities of the vulnerability from the current state to security failure state. Furthermore in order to improve accuracy of our algorithms, we adjust the probabilities that they exploit the vulnerability according to the attacker's skill level. In the light of the preconditions and post-conditions of vulnerabilities in the network, attack graph is built to visualize security situation in real time. Subsequently, we predict attack path, recognize attack intention and estimate the impact through analysis of attack graph. These help administrators to insight into intrusion steps, determine security state and assess threat. Finally testing in a network shows that this method is reasonable and feasible, and can undertake tremendous analysis task to facilitate administrators' work.

Geologic, hydrologic, and geochemical identification of flow paths in the Edwards Aquifer, northeastern Bexar and southern Comal Counties, Texas

USGS Publications Warehouse

Otero, Cassi L.

2007-01-01

The U.S. Geological Survey, in cooperation with the San Antonio Water System, conducted a 4-year study during 2002?06 to identify major flow paths in the Edwards aquifer in northeastern Bexar and southern Comal Counties (study area). In the study area, faulting directs ground water into three hypothesized flow paths that move water, generally, from the southwest to the northeast. These flow paths are identified as the southern Comal flow path, the central Comal flow path, and the northern Comal flow path. Statistical correlations between water levels for six observation wells and between the water levels and discharges from Comal Springs and Hueco Springs yielded evidence for the hypothesized flow paths. Strong linear correlations were evident between the datasets from wells and springs within the same flow path and the datasets from wells in areas where flow between flow paths was suspected. Geochemical data (major ions, stable isotopes, sulfur hexafluoride, and tritium and helium) were used in graphical analyses to obtain evidence of the flow path from which wells or springs derive water. Major-ion geochemistry in samples from selected wells and springs showed relatively little variation. Samples from the southern Comal flow path were characterized by relatively high sulfate and chloride concentrations, possibly indicating that the water in the flow path was mixing with small amounts of saline water from the freshwater/saline-water transition zone. Samples from the central Comal flow path yielded the most varied major-ion geochemistry of the three hypothesized flow paths. Central Comal flow path samples were characterized, in general, by high calcium concentrations and low magnesium concentrations. Samples from the northern Comal flow path were characterized by relatively low sulfate and chloride concentrations and high magnesium concentrations. The high magnesium concentrations characteristic of northern Comal flow path samples from the recharge zone in Comal County might indicate that water from the Trinity aquifer is entering the Edwards aquifer in the subsurface. A graph of the relation between the stable isotopes deuterium and delta-18 oxygen showed that, except for samples collected following an unusually intense rain storm, there was not much variation in stable isotope values among the flow paths. In the study area deuterium ranged from -36.00 to -20.89 per mil and delta-18 oxygen ranged from -6.03 to -3.70 per mil. Excluding samples collected following the intense rain storm, the deuterium range in the study area was -33.00 to -20.89 per mil and the delta-18 oxygen range was -4.60 to -3.70 per mil. Two ground-water age-dating techniques, sulfur hexafluoride concentrations and tritium/helium-3 isotope ratios, were used to compute apparent ages (time since recharge occurred) of water samples collected in the study area. In general, the apparent ages computed by the two methods do not seem to indicate direction of flow. Apparent ages computed for water samples in northeastern Bexar and southern Comal Counties do not vary greatly except for some very young water in the recharge zone in central Comal County.

Transition Induced by Fence Geometrics on Shuttle Orbiter at Mach 10

NASA Technical Reports Server (NTRS)

Everhart, Joel L.

2010-01-01

Fence-induced transition data simulating a raised gap filler have been acquired on the wing lower surface of a Shuttle Orbiter model in the Langley 31-Inch Mach 10 Tunnel to compare with the Shuttle Boundary Layer Transition Flight and HYTHIRM Experiments, and to provide additional correlation data for the Boundary Layer Transition Tool. In a qualitative assessment, the data exhibit the expected response to all parameter variations; however, it is unclear whether fully effective tripping at the fence was ever realized at any test condition with the present model hardware. A preliminary, qualitative comparison of the ground-based transition measurements with those obtained from the STS-128 HYTHIRM imagery at Mach 15 reveal similar transition-wake response characteristics in terms of the spreading and the path along the vehicle surface.

Weinberg propagator of a massive particle with an arbitrary spin (in Ukrainian)

NASA Astrophysics Data System (ADS)

Zima, V. G.; Fedoruk, S. O.

The transition amplitude is obtained for a free massive particle of an arbitrary spin by calculating the path integral in the index--spinor formulation within the BFV--BRST approach. None renormalizations of the path integral measure were applied. The calculation has given the Weinberg propagator written in the index--free form with the use of an index spinor. The choice of boundary conditions on the index spinor determines holomorphic or antiholomorphic representation for the canonical description of particle/antiparticle spin.

Systems and methods for separating a multiphase fluid

NASA Technical Reports Server (NTRS)

Weislogel, Mark M. (Inventor); Thomas, Evan A. (Inventor); Graf, John C. (Inventor)

2011-01-01

Apparatus and methods for separating a fluid are provided. The apparatus can include a separator and a collector having an internal volume defined at least in part by one or more surfaces narrowing toward a bottom portion of the volume. The separator can include an exit port oriented toward the bottom portion of the volume. The internal volume can receive a fluid expelled from the separator into a flow path in the collector and the flow path can include at least two directional transitions within the collector.

Transitioning NWChem to the Next Generation of Manycore Machines

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

Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

Transition from homogeneous to inhomogeneous limit cycles: Effect of local filtering in coupled oscillators

NASA Astrophysics Data System (ADS)

Banerjee, Tanmoy; Biswas, Debabrata; Ghosh, Debarati; Bandyopadhyay, Biswabibek; Kurths, Jürgen

2018-04-01

We report an interesting symmetry-breaking transition in coupled identical oscillators, namely, the continuous transition from homogeneous to inhomogeneous limit cycle oscillations. The observed transition is the oscillatory analog of the Turing-type symmetry-breaking transition from amplitude death (i.e., stable homogeneous steady state) to oscillation death (i.e., stable inhomogeneous steady state). This novel transition occurs in the parametric zone of occurrence of rhythmogenesis and oscillation death as a consequence of the presence of local filtering in the coupling path. We consider paradigmatic oscillators, such as Stuart-Landau and van der Pol oscillators, under mean-field coupling with low-pass or all-pass filtered self-feedback and through a rigorous bifurcation analysis we explore the genesis of this transition. Further, we experimentally demonstrate the observed transition, which establishes its robustness in the presence of parameter fluctuations and noise.

(Un)Folding Mechanisms of the FBP28 WW Domain in Explicit Solvent Revealed by Multiple Rare Event Simulation Methods

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2010-01-01

Abstract We report a numerical study of the (un)folding routes of the truncated FBP28 WW domain at ambient conditions using a combination of four advanced rare event molecular simulation techniques. We explore the free energy landscape of the native state, the unfolded state, and possible intermediates, with replica exchange molecular dynamics. Subsequent application of bias-exchange metadynamics yields three tentative unfolding pathways at room temperature. Using these paths to initiate a transition path sampling simulation reveals the existence of two major folding routes, differing in the formation order of the two main hairpins, and in hydrophobic side-chain interactions. Having established that the hairpin strand separation distances can act as reasonable reaction coordinates, we employ metadynamics to compute the unfolding barriers and find that the barrier with the lowest free energy corresponds with the most likely pathway found by transition path sampling. The unfolding barrier at 300 K is ∼17 kBT ≈ 42 kJ/mol, in agreement with the experimental unfolding rate constant. This work shows that combining several powerful simulation techniques provides a more complete understanding of the kinetic mechanism of protein folding. PMID:20159161

A Random Walk Down University Avenue: Life Paths, Life Events, and Personality Trait Change at the Transition to University Life

