Push-pull tracer tests: Their information content and use for characterizing non-Fickian, mobile-immobile behavior: INFORMATION CONTENT OF PUSH-PULL TESTS

DOE PAGES

Hansen, Scott K.; Berkowitz, Brian; Vesselinov, Velimir V.; ...

2016-12-01

Path reversibility and radial symmetry are often assumed in push-pull tracer test analysis. In reality, heterogeneous flow fields mean that both assumptions are idealizations. In this paper, to understand their impact, we perform a parametric study which quantifies the scattering effects of ambient flow, local-scale dispersion, and velocity field heterogeneity on push-pull breakthrough curves and compares them to the effects of mobile-immobile mass transfer (MIMT) processes including sorption and diffusion into secondary porosity. We identify specific circumstances in which MIMT overwhelmingly determines the breakthrough curve, which may then be considered uninformative about drift and local-scale dispersion. Assuming path reversibility, wemore » develop a continuous-time-random-walk-based interpretation framework which is flow-field-agnostic and well suited to quantifying MIMT. Adopting this perspective, we show that the radial flow assumption is often harmless: to the extent that solute paths are reversible, the breakthrough curve is uninformative about velocity field heterogeneity. Our interpretation method determines a mapping function (i.e., subordinator) from travel time in the absence of MIMT to travel time in its presence. A mathematical theory allowing this function to be directly “plugged into” an existing Laplace-domain transport model to incorporate MIMT is presented and demonstrated. Algorithms implementing the calibration are presented and applied to interpretation of data from a push-pull test performed in a heterogeneous environment. A successful four-parameter fit is obtained, of comparable fidelity to one obtained using a million-node 3-D numerical model. In conclusion, we demonstrate analytically and numerically how push-pull tests quantifying MIMT are sensitive to remobilization, but not immobilization, kinetics.« less

Push-pull tracer tests: Their information content and use for characterizing non-Fickian, mobile-immobile behavior: INFORMATION CONTENT OF PUSH-PULL TESTS

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

Hansen, Scott K.; Berkowitz, Brian; Vesselinov, Velimir V.

Path reversibility and radial symmetry are often assumed in push-pull tracer test analysis. In reality, heterogeneous flow fields mean that both assumptions are idealizations. In this paper, to understand their impact, we perform a parametric study which quantifies the scattering effects of ambient flow, local-scale dispersion, and velocity field heterogeneity on push-pull breakthrough curves and compares them to the effects of mobile-immobile mass transfer (MIMT) processes including sorption and diffusion into secondary porosity. We identify specific circumstances in which MIMT overwhelmingly determines the breakthrough curve, which may then be considered uninformative about drift and local-scale dispersion. Assuming path reversibility, wemore » develop a continuous-time-random-walk-based interpretation framework which is flow-field-agnostic and well suited to quantifying MIMT. Adopting this perspective, we show that the radial flow assumption is often harmless: to the extent that solute paths are reversible, the breakthrough curve is uninformative about velocity field heterogeneity. Our interpretation method determines a mapping function (i.e., subordinator) from travel time in the absence of MIMT to travel time in its presence. A mathematical theory allowing this function to be directly “plugged into” an existing Laplace-domain transport model to incorporate MIMT is presented and demonstrated. Algorithms implementing the calibration are presented and applied to interpretation of data from a push-pull test performed in a heterogeneous environment. A successful four-parameter fit is obtained, of comparable fidelity to one obtained using a million-node 3-D numerical model. In conclusion, we demonstrate analytically and numerically how push-pull tests quantifying MIMT are sensitive to remobilization, but not immobilization, kinetics.« less

Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

PubMed

Gao, J

2016-01-01

Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects. © 2016 Elsevier Inc. All rights reserved.

Simplified path integral for supersymmetric quantum mechanics and type-A trace anomalies

NASA Astrophysics Data System (ADS)

Bastianelli, Fiorenzo; Corradini, Olindo; Iacconi, Laura

2018-05-01

Particles in a curved space are classically described by a nonlinear sigma model action that can be quantized through path integrals. The latter require a precise regularization to deal with the derivative interactions arising from the nonlinear kinetic term. Recently, for maximally symmetric spaces, simplified path integrals have been developed: they allow to trade the nonlinear kinetic term with a purely quadratic kinetic term (linear sigma model). This happens at the expense of introducing a suitable effective scalar potential, which contains the information on the curvature of the space. The simplified path integral provides a sensible gain in the efficiency of perturbative calculations. Here we extend the construction to models with N = 1 supersymmetry on the worldline, which are applicable to the first quantized description of a Dirac fermion. As an application we use the simplified worldline path integral to compute the type-A trace anomaly of a Dirac fermion in d dimensions up to d = 16.

Microsolvated Model for the Kinetics and Thermodynamics of Glycosidic Bond Dissociative Cleavage of Nucleoside D4G.

PubMed

Jiang, Yang; Xue, Ying; Zeng, Yi

2018-02-15

Using the microsolvated model that involves explicit water molecules and implicit solvent in the optimization, two proposed dissociative hydrolysis mechanisms of 2',3'-didehydro-2',3'-dideoxyguanosine (d4G) have been first investigated by means of M06-2X(CPCM, water)/6-31++G(d,p) method. The glycosidic bond dissociation for the generation of the oxacarbenium ion intermediate is the rate-determining step (RDS). The subsequent nucleophilic water attack from different side of the oxacarbenium ion intermediate gives either the α-product [(2S,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] or β-product [(2R,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] and is thus referred to as α-path (inversion) and β-path (retention). Two to five explicit water molecules (n = 2-5) are considered in the microsolvated model, and n = 3 or 4 is the smallest model capable of minimizing the activation energy for α-path and β-path, respectively. Our theoretical results suggest that α-path (n = 3) is more kinetically favorable with lower free energy barrier (RDS) of 27.7 kcal mol -1 , in contrast to that of 30.7 kcal mol -1 for the β-path (n = 4). The kinetic preference of the α-path is rationalized by NBO analysis. Whereas thte β-path is more thermodynamically favorable over the α-path, where the formation of β-product and α-product are exergonic and endergonic, respectively, providing theoretical support for the experimental observation that the β-cleavage product was the major one after sufficient reaction time. Comparisons of d4G with analogous cyclo-d4G and dG from kinetic free energy barriers and thermodynamic heterolytic dissociation energies were also carried out. Our kinetic and thermodynamic results manifest that the order of glycosidic bond stability should be d4G < cyclo-d4G < dG, which agrees well with the reported experimental stability order of d4G compounds and analogues and gives further understanding on the influence of 6-cyclopropylamino and unsaturated ribose to the glycosidic bond instability of d4G.

Kinetics, bioavailability, and metabolism of RRR-alpha-tocopherol in humans supports lower requirement for vitamin E

USDA-ARS?s Scientific Manuscript database

Kinetic models enable nutrient needs and kinetic behaviors to be quantified and provide mechanistic insights into metabolism. Therefore, we modeled and quantified the kinetics, bioavailability and metabolism of RRR-alpha-tocopherol in 12 healthy adults. Six men and six women, aged 27 ± 6 y, each i...

A kinetics database and scripts for PHREEQC

NASA Astrophysics Data System (ADS)

Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

2017-12-01

Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

Studies of ion kinetic effects in OMEGA shock-driven implosions using fusion burn imaging

NASA Astrophysics Data System (ADS)

Rosenberg, M. J.; Seguin, F. H.; Rinderknecht, H. G.; Sio, H.; Zylstra, A. B.; Gatu Johnson, M.; Frenje, J. A.; Li, C. K.; Petrasso, R. D.; Amendt, P. A.; Wilks, S. C.; Zimmerman, G.; Hoffman, N. M.; Kagan, G.; Molvig, K.; Glebov, V. Yu.; Stoeckl, C.; Marshall, F. J.; Seka, W.; Delettrez, J. A.; Sangster, T. C.; Betti, R.; Meyerhofer, D. D.; Atzeni, S.; Nikroo, A.

2014-10-01

Ion kinetic effects have been inferred in a series of shock-driven implosions at OMEGA from an increasing yield discrepancy between observations and hydrodynamic simulations as the ion-ion mean free path increases. To more precisely identify the nature and impact of ion kinetic effects, spatial burn profile measurements of DD and D3He reactions in these D3He-filled shock-driven implosions are presented and contrasted to both purely hydrodynamic models and models that include ion kinetic effects. It is shown that in implosions where the ion mean free path is equal to or greater than the size of the fuel region, purely hydrodynamic models fail to capture the observed burn profiles, while a model that includes ion diffusion is able to recover the observed burn profile shape. These results further elucidate the ion kinetic mechanisms that are present under long mean-free-path conditions after shock convergence in both shock-driven and ablatively-driven implosions. This work was supported in part by the U.S. DOE, NLUF, LLE, and LLNL.

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.

Entropy-based link prediction in weighted networks

NASA Astrophysics Data System (ADS)

Xu, Zhongqi; Pu, Cunlai; Ramiz Sharafat, Rajput; Li, Lunbo; Yang, Jian

2017-01-01

Information entropy has been proved to be an effective tool to quantify the structural importance of complex networks. In the previous work (Xu et al, 2016 \\cite{xu2016}), we measure the contribution of a path in link prediction with information entropy. In this paper, we further quantify the contribution of a path with both path entropy and path weight, and propose a weighted prediction index based on the contributions of paths, namely Weighted Path Entropy (WPE), to improve the prediction accuracy in weighted networks. Empirical experiments on six weighted real-world networks show that WPE achieves higher prediction accuracy than three typical weighted indices.

A path-independent integral for the characterization of solute concentration and flux at biofilm detachments

USGS Publications Warehouse

Moran, B.; Kulkarni, S.S.; Reeves, H.W.

2007-01-01

A path-independent (conservation) integral is developed for the characterization of solute concentration and flux in a biofilm in the vicinity of a detachment or other flux limiting boundary condition. Steady state conditions of solute diffusion are considered and biofilm kinetics are described by an uptake term which can be expressed in terms of a potential (Michaelis-Menten kinetics). An asymptotic solution for solute concentration at the tip of the detachment is obtained and shown to be analogous to that of antiplane crack problems in linear elasticity. It is shown that the amplitude of the asymptotic solution can be calculated by evaluating a path-independent integral. The special case of a semi-infinite detachment in an infinite strip is considered and the amplitude of the asymptotic field is related to the boundary conditions and problem parameters in closed form for zeroth and first order kinetics and numerically for Michaelis-Menten kinetics. ?? Springer Science+Business Media, Inc. 2007.

Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations.

PubMed

Varga, Matthew J; Schwartz, Steven D

2016-04-12

In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.

Investigation of ion kinetic effects in direct-drive exploding-pusher implosions at the NIF

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

Rosenberg, M. J., E-mail: mrosenbe@mit.edu; Zylstra, A. B.; Séguin, F. H.

Measurements of yield, ion temperature, areal density (ρR), shell convergence, and bang time have been obtained in shock-driven, D{sub 2} and D{sup 3}He gas-filled “exploding-pusher” inertial confinement fusion (ICF) implosions at the National Ignition Facility to assess the impact of ion kinetic effects. These measurements probed the shock convergence phase of ICF implosions, a critical stage in hot-spot ignition experiments. The data complement previous studies of kinetic effects in shock-driven implosions. Ion temperature and fuel ρR inferred from fusion-product spectroscopy are used to estimate the ion-ion mean free path in the gas. A trend of decreasing yields relative to themore » predictions of 2D DRACO hydrodynamics simulations with increasing Knudsen number (the ratio of ion-ion mean free path to minimum shell radius) suggests that ion kinetic effects are increasingly impacting the hot fuel region, in general agreement with previous results. The long mean free path conditions giving rise to ion kinetic effects in the gas are often prevalent during the shock phase of both exploding pushers and ablatively driven implosions, including ignition-relevant implosions.« less

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 selective elbow movements during an exergame in children with neurological disorders: a pilot study.

PubMed

van Hedel, Hubertus J A; Häfliger, Nadine; Gerber, Corinna N

2016-10-21

It is difficult to distinguish between restorative and compensatory mechanisms underlying (pediatric) neurorehabilitation, as objective measures assessing selective voluntary motor control (SVMC) are scarce. We aimed to quantify SVMC of elbow movements in children with brain lesions. Children played an airplane game with the glove-based YouGrabber system. Participants were instructed to steer an airplane on a screen through a cloud-free path by correctly applying bilateral elbow flexion and extension movements. Game performance measures were (i) % time on the correct path and (ii) similarity between the ideal flight path and the actually flown path. SVMC was quantified by calculating a correlation coefficient between the derivative of the ideal path and elbow movements. A therapist scored whether the child had used compensatory movements. Thirty-three children with brain lesions (11 girls; 12.6 ± 3.6 years) participated. Clinical motor and cognitive scores correlated moderately with SVMC (0.50-0.74). Receiver Operating Characteristics analyses showed that SVMC could differentiate well and better than clinical and game performance measures between compensatory and physiological movements. We conclude that a simple measure assessed while playing a game appears promising in quantifying SVMC. We propose how to improve the methodology, and how this approach can be easily extended to other joints.

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

PubMed

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.

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.

Micro- and Nano-scale Diffusion Domains Acting as Kinetic Controls for U(VI) Release to the Hanford 300-Area Aquifer

NASA Astrophysics Data System (ADS)

Stoliker, D. L.; Hay, M. B.; Davis, J. A.; Zachara, J. M.

2008-12-01

The 300-Area of the Hanford reservation, a cold-war era nuclear processing facility, is plagued by long-term elevated concentrations of U(VI) in the underlying aquifer. While the sediment U(VI) concentration is relatively low, it continues to act as a source and sink for the contaminant, allowing for persistent groundwater concentrations well above the maximum contamination limit (MCL). Simple Kd modeling of the attenuation of U(VI) in the aquifer predicted that groundwater U(VI) concentrations would decrease to below the drinking water standard by the year 2002. However, grain-scale morphology of the aquifer material suggests that intra-grain flow paths and mineral coatings, in which sorption complexes and precipitates formed over years of waste disposal, provide a significant kinetic constraint that slows groundwater flushing of the sediments. In order to quantify the impact of diffusion kinetics on the release of U(VI), high-resolution, non-reactive tracer studies were conducted on vadose zone sediments in both column and batch reactors. Systems were equilibrated for long time scales with tritated artificial groundwater and then flushed with flow and stop-flow events included for columns. Previously collected U(VI) release data from batch dissolution/desorption studies is compared with tritium tracer diffusion kinetics as well as porosimetry and detailed microscopy characterization. The micro-scale and nano-scale diffusion regimes, including intra-granular regions as well as mineral coatings, represent a significant potential long-term source of contaminant U(VI). Understanding the physical kinetic limitations coupled with the complex chemistry of U(VI) sorption processes within natural systems is an important step forward in providing information to strengthen field-scale reactive transport simulations.

Teleconnection Paths via Climate Network Direct Link Detection.

PubMed

Zhou, Dong; Gozolchiani, Avi; Ashkenazy, Yosef; Havlin, Shlomo

2015-12-31

Teleconnections describe remote connections (typically thousands of kilometers) of the climate system. These are of great importance in climate dynamics as they reflect the transportation of energy and climate change on global scales (like the El Niño phenomenon). Yet, the path of influence propagation between such remote regions, and weighting associated with different paths, are only partially known. Here we propose a systematic climate network approach to find and quantify the optimal paths between remotely distant interacting locations. Specifically, we separate the correlations between two grid points into direct and indirect components, where the optimal path is found based on a minimal total cost function of the direct links. We demonstrate our method using near surface air temperature reanalysis data, on identifying cross-latitude teleconnections and their corresponding optimal paths. The proposed method may be used to quantify and improve our understanding regarding the emergence of climate patterns on global scales.

Effect of wall-mediated hydrodynamic fluctuations on the kinetics of a Brownian nanoparticle

NASA Astrophysics Data System (ADS)

Yu, Hsiu-Yu; Eckmann, David M.; Ayyaswamy, Portonovo S.; Radhakrishnan, Ravi

2016-12-01

The reactive flux formalism (Chandler 1978 J. Chem. Phys. 68, 2959-2970. (doi:10.1063/1.436049)) and the subsequent development of methods such as transition path sampling have laid the foundation for explicitly quantifying the rate process in terms of microscopic simulations. However, explicit methods to account for how the hydrodynamic correlations impact the transient reaction rate are missing in the colloidal literature. We show that the composite generalized Langevin equation (Yu et al. 2015 Phys. Rev. E 91, 052303. (doi:10.1103/PhysRevE.91.052303)) makes a significant step towards solving the coupled processes of molecular reactions and hydrodynamic relaxation by examining how the wall-mediated hydrodynamic memory impacts the two-stage temporal relaxation of the reaction rate for a nanoparticle transition between two bound states in the bulk, near-wall and lubrication regimes.

Method and turbine for extracting kinetic energy from a stream of two-phase fluid

NASA Technical Reports Server (NTRS)

Elliott, D. G. (Inventor)

1979-01-01

An axial flow separator turbine is described which includes a number of nozzles for delivering streams of a two-phase fluid along linear paths. A phase separator which responsively separates the vapor and liquid is characterized by concentrically related annuli supported for rotation within the paths. The separator has endless channels for confining the liquid under the influence of centrifugal forces. A vapor turbine fan extracts kinetic energy from the liquid. Angular momentum of both the liquid phase and the vapor phase of the fluid is converted to torque.

A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter

NASA Astrophysics Data System (ADS)

Razavi, Asghar M.; Khelashvili, George; Weinstein, Harel

2017-01-01

The dopamine transporter (DAT) belongs to the neurotransmitter:sodium symporter (NSS) family of membrane proteins that are responsible for reuptake of neurotransmitters from the synaptic cleft to terminate a neuronal signal and enable subsequent neurotransmitter release from the presynaptic neuron. The release of one sodium ion from the crystallographically determined sodium binding site Na2 had been identified as an initial step in the transport cycle which prepares the transporter for substrate translocation by stabilizing an inward-open conformation. We have constructed Markov State Models (MSMs) from extensive molecular dynamics simulations of human DAT (hDAT) to explore the mechanism of this sodium release. Our results quantify the release process triggered by hydration of the Na2 site that occurs concomitantly with a conformational transition from an outward-facing to an inward-facing state of the transporter. The kinetics of the release process are computed from the MSM, and transition path theory is used to identify the most probable sodium release pathways. An intermediate state is discovered on the sodium release pathway, and the results reveal the importance of various modes of interaction of the N-terminus of hDAT in controlling the pathways of release.

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

Base-Catalyzed Linkage Isomerization: An Undergraduate Inorganic Kinetics Experiment.

ERIC Educational Resources Information Center

Jackson, W. G.; And Others

1981-01-01

Describes kinetics experiments completed in a single two-hour laboratory period at 25 degrees Centigrade of nitrito to nitro rearrangement, based on the recently discovered base-catalysis path. Includes information on synthesis and characterization of linkage isomers, spectrophotometric techniques, and experimental procedures. (SK)

CO 2 Absorption and Magnesium Carbonate Precipitation in MgCl 2–NH 3–NH 4Cl Solutions: Implications for Carbon Capture and Storage

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

Zhu, Chen; Wang, Han; Li, Gen

CO 2 absorption and carbonate precipitation are the two core processes controlling the reaction rate and path of CO 2 mineral sequestration. Whereas previous studies have focused on testing reactive crystallization and precipitation kinetics, much less attention has been paid to absorption, the key process determining the removal efficiency of CO 2. In this study, adopting a novel wetted wall column reactor, we systematically explore the rates and mechanisms of carbon transformation from CO 2 gas to carbonates in MgCl 2–NH 3–NH 4Cl solutions. We find that reactive diffusion in liquid film of the wetted wall column is the rate-limitingmore » step of CO 2 absorption when proceeding chiefly through interactions between CO 2(aq) and NH 3(aq). We further quantified the reaction kinetic constant of the CO 2–NH 3 reaction. Our results indicate that higher initial concentration of NH 4Cl ( ≥2mol∙L -1) leads to the precipitation of roguinite [(NH 4) 2Mg(CO 3) 2∙4H 2O], while nesquehonite appears to be the dominant Mg-carbonate without NH 4Cl addition. We also noticed dypingite formation via phase transformation in hot water. This study provides new insight into the reaction kinetics of CO 2 mineral carbonation that indicates the potential of this technique for future application to industrial-scale CO 2 sequestration.« less

CO 2 Absorption and Magnesium Carbonate Precipitation in MgCl 2–NH 3–NH 4Cl Solutions: Implications for Carbon Capture and Storage

DOE PAGES

Zhu, Chen; Wang, Han; Li, Gen; ...