PubMed Central

Lüdtke, Oliver; Roberts, Brent W.; Trautwein, Ulrich; Nagy, Gabriel

2013-01-01

This longitudinal study examined the relation between continuity and change in the Big Five personality traits and life events. Approximately 2,000 German students were tracked from high school to university or to vocational training or work, with 3 assessments over 4 years. Life events were reported retrospectively at the 2nd and 3rd assessment. Latent curve analyses were used to assess change in personality traits, revealing 3 main findings. First, mean-level changes in the Big Five factors over the 4 years were in line with the maturity principle, indicating increasing psychological maturity from adolescence to young adulthood. Second, personality development was characterized by substantive individual differences relating to the life path followed; participants on a more vocationally oriented path showed higher increases in conscientiousness and lower increases in agreeableness than their peers at university. Third, initial level and change in the Big Five factors (especially Neuroticism and Extraversion) were linked to the occurrence of aggregated as well as single positive and negative life events. The analyses suggest that individual differences in personality development are associated with life transitions and individual life experiences. PMID:21744977

Dynamic-Stark-effect-induced coherent mixture of virtual paths in laser-dressed helium: energetic electron impact excitation

NASA Astrophysics Data System (ADS)

Agueny, Hicham; Makhoute, Abdelkader; Dubois, Alain

2017-06-01

We theoretically investigate quantum virtual path interference caused by the dynamic Stark effect in bound-bound electronic transitions. The effect is studied in an intermediate resonant region and in connection with the energetic electron impact excitation of a helium atom embedded in a weak low-frequency laser field. The process under investigation is dealt with via a Born-Floquet approach. Numerical calculations show a resonant feature in laser-assisted cross sections. The latter is found to be sensitive to the intensity of the laser field dressing. We show that this feature is a signature of quantum beats which result from the coherent mixture of different quantum virtual pathways, and that excitation may follow in order to end up with a common final channel. This mixture arises from the dynamic Stark effect, which produces a set of avoided crossings in laser-dressed states. The effect allows one to coherently control quantum virtual path interference by varying the intensity of the laser field dressing. Our findings suggest that the combination of an energetic electron and a weak laser field is a useful tool for the coherent control of nonadiabatic transitions in an intermediate resonant region.

Simulations of four-dimensional simplicial quantum gravity as dynamical triangulation

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

Agishtein, M.E.; Migdal, A.A.

1992-04-20

In this paper, Four-Dimensional Simplicial Quantum Gravity is simulated using the dynamical triangulation approach. The authors studied simplicial manifolds of spherical topology and found the critical line for the cosmological constant as a function of the gravitational one, separating the phases of opened and closed Universe. When the bare cosmological constant approaches this line from above, the four-volume grows: the authors reached about 5 {times} 10{sup 4} simplexes, which proved to be sufficient for the statistical limit of infinite volume. However, for the genuine continuum theory of gravity, the parameters of the lattice model should be further adjusted to reachmore » the second order phase transition point, where the correlation length grows to infinity. The authors varied the gravitational constant, and they found the first order phase transition, similar to the one found in three-dimensional model, except in 4D the fluctuations are rather large at the transition point, so that this is close to the second order phase transition. The average curvature in cutoff units is large and positive in one phase (gravity), and small negative in another (antigravity). The authors studied the fractal geometry of both phases, using the heavy particle propagator to define the geodesic map, as well as with the old approach using the shortest lattice paths.« less

Diode-Laser Absorption Sensor for Line-of-Sight Gas Temperature Distributions

NASA Astrophysics Data System (ADS)

Sanders, Scott T.; Wang, Jian; Jeffries, Jay B.; Hanson, Ronald K.

2001-08-01

Line-of-sight diode-laser absorption techniques have been extended to enable temperature measurements in nonuniform-property flows. The sensing strategy for such flows exploits the broad wavelength-scanning abilities ( >1.7 nm ~ 30 cm-1 ) of a vertical cavity surface-emitting laser (VCSEL) to interrogate multiple absorption transitions along a single line of sight. To demonstrate the strategy, a VCSEL-based sensor for oxygen gas temperature distributions was developed. A VCSEL beam was directed through paths containing atmospheric-pressure air with known (and relatively simple) temperature distributions in the 200 -700 K range. The VCSEL was scanned over ten transitions in the R branch of the oxygen A band near 760 nm and optionally over six transitions in the P branch. Temperature distribution information can be inferred from these scans because the line strength of each probed transition has a unique temperature dependence; the measurement accuracy and resolution depend on the details of this temperature dependence and on the total number of lines scanned. The performance of the sensing strategy can be optimized and predicted theoretically. Because the sensor exhibits a fast time response ( ~30 ms) and can be adapted to probe a variety of species over a range of temperatures and pressures, it shows promise for industrial application.

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

PubMed Central

Matsunaga, Yasuhiro; Fujisaki, Hiroshi; Terada, Tohru; Furuta, Tadaomi; Moritsugu, Kei; Kidera, Akinori

2012-01-01

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme. PMID:22685395

The Relationship between Interpersonal Violence Victimization and Smoking Behavior across Time and by Gender.

PubMed

Kristman-Valente, Allison N; Oesterle, Sabrina; Hill, Karl G; Wells, Elizabeth A; Epstein, Marina; Jones, Tiffany M; Hawkins, J David

2016-01-01

The current study examined relationships between interpersonal violence victimization and smoking from childhood to adulthood. Data were from a community-based longitudinal study (N = 808) spanning ages 10 - 33. Cross-lag path analysis was used to model concurrent, directional, and reciprocal effects. Results indicate that childhood physical abuse predicted smoking and partner violence in young adulthood; partner violence and smoking were reciprocally related in the transition from young-adulthood to adulthood. Gender differences in this relationship were not detected. Social work prevention efforts focused on interpersonal violence and interventions targeting smoking cessation may be critical factors for reducing both issues.

The Relationship between Interpersonal Violence Victimization and Smoking Behavior across Time and by Gender

PubMed Central

KRISTMAN-VALENTE, ALLISON N.; OESTERLE, SABRINA; HILL, KARL G.; WELLS, ELIZABETH A.; EPSTEIN, MARINA; JONES, TIFFANY M.; HAWKINS, J. DAVID

2016-01-01

The current study examined relationships between interpersonal violence victimization and smoking from childhood to adulthood. Data were from a community-based longitudinal study (N = 808) spanning ages 10 - 33. Cross-lag path analysis was used to model concurrent, directional, and reciprocal effects. Results indicate that childhood physical abuse predicted smoking and partner violence in young adulthood; partner violence and smoking were reciprocally related in the transition from young-adulthood to adulthood. Gender differences in this relationship were not detected. Social work prevention efforts focused on interpersonal violence and interventions targeting smoking cessation may be critical factors for reducing both issues. PMID:28243179

Microscopic Studies of Quantum Phase Transitions in Optical Lattices

NASA Astrophysics Data System (ADS)

Bakr, Waseem S.

2011-12-01

In this thesis, I report on experiments that microscopically probe quantum phase transitions of ultracold atoms in optical lattices. We have developed a "quantum gas microscope" that allowed, for the first time, optical imaging and manipulation of single atoms in a quantum-degenerate gas on individual sites of an optical lattice. This system acts as a quantum simulator of strongly correlated materials, which are currently the subject of intense research because of the technological potential of high--T c superconductors and spintronic materials. We have used our microscope to study the superfluid to Mott insulator transition in bosons and a magnetic quantum phase transition in a spin system. In our microscopic study of the superfluid-insulator transition, we have characterized the on-site number statistics in a space- and time-resolved manner. We observed Mott insulators with fidelities as high as 99%, corresponding to entropies of 0.06kB per particle. We also measured local quantum dynamics and directly imaged the shell structure of the Mott insulator. I report on the first quantum magnetism experiments in optical lattices. We have realized a quantum Ising chain in a magnetic field, and observed a quantum phase transition between a paramagnet and antiferromagnet. We achieved strong spin interactions by encoding spins in excitations of a Mott insulator in a tilted lattice. We detected the transition by measuring the total magnetization of the system across the transition using in-situ measurements as well as the Neel ordering in the antiferromagnetic state using noise-correlation techniques. We characterized the dynamics of domain formation in the system. The spin mapping introduced opens up a new path to realizing more exotic states in optical lattices including spin liquids and quantum valence bond solids. As our system sizes become larger, simulating their physics on classical computers will require exponentially larger resources because of entanglement build-up near a quantum phase transition. We have demonstrated a quantum simulator in which all degrees of freedom can be read out microscopically, allowing the simulation of quantum many-body systems with manageable resources. More generally, the ability to image and manipulate individual atoms in optical lattices opens an avenue towards scalable quantum computation.