2017-09-19

CO 2 absorption and carbonate precipitation are the two core processes controlling the reaction rate and path of CO 2 mineral sequestration. Whereas previous studies have focused on testing reactive crystallization and precipitation kinetics, much less attention has been paid to absorption, the key process determining the removal efficiency of CO 2. In this study, adopting a novel wetted wall column reactor, we systematically explore the rates and mechanisms of carbon transformation from CO 2 gas to carbonates in MgCl 2–NH 3–NH 4Cl solutions. We find that reactive diffusion in liquid film of the wetted wall column is the rate-limitingmore » step of CO 2 absorption when proceeding chiefly through interactions between CO 2(aq) and NH 3(aq). We further quantified the reaction kinetic constant of the CO 2–NH 3 reaction. Our results indicate that higher initial concentration of NH 4Cl ( ≥2mol∙L -1) leads to the precipitation of roguinite [(NH 4) 2Mg(CO 3) 2∙4H 2O], while nesquehonite appears to be the dominant Mg-carbonate without NH 4Cl addition. We also noticed dypingite formation via phase transformation in hot water. This study provides new insight into the reaction kinetics of CO 2 mineral carbonation that indicates the potential of this technique for future application to industrial-scale CO 2 sequestration.« less

FIELD EVALUATION OF A METHOD FOR ESTIMATING GASEOUS FLUXES FROM AREA SOURCES USING OPEN-PATH FTIR

EPA Science Inventory

The paper gives preliminary results from a field evaluation of a new approach for quantifying gaseous fugitive emissions of area air pollution sources. The approach combines path-integrated concentration data acquired with any path-integrated optical remote sensing (PI-ORS) ...

FIELD EVALUATION OF A METHOD FOR ESTIMATING GASEOUS FLUXES FROM AREA SOURCES USING OPEN-PATH FOURIER TRANSFORM INFRARED

EPA Science Inventory

The paper describes preliminary results from a field experiment designed to evaluate a new approach to quantifying gaseous fugitive emissions from area air pollution sources. The new approach combines path-integrated concentration data acquired with any path-integrated optical re...

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.

Broadband acoustic wave propagation across sloping topography covered by sea ice

NASA Astrophysics Data System (ADS)

Badiey, M.; Wan, L.; Eickmeier, J.; Muenchow, A.; Ryan, P. A.

2017-12-01

The Canada Basin Acoustic Propagation Experiment (CANAPE) quantifies how sound generated in the deep Basin is received on the continental shelf. The two regimes, deep basin and shallow shelves, are separated by a 30-km wide region where the bottom changes from 1000-m to 100-m. This narrow region focuses and traps kinetic energy that surface wind forcing inputs into the ocean over a wide region with periodicities of days to months. As a result, ocean temperature and speed of sound are more variable near sloping topography than they are over either deep basins or shallow shelves. In contrast to companion CANAPE presentations in this session, here we use sound speed as input to predict likely propagation paths and transmission losses across the continental slope with a two-dimensional parabolic model (2D PE). Intensity fluctuations due to the changing bathymetry, water column oceanography, and the scattering from ice cover for broadband signals are checked against measured broadband acoustic signals that were collected simultaneously with the oceanographic measurements for a long period. Differences between measured and calculated transmission loss can be the result of out of plane acoustic paths requiring 3D PE modeling for future studies. [Work supported by ONR code 322 OA].

Non-equilibrium physics of neural networks for leaning, memory and decision making: landscape and flux perspectives

NASA Astrophysics Data System (ADS)

Wang, Jin

Cognitive behaviors are determined by underlying neural networks. Many brain functions, such as learning and memory, can be described by attractor dynamics. We developed a theoretical framework for global dynamics by quantifying the landscape associated with the steady state probability distributions and steady state curl flux, measuring the degree of non-equilibrium through detailed balance breaking. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. Both landscape and flux determine the kinetic paths and speed of decision making. The kinetics and global stability of decision making are explored by quantifying the landscape topography through the barrier heights and the mean first passage time. The theoretical predictions are in agreement with experimental observations: more errors occur under time pressure. We quantitatively explored two mechanisms of the speed-accuracy tradeoff with speed emphasis and further uncovered the tradeoffs among speed, accuracy, and energy cost. Our results show an optimal balance among speed, accuracy, and the energy cost in decision making. We uncovered possible mechanisms of changes of mind and how mind changes improve performance in decision processes. Our landscape approach can help facilitate an understanding of the underlying physical mechanisms of cognitive processes and identify the key elements in neural networks.

INNOVATIVE APPROACH FOR MEASURING AMMONIA AND METHANE FLUXES FROM A HOG FARM USING OPEN-PATH FOURIER TRANSFORM INFRARED SPECTROSCOPY

EPA Science Inventory

The paper describes a new approach to quantify emissions from area air pollution sources. The approach combines path-integrated concentration data acquired with any path-integrated optical remote sensing (PI-ORS) technique and computed tomography (CT) technique. In this study, an...

Method of and apparatus for accelerating a projectile

DOEpatents

Goldstein, Yeshayahu S. A.; Tidman, Derek A.

1986-01-01

A projectile is accelerated along a confined path by supplying a pulsed high pressure, high velocity plasma jet to the rear of the projectile as the projectile traverses the path. The jet enters the confined path at a non-zero angle relative to the projectile path. The pulse is derived from a dielectric capillary tube having an interior wall from which plasma forming material is ablated in response to a discharge voltage. The projectile can be accelerated in response to the kinetic energy in the plasma jet or in response to a pressure increase of gases in the confined path resulting from the heat added to the gases by the plasma.

Tortuous Pore Path Through the Glaucomatous Lamina Cribrosa.

PubMed

Wang, Bo; Lucy, Katie A; Schuman, Joel S; Sigal, Ian A; Bilonick, Richard A; Lu, Chen; Liu, Jonathan; Grulkowski, Ireneusz; Nadler, Zachary; Ishikawa, Hiroshi; Kagemann, Larry; Fujimoto, James G; Wollstein, Gadi

2018-05-08

The lamina cribrosa is a primary site of damage in glaucoma. While mechanical distortion is hypothesized to cause reduction of axoplasmic flow, little is known about how the pores, which contains the retinal ganglion cell axons, traverse the lamina cribrosa. We investigated lamina cribrosa pore paths in vivo to quantify differences in tortuosity of pore paths between healthy and glaucomatous eyes. We imaged 16 healthy, 23 glaucoma suspect and 48 glaucomatous eyes from 70 subjects using a swept source optical coherence tomography system. The lamina cribrosa pores were automatically segmented using a previously described segmentation algorithm. Individual pore paths were automatically tracked through the depth of the lamina cribrosa using custom software. Pore path convergence to the optic nerve center and tortuosity was quantified for each eye. We found that lamina cribrosa pore pathways traverse the lamina cribrosa closer to the optic nerve center along the depth of the lamina cribrosa regardless of disease severity or diagnostic category. In addition, pores of glaucoma eyes take a more tortuous path through the lamina cribrosa compared to those of healthy eyes, suggesting a potential mechanism for reduction of axoplasmic flow in glaucoma.

Sensory Agreement Guides Kinetic Energy Optimization of Arm Movements during Object Manipulation.

PubMed

Farshchiansadegh, Ali; Melendez-Calderon, Alejandro; Ranganathan, Rajiv; Murphey, Todd D; Mussa-Ivaldi, Ferdinando A

2016-04-01

The laws of physics establish the energetic efficiency of our movements. In some cases, like locomotion, the mechanics of the body dominate in determining the energetically optimal course of action. In other tasks, such as manipulation, energetic costs depend critically upon the variable properties of objects in the environment. Can the brain identify and follow energy-optimal motions when these motions require moving along unfamiliar trajectories? What feedback information is required for such optimal behavior to occur? To answer these questions, we asked participants to move their dominant hand between different positions while holding a virtual mechanical system with complex dynamics (a planar double pendulum). In this task, trajectories of minimum kinetic energy were along curvilinear paths. Our findings demonstrate that participants were capable of finding the energy-optimal paths, but only when provided with veridical visual and haptic information pertaining to the object, lacking which the trajectories were executed along rectilinear paths.

Constraining Path-Dependent Processes During Basalt-CO2 Interactions with Observations From Flow-Through and Batch Experiments

NASA Astrophysics Data System (ADS)

Thomas, D.; Garing, C.; Zahasky, C.; Harrison, A. L.; Bird, D. K.; Benson, S. M.; Oelkers, E. H.; Maher, K.

2017-12-01

Predicting the timing and magnitude of CO2 storage in basaltic rocks relies partly on quantifying the dependence of reactivity on flow path and mineral distribution. Flow-through experiments that use intact cores are advantageous because the spatial heterogeneity of pore space and reactive phases is preserved. Combining aqueous geochemical analyses and petrologic characterization with non-destructive imaging techniques (e.g. micro-computed tomography) constrains the relationship between irreversible reactions, pore connectivity and accessible surface area. Our work enhances these capabilities by dynamically imaging flow through vesicular basalts with Positron Emission Tomography (PET) scanning. PET highlights the path a fluid takes by detecting photons produced during radioactive decay of an injected radiotracer (FDG). We have performed single-phase, CO2-saturated flow-through experiments with basaltic core from Iceland at CO2 sequestration conditions (50 °C; 76-90 bar Ptot). Constant flow rate and continuous pressure measurements at the inlet and outlet of the core constrain permeability. We monitor geochemical evolution through cation and anion analysis of outlet fluid sampled periodically. Before and after reaction, we perform PET scans and characterize the core using micro-CT. The PET scans indicate a discrete, localized flow path that appears to be a micro-crack connecting vesicles, suggesting that vesicle-lining minerals are immediately accessible and important reactants. Rapid increases in aqueous cation concentration, pH and HCO3- indicate that the rock reacts nearly immediately after CO2 injection. After 24 hours the solute release decreases, which may reflect a transition to reaction with phases with slower kinetic dissolution rates (e.g. zeolites and glasses to feldspar), a decrease in available reactive surface area or precipitation. We have performed batch experiments using crushed material of the same rock to elucidate the effect of flow path geometry and mineral accessibility on geochemical evolution. Interestingly, surface area-normalized dissolution rates as evinced by SiO2 release in all experiments approach similar values ( 10-15 mol/cm2/s). Our experiments show how imaging techniques are helpful in interpreting path-dependent processes in open systems.

Monitoring reactive microencapsulation dynamics using microfluidics

PubMed Central

Brosseau, Quentin; Baret, Jean-Christophe

2015-01-01

We use microfluidic polydimethylsiloxane (PDMS) devices to measure the kinetics of reactive encapsulations occurring at the interface of emulsion droplets. The formation of the polymeric shell is inferred from the droplet deformability measured in a series of expansion–constriction chambers along the microfluidic chip. With this tool we quantify the kinetic processes governing the encapsulation at the very early stage of shell formation with a time resolution of the order of the millisecond for overall reactions occurring in less than 0.5 s. We perform a comparison of monomer reactivities used for the encapsulation. We study the formation of polyurea microcapsules (PUMCs); the shell formation proceeds at the water–oil interface by an immediate reaction of amines dissolved in the aqueous phase and isocyanates dissolved in the oil phase. We observe that both monomers contribute differently to the encapsulation kinetics. The kinetics of the shell formation process at the oil-in-water (O/W) experiments significantly differs from the water-in-oil (W/O) systems; the component dissolved in the continuous phase has the largest impact on the kinetics. In addition, we quantified the retarding effect on the encapsulation kinetics by the interface stabilizing agent (surfactant). Our approach is valuable for quantifying in situ reactive encapsulation processes and provides guidelines to generate microcapsules with soft interfaces of tailored and controllable interfacial properties. PMID:25705975

Axioms for Obligation and Robustness with Temporal Logic

NASA Astrophysics Data System (ADS)

French, Tim; McCabe-Dansted, John C.; Reynolds, Mark

RoCTL* was proposed to model and specify the robustness of reactive systems. RoCTL* extended CTL* with the addition of Obligatory and Robustly operators, which quantify over failure-free paths and paths with one more failure respectively. This paper gives an axiomatisation for all the operators of RoCTL* with the exception of the Until operator; this fragment is able to express similar contrary-to-duty obligations to the full RoCTL* logic. We call this formal system NORA, and give a completeness proof. We also consider the fragments of the language containing only path quantifiers (but where variables are dependent on histories). We examine semantic properties and potential axiomatisations for these fragments.

Analysis of Nanoporosity in Moisture Permeation Barrier Layers by Electrochemical Impedance Spectroscopy.

PubMed

Perrotta, Alberto; García, Santiago J; Michels, Jasper J; Andringa, Anne-Marije; Creatore, Mariadriana

2015-07-29

Water permeation in inorganic moisture permeation barriers occurs through macroscale defects/pinholes and nanopores, the latter with size approaching the water kinetic diameter (0.27 nm). Both permeation paths can be identified by the calcium test, i.e., a time-consuming and expensive optical method for determining the water vapor transmission rate (WVTR) through barrier layers. Recently, we have shown that ellipsometric porosimetry (i.e., a combination of spectroscopic ellipsometry and isothermal adsorption studies) is a valid method to classify and quantify the nanoporosity and correlate it with the WVTR values. Nevertheless, no information is obtained about the macroscale defects or the kinetics of water permeation through the barrier, both essential in assessing the quality of the barrier layer. In this study, electrochemical impedance spectroscopy (EIS) is shown as a sensitive and versatile method to obtain information on nanoporosity and macroscale defects, water permeation, and diffusivity of moisture barrier layers, complementing the barrier property characterization obtained by means of EP and calcium test. EIS is performed on thin SiO2 barrier layers deposited by plasma enhanced-CVD. It allows the determination of the relative water uptake in the SiO2 layers, found to be in agreement with the nanoporosity content inferred by EP. Furthermore, the kinetics of water permeation is followed by EIS, and the diffusivity (D) is determined and found to be in accordance with literature values. Moreover, differently from EP, EIS data are shown to be sensitive to the presence of local macrodefects, correlated with the barrier failure during the calcium test.

Curvature and torsion in growing actin networks

NASA Astrophysics Data System (ADS)

Shaevitz, Joshua W.; Fletcher, Daniel A.

2008-06-01

Intracellular pathogens such as Listeria monocytogenes and Rickettsia rickettsii move within a host cell by polymerizing a comet-tail of actin fibers that ultimately pushes the cell forward. This dense network of cross-linked actin polymers typically exhibits a striking curvature that causes bacteria to move in gently looping paths. Theoretically, tail curvature has been linked to details of motility by considering force and torque balances from a finite number of polymerizing filaments. Here we track beads coated with a prokaryotic activator of actin polymerization in three dimensions to directly quantify the curvature and torsion of bead motility paths. We find that bead paths are more likely to have low rather than high curvature at any given time. Furthermore, path curvature changes very slowly in time, with an autocorrelation decay time of 200 s. Paths with a small radius of curvature, therefore, remain so for an extended period resulting in loops when confined to two dimensions. When allowed to explore a three-dimensional (3D) space, path loops are less evident. Finally, we quantify the torsion in the bead paths and show that beads do not exhibit a significant left- or right-handed bias to their motion in 3D. These results suggest that paths of actin-propelled objects may be attributed to slow changes in curvature, possibly associated with filament debranching, rather than a fixed torque.

Path Complexity in Virtual Water Maze Navigation: Differential Associations with Age, Sex, and Regional Brain Volume.

PubMed

Daugherty, Ana M; Yuan, Peng; Dahle, Cheryl L; Bender, Andrew R; Yang, Yiqin; Raz, Naftali

2015-09-01

Studies of human navigation in virtual maze environments have consistently linked advanced age with greater distance traveled between the start and the goal and longer duration of the search. Observations of search path geometry suggest that routes taken by older adults may be unnecessarily complex and that excessive path complexity may be an indicator of cognitive difficulties experienced by older navigators. In a sample of healthy adults, we quantify search path complexity in a virtual Morris water maze with a novel method based on fractal dimensionality. In a two-level hierarchical linear model, we estimated improvement in navigation performance across trials by a decline in route length, shortening of search time, and reduction in fractal dimensionality of the path. While replicating commonly reported age and sex differences in time and distance indices, a reduction in fractal dimension of the path accounted for improvement across trials, independent of age or sex. The volumes of brain regions associated with the establishment of cognitive maps (parahippocampal gyrus and hippocampus) were related to path dimensionality, but not to the total distance and time. Thus, fractal dimensionality of a navigational path may present a useful complementary method of quantifying performance in navigation. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Relationships between molecular structure and kinetic and thermodynamic controls in lipid systems. Part II: Phase behavior and transformation paths of SSS, PSS and PPS saturated triacylglycerols--effect of chain length mismatch.

PubMed

Bouzidi, Laziz; Narine, Suresh S

2012-01-01

The kinetic phase behavior and phase transformation paths of purified tristearoylglycerol (SSS), 3-palmitoyl-1,2-distearoyl-sn-glycerol (PSS) and 1,2-dipalmitoyl-3-stearoyl-sn-glycerol (PPS) were investigated in terms of polymorphism, crystallization and melting. The details of the phase transformation paths were obtained using the heating cycles of two sets of experiments: (a) cooling rate was varied and heating rate fixed and (b) cooling rate was fixed and heating rate varied. Kinetic effects were manifest in all measured properties, underscoring the complexity of the phase transformation paths for each TAG, and the intricate thermodynamics-molecular relationships. For the first time, XRD data obtained for SSS, PSS and PPS TAGs, cooled at rates higher than 0.5°C/min, suggested the formation of a transient structure similar to the so-called α(2)-phase which has been observed in mixed saturated-unsaturated TAGs quenched from the melt. The more stable phases (β' in PSS and PPS, and β in SSS) were only observed for cooling rates lower than 1.0°C/min. The kinetic and thermodynamic differences observed in the crystallization, structure and melting of SSS, PSS and PPS are proposed to be mainly due to the disturbances introduced at the "terrace" level via methyl-end group interactions, i.e., the missing of two or four CH(2) groups compared to SSS. The symmetrical SSS with a relatively flat "terrace" crystallizes preferably in the most stable β-form. Two missing CH(2) groups at the sn-1 position (PSS) introduces enough structural disturbances to promote the relative prevalence and persistence of the β'-phase, and four missing CH(2) groups at the sn-1 and sn-2 positions (PPS) is relatively too large of a disturbance and therefore favors the α-form. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Kinetic model for the collisionless sheath of a collisional plasma

DOE PAGES

Tang, Xian-Zhu; Guo, Zehua

2016-08-04

Collisional plasmas typically have mean-free-path still much greater than the Debye length, so the sheath is mostly collisionless. Once the plasma density, temperature, and flow are specified at the sheath entrance, the profile variation of electron and ion density, temperature, flow speed, and conductive heat fluxes inside the sheath is set by collisionless dynamics, and can be predicted by an analytical kinetic model distribution. Finally, these predictions are contrasted in this paper with direct kinetic simulations, showing good agreement.

Kinetic Boltzmann approach adapted for modeling highly ionized matter created by x-ray irradiation of a solid.

PubMed

Ziaja, Beata; Saxena, Vikrant; Son, Sang-Kil; Medvedev, Nikita; Barbrel, Benjamin; Woloncewicz, Bianca; Stransky, Michal

2016-05-01

We report on the kinetic Boltzmann approach adapted for simulations of highly ionized matter created from a solid by its x-ray irradiation. X rays can excite inner-shell electrons, which leads to the creation of deeply lying core holes. Their relaxation, especially in heavier elements, can take complicated paths, leading to a large number of active configurations. Their number can be so large that solving the set of respective evolution equations becomes computationally inefficient and another modeling approach should be used instead. To circumvent this complexity, the commonly used continuum models employ a superconfiguration scheme. Here, we propose an alternative approach which still uses "true" atomic configurations but limits their number by restricting the sample relaxation to the predominant relaxation paths. We test its reliability, performing respective calculations for a bulk material consisting of light atoms and comparing the results with a full calculation including all relaxation paths. Prospective application for heavy elements is discussed.

Analyzing bean extracts using time-dependent SDS trapping to quantify the kinetic stability of phaseolin proteins.