Synthetic receiver function profiles through the upper mantle and the transition zone for upwelling scenarios

NASA Astrophysics Data System (ADS)

Nagel, Thorsten; Düsterhöft, Erik; Schiffer, Christian

2017-04-01

We investigate the signature relevant mantle lithologies leave in the receiver function record for different adiabatic thermal gradients down to 800 kilometers depth. The parameter space is chosen to target the visibility of upwelling mantle (a plume). Seismic velocities for depleted mantle, primitive mantle, and three pyroxenites are extracted from thermodynamically calculated phases diagrams, which also provide the adiabatic decompression paths. Results suggest that compositional variations, i.e. the presence or absence of considerable amounts of pyroxenites in primitive mantle should produce a clear footprint while horizontal differences in thermal gradients for similar compositions might be more subtle. Peridotites best record the classic discontinuities at around 410 and 650 kilometers depth, which are associated with the olivin-wadsleyite and ringwoodite-perovskite transitions, respectively. Pyroxenites, instead, show the garnet-perovskite transition below 700 kilometers depth and SiO2-supersaturated compositions like MORB display the coesite-stishovite transition between 300 and 340 kilometers depth. The latter shows the strongest temperature-depth dependency of all significant transitions potentially allowing to infer information about the thermal state if the mantle contains a sufficient fraction of MORB-like compositions. For primitive and depleted mantle compositions, the olivin-wadsleyite transition shows a certain temperature-depth dependency reflected in slightly larger delay times for higher thermal gradients. The lower-upper-mantle discontinuity, however, is predicted to display larger delay times for higher thermal gradients although the associated assemblage transition occurs at shallower depths thus requiring a very careful depth migration if a thermal anomaly should be recognized. This counterintuitive behavior results from the downward replacement of the assemblage wadsleyite+garnet with the assemblage garnet+periclase at high temperatures. This transition causes even lower seismic velocities with greater depth (following an adiabatic gradient), the highly continuous nature of the reaction, however, should produce only a smooth negative conversion. In contrast, a small positive conversion is expected at normal thermal gradients in the same depth range between 500 and 550 kilometers because of the wadsleyite-ringwoodite-transition. Hence, the polarity of the 520 discontinuity also offers a possibility to recognize the thermal state of the upper mantle.

Effects of the thermal and magnetic paths on first order martensite transition of disordered Ni45Mn44Sn9In2 Heusler alloy exhibiting a giant magnetocaloric effect and magnetoresistance near room temperature

NASA Astrophysics Data System (ADS)

Chabri, T.; Ghosh, A.; Nair, Sunil; Awasthi, A. M.; Venimadhav, A.; Nath, T. K.

2018-05-01

The existence of a first order martensite transition in off-stoichiometric Ni45Mn44Sn9In2 ferromagnetic shape memory Heusler alloy has been clearly observed by thermal, magnetic, and magneto-transport measurements. Field and thermal path dependence of the change in large magnetic entropy and negative magnetoresistance are observed, which originate due to the sharp change in magnetization driven by metamagnetic transition from the weakly magnetic martensite phase to the ferromagnetic austenite phase in the vicinity of the martensite transition. The noticeable shift in the martensite transition with the application of a magnetic field is the most significant feature of the present study. This shift is due to the interplay of the austenite and martensite phase fraction in the alloy. The different aspects of the first order martensite transition, e.g. broadening of the martensite transition and the field induced arrest of the austenite phase are mainly related to the dynamics of coexisting phases in the vicinity of the martensite transition. The alloy also shows a second order ferromagnetic  →  paramagnetic transition near the Curie temperature of the austenite phase. A noticeably large change in magnetic entropy (ΔS M   =  24 J kg‑1 K‑1 at 298 K) and magnetoresistance (=  ‑33% at 295 K) has been observed for the change in 5 and 8 T magnetic fields, respectively. The change in adiabatic temperature for the change in a magnetic field of 5 T is found to be  ‑3.8 K at 299 K. The low cost of the ingredients and the large change in magnetic entropy very near to the room temperature makes Ni45Mn44Sn9In2 alloy a promising magnetic refrigerant for real technological application.

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems.

PubMed

Velez-Vega, Camilo; Gilson, Michael K

2012-03-13

The field of host-guest chemistry provides computationally tractable yet informative model systems for biomolecular recognition. We applied molecular dynamics simulations to study the forces and mechanical stresses associated with forced dissociation of aqueous cucurbituril-guest complexes with high binding affinities. First, the unbinding transitions were modeled with constant velocity pulling (steered dynamics) and a soft spring constant, to model atomic force microscopy (AFM) experiments. The computed length-force profiles yield rupture forces in good agreement with available measurements. We also used steered dynamics with high spring constants to generate paths characterized by a tight control over the specified pulling distance; these paths were then equilibrated via umbrella sampling simulations and used to compute time-averaged mechanical stresses along the dissociation pathways. The stress calculations proved to be informative regarding the key interactions determining the length-force profiles and rupture forces. In particular, the unbinding transition of one complex is found to be a stepwise process, which is initially dominated by electrostatic interactions between the guest's ammoniums and the host's carbonyl groups, and subsequently limited by the extraction of the guest's bulky bicyclooctane moiety; the latter step requires some bond stretching at the cucurbituril's extraction portal. Conversely, the dissociation of a second complex with a more slender guest is mainly driven by successive electrostatic interactions between the different guest's ammoniums and the host's carbonyl groups. The calculations also provide information on the origins of thermodynamic irreversibilities in these forced dissociation processes.

A mathematical model to optimize the drain phase in gravity-based peritoneal dialysis systems.

PubMed

Akonur, Alp; Lo, Ying-Cheng; Cizman, Borut

2010-01-01

Use of patient-specific drain-phase parameters has previously been suggested to improve peritoneal dialysis (PD) adequacy. Improving management of the drain period may also help to minimize intraperitoneal volume (IPV). A typical gravity-based drain profile consists of a relatively constant initial fast-flow period, followed by a transition period and a decaying slow-flow period. That profile was modeled using the equation VD(t) = (V(D0) - Q(MAX) x t) xphi + (V(D0) x e(-alphat)) x (1 - phi), where V(D)(t) is the time-dependent dialysate volume; V(D0), the dialysate volume at the start of the drain; Q(MAX), the maximum drain flow rate; alpha, the exponential drain constant; and phi, the unit step function with respect to the flow transition. We simulated the effects of the assumed patient-specific maximum drain flow (Q(MAX)) and transition volume (psi), and the peritoneal volume percentage when transition occurs,for fixed device-specific drain parameters. Average patient transport parameters were assumed during 5-exchange therapy with 10 L of PD solution. Changes in therapy performance strongly depended on the drain parameters. Comparing 400 mL/85% with 200 mL/65% (Q(MAX/psi), drain time (7.5 min vs. 13.5 min) and IPV (2769 mL vs. 2355 mL) increased when the initial drain flow was low and the transition quick. Ultrafiltration and solute clearances remained relatively similar. Such differences were augmented up to a drain time of 22 minutes and an IPV of more than 3 L when Q(MAX) was 100 mL/min. The ability to model individual drain conditions together with water and solute transport may help to prevent patient discomfort with gravity-based PD. However, it is essential to note that practical difficulties such as displaced catheters and obstructed flow paths cause variability in drain characteristics even for the same patient, limiting the clinical applicability of this model.

Detecting reactive islands using Lagrangian descriptors and the relevance to transition path sampling.

PubMed

Patra, Sarbani; Keshavamurthy, Srihari

2018-02-14

It has been known for sometime now that isomerization reactions, classically, are mediated by phase space structures called reactive islands (RI). RIs provide one possible route to correct for the nonstatistical effects in the reaction dynamics. In this work, we map out the reactive islands for the two dimensional Müller-Brown model potential and show that the reactive islands are intimately linked to the issue of rare event sampling. In particular, we establish the sensitivity of the so called committor probabilities, useful quantities in the transition path sampling technique, to the hierarchical RI structures. Mapping out the RI structure for high dimensional systems, however, is a challenging task. Here, we show that the technique of Lagrangian descriptors is able to effectively identify the RI hierarchy in the model system. Based on our results, we suggest that the Lagrangian descriptors can be useful for detecting RIs in high dimensional systems.

Effects of snowmelt on watershed transit time distributions

NASA Astrophysics Data System (ADS)

Fang, Z.; Carroll, R. W. H.; Harman, C. J.; Wilusz, D. C.; Schumer, R.

2017-12-01

Snowmelt is the principal control of the timing and magnitude of water flow through alpine watersheds, but the streamflow generated may be displaced groundwater. To quantify this effect, we use a rank StorAge Selection (rSAS) model to estimate time-dependent travel time distributions (TTDs) for the East River Catchment (ERC, 84 km2) - a headwater basin of the Colorado River, and newly designated as the Lawrence Berkeley National Laboratory's Watershed Function Science Focus Area (SFA). Through the SFA, observational networks related to precipitation and stream fluxes have been established with a focus on environmental tracers and stable isotopes. The United Stated Geological Survey Precipitation Runoff Modeling System (PRMS) was used to estimate spatially- and temporally-variable boundary fluxes of effective precipitation (snowmelt & rain), evapotranspiration, and subsurface storage. The DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm was used to calibrate the rSAS model to observed stream isotopic concentration data and quantify uncertainty. The sensitivity of the simulated TTDs to systematic changes in the boundary fluxes was explored. Different PRMS and rSAS model parameters setup were tested to explore how they affect the relationship between input precipitation, especially snowmelt, and the estimated TTDs. Wavelet Coherence Analysis (WCA) was applied to investigate the seasonality of TTD simulations. Our ultimate goal is insight into how the Colorado River headwater catchments store and route water, and how sensitive flow paths and transit times are to climatic changes.

Tunable, high-sensitive measurement of inter-dot transition via tunneling induced absorption

NASA Astrophysics Data System (ADS)

Peng, Yandong; Yang, Aihong; Chen, Bing; Li, Lei; Liu, Shande; Guo, Hongju

2016-10-01

A tunable, narrow absorption spectrum induced by resonant tunneling is demonstrated and proposed for measuring interdot tunneling. Tunneling-induced absorption (TIA) arises from constructive interference between different transition paths, and the large nonlinear TIA significantly enhances the total absorption. The narrow nonlinear TIA spectrum is sensitive to inter-dot tunneling, and its sensor characteristics, including sensitivity and bandwidth, are investigated in weak-coupling and strong-coupling regimes, respectively.

Mandatory bundled payment getting into formation for value-based care.

PubMed

Fink, John

2015-10-01

Succeeding under Medicare's enterprise Comprehensive Care for Joint Replacement Model will require collaboration among caregivers and financial arrangements to align incentives Priorities for most organization's transition to becoming a value-based hospitals will be care redesign, supply-purchasing strategy, and post-acute care provider partnering. Pursuing value for your joint replacement program will chart a path for other service lines and lead your organization's transition to becoming a value-based enterprise.

HIFiRE-5 Flight Test Preliminary Results (Postprint)

DTIC Science & Technology

2013-11-01

DMARS-R) IMU and Ashtech DG14 Global Positioning System receiver. Results show that a tripped transition occurred on the test article leading edge...Reference System (DMARS-R) IMU and Ashtech DG14 Global Positioning System receiver. Results show that a tripped transition occurred on the test...pitch angle relative to earth as measured by IMU , or flight-path elevation angle as measured by GPS or IMU , degrees  = body-fixed angular coordinate

On the mode-coupling treatment of collective density fluctuations for quantum liquids: para-hydrogen and normal liquid helium.

PubMed

Kletenik-Edelman, Orly; Reichman, David R; Rabani, Eran

2011-01-28

A novel quantum mode coupling theory combined with a kinetic approach is developed for the description of collective density fluctuations in quantum liquids characterized by Boltzmann statistics. Three mode-coupling approximations are presented and applied to study the dynamic response of para-hydrogen near the triple point and normal liquid helium above the λ-transition. The theory is compared with experimental results and to the exact imaginary time data generated by path integral Monte Carlo simulations. While for liquid para-hydrogen the combination of kinetic and quantum mode-coupling theory provides semi-quantitative results for both short and long time dynamics, it fails for normal liquid helium. A discussion of this failure based on the ideal gas limit is presented.

Sexual revictimization during women's first year of college: self-blame and sexual refusal assertiveness as possible mechanisms.

PubMed

Katz, Jennifer; May, Pamela; Sörensen, Silvia; DelTosta, Jill

2010-11-01

Although sexual victimization during adolescence increases risk for later revictimization, mechanisms for increased risk among new college students have not been identified. Female undergraduates (N = 87) were assessed at the start and end of their first academic year. Those who reported initial sexual victimization at Time 1 were more likely than other women to report later college victimization at Time 2. Path analyses showed that self-blame and decreased sexual refusal assertiveness (SRA) explained this effect. Specifically, initial victimization was associated with increased self-blame; in turn, self-blame indirectly predicted later college victimization via decreased sexual refusal assertiveness. Prevention efforts focused on self-blame and other barriers to SRA may reduce risk for revictimization during women's transition to college.

Routing optimization in networks based on traffic gravitational field model

NASA Astrophysics Data System (ADS)

Liu, Longgeng; Luo, Guangchun

2017-04-01

For research on the gravitational field routing mechanism on complex networks, we further analyze the gravitational effect of paths. In this study, we introduce the concept of path confidence degree to evaluate the unblocked reliability of paths that it takes the traffic state of all nodes on the path into account from the overall. On the basis of this, we propose an improved gravitational field routing protocol considering all the nodes’ gravities on the path and the path confidence degree. In order to evaluate the transmission performance of the routing strategy, an order parameter is introduced to measure the network throughput by the critical value of phase transition from a free-flow phase to a jammed phase, and the betweenness centrality is used to evaluate the transmission performance and traffic congestion of the network. Simulation results show that compared with the shortest-path routing strategy and the previous gravitational field routing strategy, the proposed algorithm improves the network throughput considerably and effectively balances the traffic load within the network, and all nodes in the network are utilized high efficiently. As long as γ ≥ α, the transmission performance can reach the maximum and remains unchanged for different α and γ, which ensures that the proposed routing protocol is high efficient and stable.

Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths

PubMed Central

Li, Chunhe; Wang, Jin

2013-01-01

Cellular reprogramming has been recently intensively studied experimentally. We developed a global potential landscape and kinetic path framework to explore a human stem cell developmental network composed of 52 genes. We uncovered the underlying landscape for the stem cell network with two basins of attractions representing stem and differentiated cell states, quantified and exhibited the high dimensional biological paths for the differentiation and reprogramming process, connecting the stem cell state and differentiated cell state. Both the landscape and non-equilibrium curl flux determine the dynamics of cell differentiation jointly. Flux leads the kinetic paths to be deviated from the steepest descent gradient path, and the corresponding differentiation and reprogramming paths are irreversible. Quantification of paths allows us to find out how the differentiation and reprogramming occur and which important states they go through. We show the developmental process proceeds as moving from the stem cell basin of attraction to the differentiation basin of attraction. The landscape topography characterized by the barrier heights and transition rates quantitatively determine the global stability and kinetic speed of cell fate decision process for development. Through the global sensitivity analysis, we provided some specific predictions for the effects of key genes and regulation connections on the cellular differentiation or reprogramming process. Key links from sensitivity analysis and biological paths can be used to guide the differentiation designs or reprogramming tactics. PMID:23935477

Curvature Continuous and Bounded Path Planning for Fixed-Wing UAVs

PubMed Central

Jiang, Peng; Li, Deshi; Sun, Tao

2017-01-01

Unmanned Aerial Vehicles (UAVs) play an important role in applications such as data collection and target reconnaissance. An accurate and optimal path can effectively increase the mission success rate in the case of small UAVs. Although path planning for UAVs is similar to that for traditional mobile robots, the special kinematic characteristics of UAVs (such as their minimum turning radius) have not been taken into account in previous studies. In this paper, we propose a locally-adjustable, continuous-curvature, bounded path-planning algorithm for fixed-wing UAVs. To deal with the curvature discontinuity problem, an optimal interpolation algorithm and a key-point shift algorithm are proposed based on the derivation of a curvature continuity condition. To meet the upper bound for curvature and to render the curvature extrema controllable, a local replanning scheme is designed by combining arcs and Bezier curves with monotonic curvature. In particular, a path transition mechanism is built for the replanning phase using minimum curvature circles for a planning philosophy. Numerical results demonstrate that the analytical planning algorithm can effectively generate continuous-curvature paths, while satisfying the curvature upper bound constraint and allowing UAVs to pass through all predefined waypoints in the desired mission region. PMID:28925960

Curvature Continuous and Bounded Path Planning for Fixed-Wing UAVs.

PubMed

Wang, Xiaoliang; Jiang, Peng; Li, Deshi; Sun, Tao

2017-09-19

Unmanned Aerial Vehicles (UAVs) play an important role in applications such as data collection and target reconnaissance. An accurate and optimal path can effectively increase the mission success rate in the case of small UAVs. Although path planning for UAVs is similar to that for traditional mobile robots, the special kinematic characteristics of UAVs (such as their minimum turning radius) have not been taken into account in previous studies. In this paper, we propose a locally-adjustable, continuous-curvature, bounded path-planning algorithm for fixed-wing UAVs. To deal with the curvature discontinuity problem, an optimal interpolation algorithm and a key-point shift algorithm are proposed based on the derivation of a curvature continuity condition. To meet the upper bound for curvature and to render the curvature extrema controllable, a local replanning scheme is designed by combining arcs and Bezier curves with monotonic curvature. In particular, a path transition mechanism is built for the replanning phase using minimum curvature circles for a planning philosophy. Numerical results demonstrate that the analytical planning algorithm can effectively generate continuous-curvature paths, while satisfying the curvature upper bound constraint and allowing UAVs to pass through all predefined waypoints in the desired mission region.

TDR method for determine IC's parameters

NASA Astrophysics Data System (ADS)

Timoshenkov, V.; Rodionov, D.; Khlybov, A.

2016-12-01

Frequency domain simulation is a widely used approach for determine integrated circuits parameters. This approach can be found in most of software tools used in IC industry. Time domain simulation approach shows intensive usage last years due to some advantages. In particular it applicable for analysis of nonlinear and nonstationary systems where frequency domain is inapplicable. Resolution of time domain systems allow see heterogeneities on distance 1mm, determine it parameters and properties. Authors used approach based on detecting reflected signals from heterogeneities - time domain reflectometry (TDR). Field effect transistor technology scaling up to 30-60nm gate length and 10nm gate dielectric, heterojunction bi-polar transistors with 10-30nm base width allows fabricate digital IC's with 20GHz clock frequency and RF-IC's with tens GHz bandwidth. Such devices and operation speed suppose transit signal by use microwave lines. There are local heterogeneities can be found inside of the signal path due to connections between different parts of signal lines (stripe line-RF-connector pin, stripe line - IC package pin). These heterogeneities distort signals that cause bandwidth decrease for RF-devices. Time domain research methods of transmission and reflected signals give the opportunities to determine heterogeneities, it properties, parameters and built up equivalent circuits. Experimental results are provided and show possibility for inductance and capacitance measurement up to 25GHz. Measurements contains result of signal path research on IC and printed circuit board (PCB) used for 12GHz RF chips. Also dielectric constant versus frequency was measured up to 35GHz.

Performance Analysis of Stop-Skipping Scheduling Plans in Rail Transit under Time-Dependent Demand

PubMed Central

Cao, Zhichao; Yuan, Zhenzhou; Zhang, Silin

2016-01-01

Stop-skipping is a key method for alleviating congestion in rail transit, where schedules are sometimes difficult to implement. Several mechanisms have been proposed and analyzed in the literature, but very few performance comparisons are available. This study formulated train choice behavior estimation into the model considering passengers’ perception. If a passenger’s train path can be identified, this information would be useful for improving the stop-skipping schedule service. Multi-performance is a key characteristic of our proposed five stop-skipping schedules, but quantified analysis can be used to illustrate the different effects of well-known deterministic and stochastic forms. Problems in the novel category of forms were justified in the context of a single line rather than transit network. We analyzed four deterministic forms based on the well-known A/B stop-skipping operating strategy. A stochastic form was innovatively modeled as a binary integer programming problem. We present a performance analysis of our proposed model to demonstrate that stop-skipping can feasibly be used to improve the service of passengers and enhance the elasticity of train operations under demand variations along with an explicit parametric discussion. PMID:27420087

Performance Analysis of Stop-Skipping Scheduling Plans in Rail Transit under Time-Dependent Demand.

PubMed

Cao, Zhichao; Yuan, Zhenzhou; Zhang, Silin

2016-07-13

Stop-skipping is a key method for alleviating congestion in rail transit, where schedules are sometimes difficult to implement. Several mechanisms have been proposed and analyzed in the literature, but very few performance comparisons are available. This study formulated train choice behavior estimation into the model considering passengers' perception. If a passenger's train path can be identified, this information would be useful for improving the stop-skipping schedule service. Multi-performance is a key characteristic of our proposed five stop-skipping schedules, but quantified analysis can be used to illustrate the different effects of well-known deterministic and stochastic forms. Problems in the novel category of forms were justified in the context of a single line rather than transit network. We analyzed four deterministic forms based on the well-known A/B stop-skipping operating strategy. A stochastic form was innovatively modeled as a binary integer programming problem. We present a performance analysis of our proposed model to demonstrate that stop-skipping can feasibly be used to improve the service of passengers and enhance the elasticity of train operations under demand variations along with an explicit parametric discussion.

Phase transitions in the system CaCO3 at high P and T determined by in situ vibrational spectroscopy in diamond anvil cells and first-principles simulations

NASA Astrophysics Data System (ADS)

Koch-Müller, Monika; Jahn, Sandro; Birkholz, Natalie; Ritter, Eglof; Schade, Ulrich

2016-09-01

The stability of the high-pressure CaCO3 calcite (cc)-related polymorphs was studied in experiments that were performed in conventional diamond anvil cells (DAC) at room temperature as a function of pressure up to 30 GPa as well as in internally heated diamond anvil cells (DAC-HT) at pressures and temperatures up to 20 GPa and 800 K. To probe structural changes, we used Raman and FTIR spectroscopy. For the latter, we applied conventional and synchrotron mid-infrared as well as synchrotron far-infrared radiation. Within the cc-III stability field (2.2-15 GPa at room temperature, e.g., Catalli and Williams in Phys Chem Miner 32(5-6):412-417, 2005), we observed in the Raman spectra consistently three different spectral patterns: Two patterns at pressures below and above 3.3 GPa were already described in Pippinger et al. (Phys Chem Miner 42(1):29-43, 2015) and assigned to the phase transition of cc-IIIb to cc-III at 3.3 GPa. In addition, we observed a clear change between 5 and 6 GPa that is independent of the starting material and the pressure path and time path of the experiments. This apparent change in the spectral pattern is only visible in the low-frequency range of the Raman spectra—not in the infrared spectra. Complementary electronic structure calculations confirm the existence of three distinct stability regions of cc-III-type phases at pressures up to about 15 GPa. By combining experimental and simulation data, we interpret the transition at 5-6 GPa as a re-appearance of the cc-IIIb phase. In all types of experiments, we confirmed the transition from cc-IIIb to cc-VI at about 15 GPa at room temperature. We found that temperature stabilizes cc-VI to lower pressure. The reaction cc-IIIb to cc-VI has a negative slope of -7.0 × 10-3 GPa K-1. Finally, we discuss the possibility of the dense cc-VI phase being more stable than aragonite at certain pressure and temperature conditions relevant to the Earth's mantle.