PubMed

Thibeault, Jane; Church, Jennifer; Ortiz-Perez, Brian; Addo, Samuel; Hill, Shakeema; Khalil, Areeg; Young, Malaney; Xia, Ke; Colón, Wilfredo

2017-09-30

In common beans and lima bean, the storage protein phaseolin is difficult to degrade and SDS-resistant, a sign of kinetic stability. Kinetically stable proteins (KSPs) are characterized by having a high-energy barrier between the native and denatured states that results in very slow unfolding. Such proteins are resistant to proteolytic degradation and detergents, such as SDS. Here the method SDS-Trapping of Proteins (S-TraP) is applied directly on bean extracts to quantify the kinetic stability of phaseolin in lima bean and several common beans, including black bean, navy bean, and small red bean. The bean extracts were incubated in SDS at various temperatures (60-75 °C) for different time periods, followed by SDS-PAGE analysis at room temperature, and subsequent band quantification to determine the kinetics of phaseolin unfolding. Eyring plot analysis showed that the phaseolin from each bean has high kinetic stability, with an SDS-trapping (i.e. unfolding) half-life ranging from about 20-100 years at 24 °C and 2-7 years at 37 °C. The remarkably high kinetic stability of these phaseolin proteins is consistent with the low digestibility of common beans and lima bean, as well as their relatively high germination temperatures. From a practical perspective, this work exemplifies that S-TraP is a useful and cost-effective method for quantifying the kinetic stability of proteins in biological extracts or lysates. Depending on the protein to be studied and its abundance, S-TraP may be performed directly on the extract without need for protein purification. Copyright © 2017 Elsevier Inc. All rights reserved.

Quantifying tight-gas sandstone permeability via critical path analysis

USDA-ARS?s Scientific Manuscript database

Rock permeability has been actively investigated over the past several decades by the geosciences community. However, its accurate estimation still presents significant technical challenges, especially in spatially complex rocks. In this letter, we apply critical path analysis (CPA) to estimate perm...

Energy Index For Aircraft Maneuvers

NASA Technical Reports Server (NTRS)

Chidester, Thomas R. (Inventor); Lynch, Robert E. (Inventor); Lawrence, Robert E. (Inventor); Amidan, Brett G. (Inventor); Ferryman, Thomas A. (Inventor); Drew, Douglas A. (Inventor); Ainsworth, Robert J. (Inventor); Prothero, Gary L. (Inventor); Romanowski, Tomothy P. (Inventor); Bloch, Laurent (Inventor)

2006-01-01

Method and system for analyzing, separately or in combination, kinetic energy and potential energy and/or their time derivatives, measured or estimated or computed, for an aircraft in approach phase or in takeoff phase, to determine if the aircraft is or will be put in an anomalous configuration in order to join a stable approach path or takeoff path. A 3 reference value of kinetic energy andor potential energy (or time derivatives thereof) is provided, and a comparison index .for the estimated energy and reference energy is computed and compared with a normal range of index values for a corresponding aircraft maneuver. If the computed energy index lies outside the normal index range, this phase of the aircraft is identified as anomalous, non-normal or potentially unstable.

A Kinetic Study of the Reaction of Ch3 02 with N02. Volume I,

DTIC Science & Technology

1980-01-01

Ravishankara F.L. Eisele IP.H. Wine ABSTRACT The technique of pulsed laser photolysis-long path laser aborption is employed to study the kinetics of the...Inrad Corp.) which was housed in a gold plated copper block. This copper block was in snug contact with a gold plated pedestal which was backed by a

Incorporating both physical and kinetic limitations in quantifying dissolved oxygen flux to aquatic sediments

USGS Publications Warehouse

O'Connor, B.L.; Hondzo, Miki; Harvey, J.W.

2009-01-01

Traditionally, dissolved oxygen (DO) fluxes have been calculated using the thin-film theory with DO microstructure data in systems characterized by fine sediments and low velocities. However, recent experimental evidence of fluctuating DO concentrations near the sediment-water interface suggests that turbulence and coherent motions control the mass transfer, and the surface renewal theory gives a more mechanistic model for quantifying fluxes. Both models involve quantifying the mass transfer coefficient (k) and the relevant concentration difference (??C). This study compared several empirical models for quantifying k based on both thin-film and surface renewal theories, as well as presents a new method for quantifying ??C (dynamic approach) that is consistent with the observed DO concentration fluctuations near the interface. Data were used from a series of flume experiments that includes both physical and kinetic uptake limitations of the flux. Results indicated that methods for quantifying k and ??C using the surface renewal theory better estimated the DO flux across a range of fluid-flow conditions. ?? 2009 ASCE.

Optimization of Turbine Rim Seals

NASA Technical Reports Server (NTRS)

Wagner, J. H.; Tew, D. E.; Stetson, G. M.; Sabnis, J. S.

2006-01-01

Experiments are being conducted to gain an understanding of the physics of rim scale cavity ingestion in a turbine stage with the high-work, single-stage characteristics envisioned for Advanced Subsonic Transport (AST) aircraft gas turbine engines fo the early 21st century. Initial experimental measurements to be presented include time-averaged turbine rim cavity and main gas path static pressure measurements for rim seal coolant to main gas path mass flow ratios between 0 and 0.02. The ultimate objective of this work is develop improved rim seal design concepts for use in modern high-work, single sage turbines n order to minimize the use of secondary coolant flow. Toward this objective the time averaged and unsteady data to be obtained in these experiments will be used to 1) Quantify the impact of the rim cavity cooling air on the ingestion process. 2) Quantify the film cooling benefits of the rim cavity purge flow in the main gas path. 3) Quantify the impact of the cooling air on turbine efficiency. 4) Develop/evaluate both 3D CFD and analytical models of the ingestion/cooling process.

Repeatable source, site, and path effects on the standard deviation for empirical ground-motion prediction models

USGS Publications Warehouse

Lin, P.-S.; Chiou, B.; Abrahamson, N.; Walling, M.; Lee, C.-T.; Cheng, C.-T.

2011-01-01

In this study, we quantify the reduction in the standard deviation for empirical ground-motion prediction models by removing ergodic assumption.We partition the modeling error (residual) into five components, three of which represent the repeatable source-location-specific, site-specific, and path-specific deviations from the population mean. A variance estimation procedure of these error components is developed for use with a set of recordings from earthquakes not heavily clustered in space.With most source locations and propagation paths sampled only once, we opt to exploit the spatial correlation of residuals to estimate the variances associated with the path-specific and the source-location-specific deviations. The estimation procedure is applied to ground-motion amplitudes from 64 shallow earthquakes in Taiwan recorded at 285 sites with at least 10 recordings per site. The estimated variance components are used to quantify the reduction in aleatory variability that can be used in hazard analysis for a single site and for a single path. For peak ground acceleration and spectral accelerations at periods of 0.1, 0.3, 0.5, 1.0, and 3.0 s, we find that the singlesite standard deviations are 9%-14% smaller than the total standard deviation, whereas the single-path standard deviations are 39%-47% smaller.

Kinetics of enzymatic trans-esterification of glycerides for biodiesel production.

PubMed

Calabrò, Vincenza; Ricca, Emanuele; De Paola, Maria Gabriela; Curcio, Stefano; Iorio, Gabriele

2010-08-01

In this paper, the reaction of enzymatic trans-esterification of glycerides with ethanol in a reaction medium containing hexane at a temperature of 37 degrees C has been studied. The enzyme was Lipase from Mucor miehei, immobilized on ionic exchange resin, aimed at achieving high catalytic specific surface and recovering, regenerating and reusing the biocatalyst. A kinetic analysis has been carried out to identify the reaction path; the rate equation and kinetic parameters have been also calculated. The kinetic model has been validated by comparison between predicted and experimental results. Mass transport resistances estimation was undertaken in order to verify that the kinetics found was intrinsic. Model potentialities in terms of reactors design and optimization are also shown.

SIMULATION STUDY FOR GASEOUS FLUXES FROM AN AREA SOURCE USING COMPUTED TOMOGRAPHY AND OPTICAL REMOTE SENSING

EPA Science Inventory

The paper presents a new approach to quantifying emissions from fugitive gaseous air pollution sources. Computed tomography (CT) and path-integrated optical remote sensing (PI-ORS) concentration data are combined in a new field beam geometry. Path-integrated concentrations are ...

3D-printed phantom for the characterization of non-uniform rotational distortion (Conference Presentation)

NASA Astrophysics Data System (ADS)

Hohert, Geoffrey; Pahlevaninezhad, Hamid; Lee, Anthony; Lane, Pierre M.

2016-03-01

Endoscopic catheter-based imaging systems that employ a 2-dimensional rotary or 3-dimensional rotary-pullback scanning mechanism require constant angular velocity at the distal tip to ensure correct angular registration of the collected signal. Non-uniform rotational distortion (NURD) - often present due to a variety of mechanical issues - can result in inconsistent position and velocity profiles at the tip, limiting the accuracy of any measurements. Since artifacts like NURD are difficult to identify and characterize during tissue imaging, phantoms with well-defined patterns have been used to quantify position and/or velocity error. In this work we present a fast, versatile, and cost-effective method for making fused deposition modeling 3D printed phantoms for identifying and quantifying NURD errors along an arbitrary user-defined pullback path. Eight evenly-spaced features are present at the same orientation at all points on the path such that deviations from expected geometry can be quantified for the imaging catheter. The features are printed vertically and then folded together around the path to avoid issues with printer head resolution. This method can be adapted for probes of various diameters and for complex imaging paths with multiple bends. We demonstrate imaging using the 3D printed phantoms with a 1mm diameter rotary-pullback OCT catheter and system as a means of objectively evaluating the mechanical performance of similarly constructed probes.

Kinetic-freezing and unfreezing of local-region fluctuations in a glass structure observed by heat capacity hysteresis

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

Aji, D. P. B.; Johari, G. P., E-mail: joharig@mcmaster.ca

Fluctuations confined to local regions in the structure of a glass are observed as the Johari-Goldstein (JG) relaxation. Properties of these regions and their atomic configuration are currently studied by relaxation techniques, by electron microscopy, and by high-energy X-ray scattering and extended x-ray absorption fine structure methods. One expects that these fluctuations (i) would kinetically freeze on cooling a glass, and the temperature coefficient of its enthalpy, dH/dT, would consequently show a gradual decrease with decrease in T, (ii) would kinetically unfreeze on heating the glass toward the glass-liquid transition temperature, T{sub g}, and dH/dT would gradually increase, and (iii)more » there would be a thermal hysteresis indicating the time and temperature dependence of the enthalpy. Since no such features have been found, thermodynamic consequences of these fluctuations are debated. After searching for these features in glasses of different types, we found it in one of the most stable metal alloy glasses of composition Pd{sub 40}Ni{sub 10}Cu{sub 30}P{sub 20}. On cooling from its T{sub g}, dH/dT decreased along a broad sigmoid-shape path as local-region fluctuations kinetically froze. On heating thereafter, dH/dT increased along a similar path as these fluctuations unfroze, and there is hysteresis in the cooling and heating paths, similar to that observed in the T{sub g}-endotherm range. After eliminating other interpretations, we conclude that local-region fluctuations seen as the JG relaxation in the non-equilibrium state of a glass contribute to its entropy, and we suggest conditions under which such fluctuations may be observed.« less

Kinetic-freezing and unfreezing of local-region fluctuations in a glass structure observed by heat capacity hysteresis.