Water evaporation: a transition path sampling study.

PubMed

Varilly, Patrick; Chandler, David

2013-02-07

We use transition path sampling to study evaporation in the SPC/E model of liquid water. On the basis of thousands of evaporation trajectories, we characterize the members of the transition state ensemble (TSE), which exhibit a liquid-vapor interface with predominantly negative mean curvature at the site of evaporation. We also find that after evaporation is complete, the distributions of translational and angular momenta of the evaporated water are Maxwellian with a temperature equal to that of the liquid. To characterize the evaporation trajectories in their entirety, we find that it suffices to project them onto just two coordinates: the distance of the evaporating molecule to the instantaneous liquid-vapor interface and the velocity of the water along the average interface normal. In this projected space, we find that the TSE is well-captured by a simple model of ballistic escape from a deep potential well, with no additional barrier to evaporation beyond the cohesive strength of the liquid. Equivalently, they are consistent with a near-unity probability for a water molecule impinging upon a liquid droplet to condense. These results agree with previous simulations and with some, but not all, recent experiments.

Chirped quantum cascade laser induced rapid passage signatures in an optically thick gas

NASA Astrophysics Data System (ADS)

Northern, J. H.; Ritchie, G. A. D.; Smakman, E. P.; van Helden, J. H.; Walker, R. J.; Duxbury, G.

2011-01-01

We report observations of rapid passage signals induced in samples of N2O and CH4 present in a multipass cell with an optical path length of 5 m. The effect of laser power and chirp rate upon the signals has been studied by utilising two different chirped quantum cascade lasers operating around 8 μm. The rapid passage signals exhibit an increasing delay in the switch from absorption to emission as a function of increased gas pressure (up to 8 Torr of gas). By comparing a selection of transitions in N2O and CH4, we show that, unlike ammonia, this `pressure shift' is independent of the transition dipole moment, spectroscopic branch probed and laser chirp rate. As the transition dipole moment is much larger in nitrous oxide than methane, we believe that this indicates that N2O-N2O collisions are more efficient at removing coherence from the polarised sample than CH4-CH4 collisions. We have also observed this pressure shift in a short path length of 40 cm, although with a much reduced value, indicating that propagation effects are important in this optically thick minimally damped system.

A study of electron transfer using a three-level system coupled to an ohmic bath

NASA Technical Reports Server (NTRS)

Takasu, Masako; Chandler, David

1993-01-01

Electron transfer is studied using a multi-level system coupled to a bosonic bath. Two body correlation functions are obtained using both exact enumeration of spin paths and Monte Carlo simulation. It was found that the phase boundary for the coherent-incoherent transition lies at a smaller friction in the asymmetric two-level model than in the symmetric two-level model. A similar coherent-incoherent transition is observed for three-level system.

Evaluating methods for estimating space-time paths of individuals in calculating long-term personal exposure to air pollution

NASA Astrophysics Data System (ADS)

Schmitz, Oliver; Soenario, Ivan; Vaartjes, Ilonca; Strak, Maciek; Hoek, Gerard; Brunekreef, Bert; Dijst, Martin; Karssenberg, Derek

2016-04-01

Air pollution is one of the major concerns for human health. Associations between air pollution and health are often calculated using long-term (i.e. years to decades) information on personal exposure for each individual in a cohort. Personal exposure is the air pollution aggregated along the space-time path visited by an individual. As air pollution may vary considerably in space and time, for instance due to motorised traffic, the estimation of the spatio-temporal location of a persons' space-time path is important to identify the personal exposure. However, long term exposure is mostly calculated using the air pollution concentration at the x, y location of someone's home which does not consider that individuals are mobile (commuting, recreation, relocation). This assumption is often made as it is a major challenge to estimate space-time paths for all individuals in large cohorts, mostly because limited information on mobility of individuals is available. We address this issue by evaluating multiple approaches for the calculation of space-time paths, thereby estimating the personal exposure along these space-time paths with hyper resolution air pollution maps at national scale. This allows us to evaluate the effect of the space-time path and resulting personal exposure. Air pollution (e.g. NO2, PM10) was mapped for the entire Netherlands at a resolution of 5×5 m2 using the land use regression models developed in the European Study of Cohorts for Air Pollution Effects (ESCAPE, http://escapeproject.eu/) and the open source software PCRaster (http://www.pcraster.eu). The models use predictor variables like population density, land use, and traffic related data sets, and are able to model spatial variation and within-city variability of annual average concentration values. We approximated space-time paths for all individuals in a cohort using various aggregations, including those representing space-time paths as the outline of a persons' home or associated parcel of land, the 4 digit postal code area or neighbourhood of a persons' home, circular areas around the home, and spatial probability distributions of space-time paths during commuting. Personal exposure was estimated by averaging concentrations over these space-time paths, for each individual in a cohort. Preliminary results show considerable differences of a persons' exposure using these various approaches of space-time path aggregation, presumably because air pollution shows large variation over short distances.

Precursor to the Matuyama/Brunhes Polarity Transition 0.78 Million Years Ago at Bishop, CA

NASA Astrophysics Data System (ADS)

Kravchinsky, Vadim; Liddicoat, Joseph

2013-04-01

Van Zijl et al.'s 1962 report of a polarity transition in Stormberg lavas was the first of many investigations of the Matuyama/Brunhes polarity transition (MBPT) about 0.78 m.y. ago. Among the earliest of those investigations was a study of bathyal siltstone in the Boso Peninsula in Japan (Niitsuma, 1971; Okada and Niitsuma, 1989). That investigation was preceded by a report that the relative intensity of the palaeomagnetic field as recorded in a marine core is reduced for a longer period of time than is required for the field directions to reverse (Ninkovich et al., 1966), a discovery that was summarized for other reversals in cored marine sediment (Opdyke, 1973). In the U.S., Hillhouse and Cox (1976) documented the field directions and relative intensity during the MBPT using exposed Pleistocene Lake Tecopa sediments in southeastern California. They reported a generally smooth path of the Virtual Geomagnetic Poles (VGPs) as the field changed from reverse to normal that does not coincide with the VGP path for the MBPT in Japan, concluding that the transitional field is predominantly the non-dipole field. At Lake Tecopa, as in the marine record, the reduction in field strength occurred sooner and lasted longer by a factor of at least two the time required for the directions to reverse polarity, which was confirmed by Valet et al. (1988) in a restudy of the Lake Tecopa sediments. The Lake Tecopa study by Hillhouse and Cox (1976) was followed by one of Pleistocene lacustrine sediments exposed beneath the Bishop Tuff (Dalrymple et al., 1965) near Bishop, California (37.4˚ N, 241˚ E) (Liddicoat, 1982, 1993). The data we report are for directional and normalized relative intensity measurements of additional samples from each horizon at the Bishop locality that indicate the time spanned by the reduction in relative intensity for the full transition exceeds by about 20 percent the time during which the palaeomagnetic directions reverse. Although the change in field direction is difficult to establish with much certainty because there is a large scatter of directions for multiple (usually six) samples for each measured horizon (Liddicoat, 1993), it is possible to record a brief interval of opposite polarity near each end of the transition. During the onset of the transition, an estimated 1,000 years of normal polarity occurs at three sites separated along strike by 15 m. The change in polarity is in unweathered siltstone in cubes 2 cm on a side that were either demagnetized in an alternating field to 100 mT or heated to 600˚C. The interval of normal polarity has approximately 0.5 m of reverse polarity above it, which is overlain by 5 m of unconsolidated coarse sand. The time represented by the sand bed is not known, but it is reasonable to expect it could be considerable, but maybe no longer than 10,000 years. On that assumption, the normal polarity at Bishop might be the precursor to the MBPT Hartl and Tauxe (1996) discovered at ODP Hole 804C in the equatorial Pacific Ocean (1.0˚ N, 161.4˚ E.), or is in loess in China (35.7˚ N, 109.4˚ E) and elsewhere as referenced in Jin et al. (2012). In the upper third of the MBPT there is a partial recovery of the relative intensity, and in the Brunhes Normal Chron there is a brief interval of reverse polarity that might be the reverse interval Coe et al. (2004) located in volcanic rocks at Maui, Hawaii (20.8˚ N, 203.7˚ E).