PubMed

Aji, D P B; Johari, G P

2015-06-07

Fluctuations confined to local regions in the structure of a glass are observed as the Johari-Goldstein (JG) relaxation. Properties of these regions and their atomic configuration are currently studied by relaxation techniques, by electron microscopy, and by high-energy X-ray scattering and extended x-ray absorption fine structure methods. One expects that these fluctuations (i) would kinetically freeze on cooling a glass, and the temperature coefficient of its enthalpy, dH/dT, would consequently show a gradual decrease with decrease in T, (ii) would kinetically unfreeze on heating the glass toward the glass-liquid transition temperature, Tg, and dH/dT would gradually increase, and (iii) there would be a thermal hysteresis indicating the time and temperature dependence of the enthalpy. Since no such features have been found, thermodynamic consequences of these fluctuations are debated. After searching for these features in glasses of different types, we found it in one of the most stable metal alloy glasses of composition Pd40Ni10Cu30P20. On cooling from its Tg, dH/dT decreased along a broad sigmoid-shape path as local-region fluctuations kinetically froze. On heating thereafter, dH/dT increased along a similar path as these fluctuations unfroze, and there is hysteresis in the cooling and heating paths, similar to that observed in the Tg-endotherm range. After eliminating other interpretations, we conclude that local-region fluctuations seen as the JG relaxation in the non-equilibrium state of a glass contribute to its entropy, and we suggest conditions under which such fluctuations may be observed.

Measurement of Enzyme Kinetics by Use of a Blood Glucometer: Hydrolysis of Sucrose and Lactose

ERIC Educational Resources Information Center

Heinzerling, Peter; Schrader, Frank; Schanze, Sascha

2012-01-01

An alternative analytical method for measuring the kinetic parameters of the enzymes invertase and lactase is described. Invertase hydrolyzes sucrose to glucose and fructose and lactase hydrolyzes lactose to glucose and galactose. In most enzyme kinetics studies, photometric methods or test strips are used to quantify the derivates of the…

The Use of a Multidimensional Measure of Dialysis Adequacy—Moving beyond Small Solute Kinetics

PubMed Central

Perl, Jeffrey; Dember, Laura M.; Bargman, Joanne M.; Browne, Teri; Charytan, David M.; Flythe, Jennifer E.; Hickson, LaTonya J.; Hung, Adriana M.; Jadoul, Michel; Lee, Timmy Chang; Meyer, Klemens B.; Moradi, Hamid; Shafi, Tariq; Teitelbaum, Isaac; Wong, Leslie P.

2017-01-01

Urea removal has become a key measure of the intensity of dialysis treatment for kidney failure. Small solute removal, exemplified by Kt/Vurea, has been broadly applied as a means to quantify the dose of thrice weekly hemodialysis. Yet, the reliance on small solute clearances alone as a measure of dialysis adequacy fails fully to quantify the intended clinical effects of dialysis therapy. This review aims to (1) understand the strengths and limitations of small solute kinetics as a surrogate marker of dialysis dose, and (2) present the prospect of a more comprehensive construct for dialysis dose, one that considers more broadly the goals of ESRD care to maximize both quality of life and survival. On behalf of the American Society of Nephrology Dialysis Advisory Group, we propose the need to ascertain the validity and utility of a multidimensional measure that moves beyond small solute kinetics alone to quantify optimal dialysis derived from both patient-reported and comprehensive clinical and dialysis-related measures. PMID:28314806

Dynamical characterization of inactivation path in voltage-gated Na+ ion channel by non-equilibrium response spectroscopy

PubMed Central

Pal, Krishnendu; Gangopadhyay, Gautam

2016-01-01

ABSTRACT Inactivation path of voltage gated sodium channel has been studied here under various voltage protocols as it is the main governing factor for the periodic occurrence and shape of the action potential. These voltage protocols actually serve as non-equilibrium response spectroscopic tools to study the ion channel in non-equilibrium environment. In contrast to a lot of effort in finding the crystal structure based molecular mechanism of closed-state(CSI) and open-state inactivation(OSI); here our approach is to understand the dynamical characterization of inactivation. The kinetic flux as well as energetic contribution of the closed and open- state inactivation path is compared here for voltage protocols, namely constant, pulsed and oscillating. The non-equilibrium thermodynamic quantities used in response to these voltage protocols serve as improved characterization tools for theoretical understanding which not only agrees with the previously known kinetic measurements but also predict the energetically optimum processes to sustain the auto-regulatory mechanism of action potential and the consequent inactivation steps needed. The time dependent voltage pattern governs the population of the conformational states which when couple with characteristic rate parameters, the CSI and OSI selectivity arise dynamically to control the inactivation path. Using constant, pulsed and continuous oscillating voltage protocols we have shown that during depolarization the OSI path is more favored path of inactivation however, in the hyper-polarized situation the CSI is favored. It is also shown that the re-factorisation of inactivated sodium channel to resting state occurs via CSI path. Here we have shown how the subtle energetic and entropic cost due to the change in the depolarization magnitude determines the optimum path of inactivation. It is shown that an efficient CSI and OSI dynamical profile in principle can characterize the open-state drug blocking phenomena. PMID:27367642

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

Quantification of Transthyretin Kinetic Stability in Human Plasma Using Subunit Exchange

PubMed Central

2015-01-01

The transthyretin (TTR) amyloidoses are a group of degenerative diseases caused by TTR aggregation, requiring rate-limiting tetramer dissociation. Kinetic stabilization of TTR, by preferential binding of a drug to the native tetramer over the dissociative transition state, dramatically slows the progression of familial amyloid polyneuropathy. An established method for quantifying the kinetic stability of recombinant TTR tetramers in buffer is subunit exchange, in which tagged TTR homotetramers are added to untagged homotetramers at equal concentrations to measure the rate at which the subunits exchange. Herein, we report a subunit exchange method for quantifying the kinetic stability of endogenous TTR in human plasma. The subunit exchange reaction is initiated by the addition of a substoichiometric quantity of FLAG-tagged TTR homotetramers to endogenous TTR in plasma. Aliquots of the subunit exchange reaction, taken as a function of time, are then added to an excess of a fluorogenic small molecule, which immediately arrests further subunit exchange. After binding, the small molecule reacts with the TTR tetramers, rendering them fluorescent and detectable in human plasma after subsequent ion exchange chromatography. The ability to report on the extent of TTR kinetic stabilization resulting from treatment with oral tafamidis is important, especially for selection of the appropriate dose for patients carrying rare mutations. This method could also serve as a surrogate biomarker for the prediction of the clinical outcome. Subunit exchange was used to quantify the stabilization of WT TTR from senile systemic amyloidosis patients currently being treated with tafamidis (20 mg orally, once daily). TTR kinetic stability correlated with the tafamidis plasma concentration. PMID:24661308

Relationships Between the Phase Transformation Kinetics, Texture Evolution, and Microstructure Development in a 304L Stainless Steel Under Biaxial Loading Conditions: Synchrotron X-ray and Electron Backscatter Diffraction Studies

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

Cakmak, Ercan; Choo, Hahn; Kang, Jun-Yun

2015-02-11

The relationships between the martensitic phase transformation kinetics, texture evolution, and the microstructure development in the parent austenite phase were studied for a 304L stainless steel that exhibits the transformation-induced plasticity effect under biaxial loading conditions at ambient temperature. The applied loading paths included: pure torsion, simultaneous biaxial torsion/tension, simultaneous biaxial torsion/compression, and stepwise loading of tension followed by torsion (i.e., first loading by uniaxial tension and then by pure torsion in sequence). Synchrotron X-ray and electron backscatter diffraction techniques were used to measure the evolution of the phase fractions, textures, and microstructures as a function of the applied strains.more » The influence of loading character and path on the changes in martensitic phase transformation kinetics is discussed in the context of (1) texture-transformation relationship and the preferred transformation of grains belonging to certain texture components over the others, (2) effects of axial strains on shear band evolutions, and (3) volume changes associated with martensitic transformation.« less

Kinetic isotope effect in malonaldehyde determined from path integral Monte Carlo simulations.

PubMed

Huang, Jing; Buchowiecki, Marcin; Nagy, Tibor; Vaníček, Jiří; Meuwly, Markus

2014-01-07

The primary H/D kinetic isotope effect on the intramolecular proton transfer in malonaldehyde is determined from quantum instanton path integral Monte Carlo simulations on a fully dimensional and validated potential energy surface for temperatures between 250 and 1500 K. Our calculations, based on thermodynamic integration with respect to the mass of the transferring particle, are significantly accelerated by the direct evaluation of the kinetic isotope effect instead of computing it as a ratio of two rate constants. At room temperature, the KIE from the present simulations is 5.2 ± 0.4. The KIE is found to vary considerably as a function of temperature and the low-T behaviour is dominated by the fact that the free energy derivative in the reactant state increases more rapidly than in the transition state. Detailed analysis of the various contributions to the quantum rate constant together with estimates for rates from conventional transition state theory and from periodic orbit theory suggest that the KIE in malonaldehyde is dominated by zero point energy effects and that tunneling plays a minor role at room temperature.

An estimate of the shadow price of water in the southern Ogallala Aquifer

USDA-ARS?s Scientific Manuscript database

In this paper, we attempt to quantify the shadow price of an additional inch of groundwater resource left in situ for the Southern Ogallala Aquifer. Previous authors have shown the degree to which the optimal resource extraction path may diverge from the competitive extraction path based upon varyin...

Insights into vehicle trajectories at the handling limits: analysing open data from race car drivers

NASA Astrophysics Data System (ADS)

Kegelman, John C.; Harbott, Lene K.; Gerdes, J. Christian

2017-02-01

Race car drivers can offer insights into vehicle control during extreme manoeuvres; however, little data from race teams is publicly available for analysis. The Revs Program at Stanford has built a collection of vehicle dynamics data acquired from vintage race cars during live racing events with the intent of making this database publicly available for future analysis. This paper discusses the data acquisition, post-processing, and storage methods used to generate the database. An analysis of available data quantifies the repeatability of professional race car driver performance by examining the statistical dispersion of their driven paths. Certain map features, such as sections with high path curvature, consistently corresponded to local minima in path dispersion, quantifying the qualitative concept that drivers anchor their racing lines at specific locations around the track. A case study explores how two professional drivers employ distinct driving styles to achieve similar lap times, supporting the idea that driving at the limits allows a family of solutions in terms of paths and speed that can be adapted based on specific spatial, temporal, or other constraints and objectives.