Killing (absorption) versus survival in random motion

NASA Astrophysics Data System (ADS)

Garbaczewski, Piotr

2017-09-01

We address diffusion processes in a bounded domain, while focusing on somewhat unexplored affinities between the presence of absorbing and/or inaccessible boundaries. For the Brownian motion (Lévy-stable cases are briefly mentioned) model-independent features are established of the dynamical law that underlies the short-time behavior of these random paths, whose overall lifetime is predefined to be long. As a by-product, the limiting regime of a permanent trapping in a domain is obtained. We demonstrate that the adopted conditioning method, involving the so-called Bernstein transition function, works properly also in an unbounded domain, for stochastic processes with killing (Feynman-Kac kernels play the role of transition densities), provided the spectrum of the related semigroup operator is discrete. The method is shown to be useful in the case, when the spectrum of the generator goes down to zero and no isolated minimal (ground state) eigenvalue is in existence, like in the problem of the long-term survival on a half-line with a sink at origin.

Demonstration of Synaptic Behaviors and Resistive Switching Characterizations by Proton Exchange Reactions in Silicon Oxide

PubMed Central

Chang, Yao-Feng; Fowler, Burt; Chen, Ying-Chen; Zhou, Fei; Pan, Chih-Hung; Chang, Ting-Chang; Lee, Jack C.

2016-01-01

We realize a device with biological synaptic behaviors by integrating silicon oxide (SiOx) resistive switching memory with Si diodes. Minimal synaptic power consumption due to sneak-path current is achieved and the capability for spike-induced synaptic behaviors is demonstrated, representing critical milestones for the use of SiO2–based materials in future neuromorphic computing applications. Biological synaptic behaviors such as long-term potentiation (LTP), long-term depression (LTD) and spike-timing dependent plasticity (STDP) are demonstrated systematically using a comprehensive analysis of spike-induced waveforms, and represent interesting potential applications for SiOx-based resistive switching materials. The resistive switching SET transition is modeled as hydrogen (proton) release from (SiH)2 to generate the hydrogen bridge defect, and the RESET transition is modeled as an electrochemical reaction (proton capture) that re-forms (SiH)2. The experimental results suggest a simple, robust approach to realize programmable neuromorphic chips compatible with large-scale CMOS manufacturing technology. PMID:26880381

Demonstration of Synaptic Behaviors and Resistive Switching Characterizations by Proton Exchange Reactions in Silicon Oxide

NASA Astrophysics Data System (ADS)

Chang, Yao-Feng; Fowler, Burt; Chen, Ying-Chen; Zhou, Fei; Pan, Chih-Hung; Chang, Ting-Chang; Lee, Jack C.

2016-02-01

We realize a device with biological synaptic behaviors by integrating silicon oxide (SiOx) resistive switching memory with Si diodes. Minimal synaptic power consumption due to sneak-path current is achieved and the capability for spike-induced synaptic behaviors is demonstrated, representing critical milestones for the use of SiO2-based materials in future neuromorphic computing applications. Biological synaptic behaviors such as long-term potentiation (LTP), long-term depression (LTD) and spike-timing dependent plasticity (STDP) are demonstrated systematically using a comprehensive analysis of spike-induced waveforms, and represent interesting potential applications for SiOx-based resistive switching materials. The resistive switching SET transition is modeled as hydrogen (proton) release from (SiH)2 to generate the hydrogen bridge defect, and the RESET transition is modeled as an electrochemical reaction (proton capture) that re-forms (SiH)2. The experimental results suggest a simple, robust approach to realize programmable neuromorphic chips compatible with large-scale CMOS manufacturing technology.

A synaptic device built in one diode-one resistor (1D-1R) architecture with intrinsic SiOx-based resistive switching memory

NASA Astrophysics Data System (ADS)

Chang, Yao-Feng; Fowler, Burt; Chen, Ying-Chen; Zhou, Fei; Pan, Chih-Hung; Chang, Kuan-Chang; Tsai, Tsung-Ming; Chang, Ting-Chang; Sze, Simon M.; Lee, Jack C.

2016-04-01

We realize a device with biological synaptic behaviors by integrating silicon oxide (SiOx) resistive switching memory with Si diodes to further minimize total synaptic power consumption due to sneak-path currents and demonstrate the capability for spike-induced synaptic behaviors, representing critical milestones for the use of SiO2-based materials in future neuromorphic computing applications. Biological synaptic behaviors such as long-term potentiation, long-term depression, and spike-timing dependent plasticity are demonstrated systemically with comprehensive investigation of spike waveform analyses and represent a potential application for SiOx-based resistive switching materials. The resistive switching SET transition is modeled as hydrogen (proton) release from the (SiH)2 defect to generate the hydrogenbridge defect, and the RESET transition is modeled as an electrochemical reaction (proton capture) that re-forms (SiH)2. The experimental results suggest a simple, robust approach to realize programmable neuromorphic chips compatible with largescale complementary metal-oxide semiconductor manufacturing technology.

Solvable four-state Landau-Zener model of two interacting qubits with path interference

DOE PAGES

Sinitsyn, Nikolai A.

2015-11-30

In this paper, I identify a nontrivial four-state Landau-Zener model for which transition probabilities between any pair of diabatic states can be determined analytically and exactly. The model describes an experimentally accessible system of two interacting qubits, such as a localized state in a Dirac material with both valley and spin degrees of freedom or a singly charged quantum dot (QD) molecule with spin orbit coupling. Application of the linearly time-dependent magnetic field induces a sequence of quantum level crossings with possibility of interference of different trajectories in a semiclassical picture. I argue that this system satisfies the criteria ofmore » integrability in the multistate Landau-Zener theory, which allows one to derive explicit exact analytical expressions for the transition probability matrix. Finally, I also argue that this model is likely a special case of a larger class of solvable systems, and present a six-state generalization as an example.« less

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.

Critical Slowing Down Governs the Transition to Neuron Spiking

PubMed Central

Meisel, Christian; Klaus, Andreas; Kuehn, Christian; Plenz, Dietmar

2015-01-01

Many complex systems have been found to exhibit critical transitions, or so-called tipping points, which are sudden changes to a qualitatively different system state. These changes can profoundly impact the functioning of a system ranging from controlled state switching to a catastrophic break-down; signals that predict critical transitions are therefore highly desirable. To this end, research efforts have focused on utilizing qualitative changes in markers related to a system’s tendency to recover more slowly from a perturbation the closer it gets to the transition—a phenomenon called critical slowing down. The recently studied scaling of critical slowing down offers a refined path to understand critical transitions: to identify the transition mechanism and improve transition prediction using scaling laws. Here, we outline and apply this strategy for the first time in a real-world system by studying the transition to spiking in neurons of the mammalian cortex. The dynamical system approach has identified two robust mechanisms for the transition from subthreshold activity to spiking, saddle-node and Hopf bifurcation. Although theory provides precise predictions on signatures of critical slowing down near the bifurcation to spiking, quantitative experimental evidence has been lacking. Using whole-cell patch-clamp recordings from pyramidal neurons and fast-spiking interneurons, we show that 1) the transition to spiking dynamically corresponds to a critical transition exhibiting slowing down, 2) the scaling laws suggest a saddle-node bifurcation governing slowing down, and 3) these precise scaling laws can be used to predict the bifurcation point from a limited window of observation. To our knowledge this is the first report of scaling laws of critical slowing down in an experiment. They present a missing link for a broad class of neuroscience modeling and suggest improved estimation of tipping points by incorporating scaling laws of critical slowing down as a strategy applicable to other complex systems. PMID:25706912

Metastable liquid-liquid transition in a molecular model of water

NASA Astrophysics Data System (ADS)

Palmer, Jeremy C.; Martelli, Fausto; Liu, Yang; Car, Roberto; Panagiotopoulos, Athanassios Z.; Debenedetti, Pablo G.