Kinetic Monte Carlo Simulation of Oxygen Diffusion in Ytterbium Disilicate

NASA Astrophysics Data System (ADS)

Good, Brian

2015-03-01

Ytterbium disilicate is of interest as a potential environmental barrier coating for aerospace applications, notably for use in next generation jet turbine engines. In such applications, the diffusion of oxygen and water vapor through these coatings is undesirable if high temperature corrosion is to be avoided. In an effort to understand the diffusion process in these materials, we have performed kinetic Monte Carlo simulations of vacancy-mediated oxygen diffusion in Ytterbium Disilicate. Oxygen vacancy site energies and diffusion barrier energies are computed using Density Functional Theory. We find that many potential diffusion paths involve large barrier energies, but some paths have barrier energies smaller than one electron volt. However, computed vacancy formation energies suggest that the intrinsic vacancy concentration is small in the pure material, with the result that the material is unlikely to exhibit significant oxygen permeability.

The Potential and Flux Landscape Theory of Ecology

PubMed Central

Zhang, Kun; Wang, Erkang; Wang, Jin

2014-01-01

The species in ecosystems are mutually interacting and self sustainable stable for a certain period. Stability and dynamics are crucial for understanding the structure and the function of ecosystems. We developed a potential and flux landscape theory of ecosystems to address these issues. We show that the driving force of the ecological dynamics can be decomposed to the gradient of the potential landscape and the curl probability flux measuring the degree of the breaking down of the detailed balance (due to in or out flow of the energy to the ecosystems). We found that the underlying intrinsic potential landscape is a global Lyapunov function monotonically going down in time and the topology of the landscape provides a quantitative measure for the global stability of the ecosystems. We also quantified the intrinsic energy, the entropy, the free energy and constructed the non-equilibrium thermodynamics for the ecosystems. We studied several typical and important ecological systems: the predation, competition, mutualism and a realistic lynx-snowshoe hare model. Single attractor, multiple attractors and limit cycle attractors emerge from these studies. We studied the stability and robustness of the ecosystems against the perturbations in parameters and the environmental fluctuations. We also found that the kinetic paths between the multiple attractors do not follow the gradient paths of the underlying landscape and are irreversible because of the non-zero flux. This theory provides a novel way for exploring the global stability, function and the robustness of ecosystems. PMID:24497975

Theoretical Proposal for the Whole Phosphate Diester Hydrolysis Mechanism Promoted by a Catalytic Promiscuous Dinuclear Copper(II) Complex.

PubMed

Esteves, Lucas F; Rey, Nicolás A; Dos Santos, Hélio F; Costa, Luiz Antônio S

2016-03-21

The catalytic mechanism that involves the cleavage of the phosphate diester model BDNPP (bis(2,4-dinitrophenyl) phosphate) catalyzed through a dinuclear copper complex is investigated in the current study. The metal complex was originally designed to catalyze catechol oxidation, and it showed an interesting catalytic promiscuity case in biomimetic systems. The current study investigates two different reaction mechanisms through quantum mechanics calculations in the gas phase, and it also includes the solvent effect through PCM (polarizable continuum model) single-point calculations using water as solvent. Two mechanisms are presented in order to fully describe the phosphate diester hydrolysis. Mechanism 1 is of the S(N)2 type, which involves the direct attack of the μ-OH bridge between the two copper(II) ions toward the phosphorus center, whereas mechanism 2 is the process in which hydrolysis takes place through proton transfer between the oxygen atom in the bridging hydroxo ligand and the other oxygen atom in the phosphate model. Actually, the present theoretical study shows two possible reaction paths in mechanism 1. Its first reaction path (p1) involves a proton transfer that occurs immediately after the hydrolytic cleavage, so that the proton transfer is the rate-determining step, which is followed by the entry of two water molecules. Its second reaction path (p2) consists of the entry of two water molecules right after the hydrolytic cleavage, but with no proton transfer; thus, hydrolytic cleavage is the rate-limiting step. The most likely catalytic path occurs in mechanism 1, following the second reaction path (p2), since it involves the lowest free energy activation barrier (ΔG(⧧) = 23.7 kcal mol(-1), in aqueous solution). A kinetic analysis showed that the experimental k(obs) value of 1.7 × 10(-5) s(-1) agrees with the calculated value k1 = 2.6 × 10(-5) s(-1); the concerted mechanism is kinetically favorable. The KIE (kinetic isotope effect) analysis applied to the second reaction path (p2) in mechanism 1 was also taken into account to assess the changes that take place in TS1-i (transition state of mechanism 1) and to perfectly characterize the mechanism described herein.

Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

PubMed Central

Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

2013-01-01

Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

Assessment of ion kinetic effects in shock-driven inertial confinement fusion implosions using fusion burn imaging

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

Rosenberg, M. J., E-mail: mros@lle.rochester.edu; Séguin, F. H.; Rinderknecht, H. G.

The significance and nature of ion kinetic effects in D{sup 3}He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, N{sub K}) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatiallymore » resolved measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (N{sub K} ∼ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.« less

Assessment of ion kinetic effects in shock-driven inertial confinement fusion (ICF) implosions using fusion burn imaging

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

Rosenberg, M. J.; Séguin, F. H.; Amendt, P. A.

The significance and nature of ion kinetic effects in D³He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, N K) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatially resolvedmore » measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (N K ~ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.« less

Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.

PubMed

Viswanath, Shruthi; Kreuzer, Steven M; Cardenas, Alfredo E; Elber, Ron

2013-11-07

Network representations are becoming increasingly popular for analyzing kinetic data from techniques like Milestoning, Markov State Models, and Transition Path Theory. Mapping continuous phase space trajectories into a relatively small number of discrete states helps in visualization of the data and in dissecting complex dynamics to concrete mechanisms. However, not only are molecular networks derived from molecular dynamics simulations growing in number, they are also getting increasingly complex, owing partly to the growth in computer power that allows us to generate longer and better converged trajectories. The increased complexity of the networks makes simple interpretation and qualitative insight of the molecular systems more difficult to achieve. In this paper, we focus on various network representations of kinetic data and algorithms to identify important edges and pathways in these networks. The kinetic data can be local and partial (such as the value of rate coefficients between states) or an exact solution to kinetic equations for the entire system (such as the stationary flux between vertices). In particular, we focus on the Milestoning method that provides fluxes as the main output. We proposed Global Maximum Weight Pathways as a useful tool for analyzing molecular mechanism in Milestoning networks. A closely related definition was made in the context of Transition Path Theory. We consider three algorithms to find Global Maximum Weight Pathways: Recursive Dijkstra's, Edge-Elimination, and Edge-List Bisection. The asymptotic efficiency of the algorithms is analyzed and numerical tests on finite networks show that Edge-List Bisection and Recursive Dijkstra's algorithms are most efficient for sparse and dense networks, respectively. Pathways are illustrated for two examples: helix unfolding and membrane permeation. Finally, we illustrate that networks based on local kinetic information can lead to incorrect interpretation of molecular mechanisms.

Assessment of ion kinetic effects in shock-driven inertial confinement fusion implosions using fusion burn imaging

NASA Astrophysics Data System (ADS)

Rosenberg, M. J.; Séguin, F. H.; Amendt, P. A.; Atzeni, S.; Rinderknecht, H. G.; Hoffman, N. M.; Zylstra, A. B.; Li, C. K.; Sio, H.; Gatu Johnson, M.; Frenje, J. A.; Petrasso, R. D.; Glebov, V. Yu.; Stoeckl, C.; Seka, W.; Marshall, F. J.; Delettrez, J. A.; Sangster, T. C.; Betti, R.; Wilks, S. C.; Pino, J.; Kagan, G.; Molvig, K.; Nikroo, A.

2015-06-01

The significance and nature of ion kinetic effects in D3He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, NK) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatially resolved measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (NK ˜ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.

Assessment of ion kinetic effects in shock-driven inertial confinement fusion (ICF) implosions using fusion burn imaging

DOE PAGES

Rosenberg, M. J.; Séguin, F. H.; Amendt, P. A.; ...

2015-06-02

The significance and nature of ion kinetic effects in D³He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, N K) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatially resolvedmore » measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (N K ~ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.« less

The Use of a Multidimensional Measure of Dialysis Adequacy-Moving beyond Small Solute Kinetics.

PubMed

Perl, Jeffrey; Dember, Laura M; Bargman, Joanne M; Browne, Teri; Charytan, David M; Flythe, Jennifer E; Hickson, LaTonya J; Hung, Adriana M; Jadoul, Michel; Lee, Timmy Chang; Meyer, Klemens B; Moradi, Hamid; Shafi, Tariq; Teitelbaum, Isaac; Wong, Leslie P; Chan, Christopher T

2017-05-08

Urea removal has become a key measure of the intensity of dialysis treatment for kidney failure. Small solute removal, exemplified by Kt/V urea, has been broadly applied as a means to quantify the dose of thrice weekly hemodialysis. Yet, the reliance on small solute clearances alone as a measure of dialysis adequacy fails fully to quantify the intended clinical effects of dialysis therapy. This review aims to ( 1 ) understand the strengths and limitations of small solute kinetics as a surrogate marker of dialysis dose, and ( 2 ) present the prospect of a more comprehensive construct for dialysis dose, one that considers more broadly the goals of ESRD care to maximize both quality of life and survival. On behalf of the American Society of Nephrology Dialysis Advisory Group, we propose the need to ascertain the validity and utility of a multidimensional measure that moves beyond small solute kinetics alone to quantify optimal dialysis derived from both patient-reported and comprehensive clinical and dialysis-related measures. Copyright © 2017 by the American Society of Nephrology.