2014-06-01

Liquid water's isothermal compressibility and isobaric heat capacity, and the magnitude of its thermal expansion coefficient, increase sharply on cooling below the equilibrium freezing point. Many experimental, theoretical and computational studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions. Some experimental evidence is consistent with this hypothesis, but no definitive proof of a liquid-liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently. Computer simulations are therefore crucial for exploring water's structure and behaviour in this regime, and have shown that some water models exhibit liquid-liquid transitions and others do not. However, recent work has argued that the liquid-liquid transition has been mistakenly interpreted, and is in fact a liquid-crystal transition in all atomistic models of water. Here we show, by studying the liquid-liquid transition in the ST2 model of water with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition. We follow the rearrangement of water's coordination shell and topological ring structure along a thermodynamically reversible path from the low-density liquid to cubic ice. We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid-liquid transition in the ST2 model of water, and point to the separation of time scales between crystallization and relaxation as being crucial for enabling it.

Metastable liquid-liquid transition in a molecular model of water.

PubMed

Palmer, Jeremy C; Martelli, Fausto; Liu, Yang; Car, Roberto; Panagiotopoulos, Athanassios Z; Debenedetti, Pablo G

2014-06-19

Liquid water's isothermal compressibility and isobaric heat capacity, and the magnitude of its thermal expansion coefficient, increase sharply on cooling below the equilibrium freezing point. Many experimental, theoretical and computational studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions. Some experimental evidence is consistent with this hypothesis, but no definitive proof of a liquid-liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently. Computer simulations are therefore crucial for exploring water's structure and behaviour in this regime, and have shown that some water models exhibit liquid-liquid transitions and others do not. However, recent work has argued that the liquid-liquid transition has been mistakenly interpreted, and is in fact a liquid-crystal transition in all atomistic models of water. Here we show, by studying the liquid-liquid transition in the ST2 model of water with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition. We follow the rearrangement of water's coordination shell and topological ring structure along a thermodynamically reversible path from the low-density liquid to cubic ice. We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid-liquid transition in the ST2 model of water, and point to the separation of time scales between crystallization and relaxation as being crucial for enabling it.

Tunable ion-photon entanglement in an optical cavity.

PubMed

Stute, A; Casabone, B; Schindler, P; Monz, T; Schmidt, P O; Brandstätter, B; Northup, T E; Blatt, R

2012-05-23

Proposed quantum networks require both a quantum interface between light and matter and the coherent control of quantum states. A quantum interface can be realized by entangling the state of a single photon with the state of an atomic or solid-state quantum memory, as demonstrated in recent experiments with trapped ions, neutral atoms, atomic ensembles and nitrogen-vacancy spins. The entangling interaction couples an initial quantum memory state to two possible light-matter states, and the atomic level structure of the memory determines the available coupling paths. In previous work, the transition parameters of these paths determined the phase and amplitude of the final entangled state, unless the memory was initially prepared in a superposition state (a step that requires coherent control). Here we report fully tunable entanglement between a single (40)Ca(+) ion and the polarization state of a single photon within an optical resonator. Our method, based on a bichromatic, cavity-mediated Raman transition, allows us to select two coupling paths and adjust their relative phase and amplitude. The cavity setting enables intrinsically deterministic, high-fidelity generation of any two-qubit entangled state. This approach is applicable to a broad range of candidate systems and thus is a promising method for distributing information within quantum networks.

Ultrafast photo-induced dynamics across the metal-insulator transition of VO2

NASA Astrophysics Data System (ADS)

Wang, Siming; Ramírez, Juan Gabriel; Jeffet, Jonathan; Bar-Ad, Shimshon; Huppert, Dan; Schuller, Ivan K.

2017-04-01

The transient reflectivity of VO2 films across the metal-insulator transition clearly shows that with low-fluence excitation, when insulating domains are dominant, energy transfer from the optically excited electrons to the lattice is not instantaneous, but precedes the superheating-driven expansion of the metallic domains. This implies that the phase transition in the coexistence regime is lattice-, not electronically-driven, at weak laser excitation. The superheated phonons provide the latent heat required for the propagation of the optically-induced phase transition. For VO2 this transition path is significantly different from what has been reported in the strong-excitation regime. We also observe a slow-down of the superheating-driven expansion of the metallic domains around the metal-insulator transition, which is possibly due to the competition among several co-existing phases, or an emergent critical-like behavior.

fastBMA: scalable network inference and transitive reduction.

PubMed

Hung, Ling-Hong; Shi, Kaiyuan; Wu, Migao; Young, William Chad; Raftery, Adrian E; Yeung, Ka Yee

2017-10-01

Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets. When using a single CPU core, fastBMA is up to 100 times faster than the next fastest method, LASSO, with increased accuracy. It is a memory-efficient, parallel, and distributed application that scales to human genome-wide expression data. A 10 000-gene regulation network can be obtained in a matter of hours using a 32-core cloud cluster (2 nodes of 16 cores). fastBMA is a significant improvement over its predecessor ScanBMA. It is more accurate and orders of magnitude faster than other fast network inference methods such as the 1 based on LASSO. The improved scalability allows it to calculate networks from genome scale data in a reasonable time frame. The transitive reduction method can improve accuracy in denser networks. fastBMA is available as code (M.I.T. license) from GitHub (https://github.com/lhhunghimself/fastBMA), as part of the updated networkBMA Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/networkBMA.html) and as ready-to-deploy Docker images (https://hub.docker.com/r/biodepot/fastbma/). © The Authors 2017. Published by Oxford University Press.

Skill of ship-following large-eddy simulations in reproducing MAGIC observations across the northeast Pacific stratocumulus to cumulus transition region

NASA Astrophysics Data System (ADS)

McGibbon, J.; Bretherton, C. S.

2017-06-01

During the Marine ARM GPCI Investigation of Clouds (MAGIC) in October 2011 to September 2012, a container ship making periodic cruises between Los Angeles, CA, and Honolulu, HI, was instrumented with surface meteorological, aerosol and radiation instruments, a cloud radar and ceilometer, and radiosondes. Here large-eddy simulation (LES) is performed in a ship-following frame of reference for 13 four day transects from the MAGIC field campaign. The goal is to assess if LES can skillfully simulate the broad range of observed cloud characteristics and boundary layer structure across the subtropical stratocumulus to cumulus transition region sampled during different seasons and meteorological conditions. Results from Leg 15A, which sampled a particularly well-defined stratocumulus to cumulus transition, demonstrate the approach. The LES reproduces the observed timing of decoupling and transition from stratocumulus to cumulus and matches the observed evolution of boundary layer structure, cloud fraction, liquid water path, and precipitation statistics remarkably well. Considering the simulations of all 13 cruises, the LES skillfully simulates the mean diurnal variation of key measured quantities, including liquid water path (LWP), cloud fraction, measures of decoupling, and cloud radar-derived precipitation. The daily mean quantities are well represented, and daily mean LWP and cloud fraction show the expected correlation with estimated inversion strength. There is a -0.6 K low bias in LES near-surface air temperature that results in a high bias of 5.6 W m-2 in sensible heat flux (SHF). Overall, these results build confidence in the ability of LES to represent the northeast Pacific stratocumulus to trade cumulus transition region.