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

Willemin, Marie-Emilie; Lumen, Annie, E-mail: Anni

Thyroid homeostasis can be disturbed due to thiocyanate exposure from the diet or tobacco smoke. Thiocyanate inhibits both thyroidal uptake of iodide, via the sodium-iodide symporter (NIS), and thyroid hormone (TH) synthesis in the thyroid, via thyroid peroxidase (TPO), but the mode of action of thiocyanate is poorly quantified in the literature. The characterization of the link between intra-thyroidal thiocyanate concentrations and dose of exposure is crucial for assessing the risk of thyroid perturbations due to thiocyanate exposure. We developed a PBPK model for thiocyanate that describes its kinetics in the whole-body up to daily doses of 0.15 mmol/kg, withmore » a mechanistic description of the thyroidal kinetics including NIS, passive diffusion, and TPO. The model was calibrated in a Bayesian framework using published studies in rats. Goodness-of-fit was satisfactory, especially for intra-thyroidal thiocyanate concentrations. Thiocyanate kinetic processes were quantified in vivo, including the metabolic clearance by TPO. The passive diffusion rate was found to be greater than NIS-mediated uptake rate. The model captured the dose-dependent kinetics of thiocyanate after acute and chronic exposures. Model behavior was evaluated using a Morris screening test. The distribution of thiocyanate into the thyroid was found to be determined primarily by the partition coefficient, followed by NIS and passive diffusion; the impact of the latter two mechanisms appears to increase at very low doses. Extrapolation to humans resulted in good predictions of thiocyanate kinetics during chronic exposure. The developed PBPK model can be used in risk assessment to quantify dose-response effects of thiocyanate on TH. - Highlights: • A PBPK model of thiocyanate (SCN{sup −}) was calibrated in rats in a Bayesian framework. • The intra-thyroidal kinetics of thiocyanate including NIS and TPO was modeled. • Passive diffusion rate for SCN{sup −} seemed to be greater than the NIS-mediated uptake. • The dose-dependent kinetics of SCN{sup −} was captured after an acute and chronic exposure. • The PBPK model of thiocyanate was successfully extrapolated to humans.« less

Quantifying fat, oil, and grease deposit formation kinetics

USDA-ARS?s Scientific Manuscript database

Fat, oil, and grease (FOG) deposits formed in sanitary sewers are calcium-based saponified solids that are responsible for a significant number of nationwide sanitary sewer overflows (SSOs) across United States. In the current study, the kinetics of lab-based saponified solids were determined to un...

Kinetic simulations of gas breakdown in the dense plasma focus

NASA Astrophysics Data System (ADS)

Bennett, N.; Blasco, M.; Breeding, K.; DiPuccio, V.; Gall, B.; Garcia, M.; Gardner, S.; Gatling, J.; Hagen, E. C.; Luttman, A.; Meehan, B. T.; Molnar, S.; O'Brien, R.; Ormond, E.; Robbins, L.; Savage, M.; Sipe, N.; Welch, D. R.

2017-06-01

The first fully kinetic, collisional, and electromagnetic simulations of the breakdown phase of a MA-scale dense plasma focus are described and shown to agree with measured electrical characteristics, including breakdown time. In the model, avalanche ionization is driven by cathode electron emission, and this results in incomplete gas breakdown along the insulator. This reinforces the importance of the conditioning process that creates a metallic layer on the insulator surface. The simulations, nonetheless, help explain the relationship between the gas pressure, the insulator length, and the coaxial gap width. Previously, researchers noted three breakdown patterns related to pressure. Simulation and analytical results show that at low pressures, long ionization path lengths lead to volumetric breakdown, while high pressures lead to breakdown across the relatively small coaxial electrode gap. In an intermediate pressure regime, ionization path lengths are comparable to the insulator length which promotes ideal breakdown along the insulator surface.

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

Unit Fractions in the Context of Proportionality: Supporting Students' Reasoning about the Inverse Order Relationship

ERIC Educational Resources Information Center

Cortina, Jose Luis; Visnovska, Jana; Zuniga, Claudia

2014-01-01

We analyze a classroom design experiment, conducted in a fourth grade classroom, that served to explore an instructional path in which the introduction of unit fractions and supporting proportional reasoning coincide. Central to this path is the use of means of support in which the objects that unit fractions quantify are not characterized as…

Multivariate curve resolution applied to kinetic-spectroscopic data matrices: Dye determination in foods by means of enzymatic oxidation.

PubMed

Boeris, Valeria; Arancibia, Juan A; Olivieri, Alejandro C

2017-07-01

In this work, the combination of chemometric techniques with kinetic-spectroscopic data allowed quantifying two dyes (tartrazine and carminic acid) in complex matrices as mustard, ketchup, asparagus soup powder, pumpkin soup powder, plum jam and orange-strawberry juice. Quantitative analysis was performed without the use of tedious sample pretreatment, due to the achievement of the second-order advantage. The results obtained showed an improvement in simplicity, speed and cost with respect to usual separation techniques, allowing to properly quantifying these dyes obtaining limits of detection below 0.6mgL -1 . In addition, to the best of our knowledge, is the first time that kinetic-spectroscopic data are obtained from the action of laccase for analytical purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

Building a mechanistic understanding of predation with GPS-based movement data.

PubMed

Merrill, Evelyn; Sand, Håkan; Zimmermann, Barbara; McPhee, Heather; Webb, Nathan; Hebblewhite, Mark; Wabakken, Petter; Frair, Jacqueline L

2010-07-27

Quantifying kill rates and sources of variation in kill rates remains an important challenge in linking predators to their prey. We address current approaches to using global positioning system (GPS)-based movement data for quantifying key predation components of large carnivores. We review approaches to identify kill sites from GPS movement data as a means to estimate kill rates and address advantages of using GPS-based data over past approaches. Despite considerable progress, modelling the probability that a cluster of GPS points is a kill site is no substitute for field visits, but can guide our field efforts. Once kill sites are identified, time spent at a kill site (handling time) and time between kills (killing time) can be determined. We show how statistical models can be used to investigate the influence of factors such as animal characteristics (e.g. age, sex, group size) and landscape features on either handling time or killing efficiency. If we know the prey densities along paths to a kill, we can quantify the 'attack success' parameter in functional response models directly. Problems remain in incorporating the behavioural complexity derived from GPS movement paths into functional response models, particularly in multi-prey systems, but we believe that exploring the details of GPS movement data has put us on the right path.

Link prediction based on local weighted paths for complex networks

NASA Astrophysics Data System (ADS)

Yao, Yabing; Zhang, Ruisheng; Yang, Fan; Yuan, Yongna; Hu, Rongjing; Zhao, Zhili

As a significant problem in complex networks, link prediction aims to find the missing and future links between two unconnected nodes by estimating the existence likelihood of potential links. It plays an important role in understanding the evolution mechanism of networks and has broad applications in practice. In order to improve prediction performance, a variety of structural similarity-based methods that rely on different topological features have been put forward. As one topological feature, the path information between node pairs is utilized to calculate the node similarity. However, many path-dependent methods neglect the different contributions of paths for a pair of nodes. In this paper, a local weighted path (LWP) index is proposed to differentiate the contributions between paths. The LWP index considers the effect of the link degrees of intermediate links and the connectivity influence of intermediate nodes on paths to quantify the path weight in the prediction procedure. The experimental results on 12 real-world networks show that the LWP index outperforms other seven prediction baselines.

Relationships Between the Phase Transformation Kinetics, Texture Evolution, and Microstructure Development in a 304L Stainless Steel Under Biaxial Loading Conditions: Synchrotron X-ray and Electron Backscatter Diffraction Studies

DOE PAGES

Cakmak, Ercan; Choo, Hahn; Kang, Jun-Yun; ...

2015-02-11

Here we report that the relationships between the martensitic phase transformation kinetics, texture evolution, and the microstructure development in the parent austenite phase were studied for a 304L stainless steel that exhibits the transformation-induced plasticity effect under biaxial loading conditions at ambient temperature. The applied loading paths included: pure torsion, simultaneous biaxial torsion/tension, simultaneous biaxial torsion/compression, and stepwise loading of tension followed by torsion (i.e., first loading by uniaxial tension and then by pure torsion in sequence). Synchrotron X-ray and electron backscatter diffraction techniques were used to measure the evolution of the phase fractions, textures, and microstructures as a functionmore » of the applied strains. The influence of loading character and path on the changes in martensitic phase transformation kinetics is discussed in the context of (1) texture-transformation relationship and the preferred transformation of grains belonging to certain texture components over the others, (2) effects of axial strains on shear band evolutions, and (3) volume changes associated with martensitic transformation.« less

Quantum path integral simulation of isotope effects in the melting temperature of ice Ih.

PubMed

Ramírez, R; Herrero, C P

2010-10-14

The isotope effect in the melting temperature of ice Ih has been studied by free energy calculations within the path integral formulation of statistical mechanics. Free energy differences between isotopes are related to the dependence of their kinetic energy on the isotope mass. The water simulations were performed by using the q-TIP4P/F model, a point charge empirical potential that includes molecular flexibility and anharmonicity in the OH stretch of the water molecule. The reported melting temperature at ambient pressure of this model (T=251 K) increases by 6.5±0.5 and 8.2±0.5 K upon isotopic substitution of hydrogen by deuterium and tritium, respectively. These temperature shifts are larger than the experimental ones (3.8 and 4.5 K, respectively). In the classical limit, the melting temperature is nearly the same as that for tritiated ice. This unexpected behavior is rationalized by the coupling between intermolecular interactions and molecular flexibility. This coupling makes the kinetic energy of the OH stretching modes larger in the liquid than in the solid phase. However, the opposite behavior is found for intramolecular modes, which display larger kinetic energy in ice than in liquid water.

75 FR 52756 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-27

... for evaluation of chemical species having unpaired electrons such as free radicals and transition.... Durnin J, Micheli J Jr, Eberly JH. Diffraction-free beams. Phys Rev Lett. 1987 Apr 13;58(15):1499-1501. 2... quantify pharmaco-kinetics and metabolic degradation kinetics of bioactive and redox sensitive free...

­Understanding Information Flow Interaction along Separable Causal Paths in Environmental Signals

NASA Astrophysics Data System (ADS)

Jiang, P.; Kumar, P.

2017-12-01

Multivariate environmental signals reflect the outcome of complex inter-dependencies, such as those in ecohydrologic systems. Transfer entropy and information partitioning approaches have been used to characterize such dependencies. However, these approaches capture net information flow occurring through a multitude of pathways involved in the interaction and as a result mask our ability to discern the causal interaction within an interested subsystem through specific pathways. We build on recent developments of momentary information transfer along causal paths proposed by Runge [2015] to develop a framework for quantifying information decomposition along separable causal paths. Momentary information transfer along causal paths captures the amount of information flow between any two variables lagged at two specific points in time. Our approach expands this concept to characterize the causal interaction in terms of synergistic, unique and redundant information flow through separable causal paths. Multivariate analysis using this novel approach reveals precise understanding of causality and feedback. We illustrate our approach with synthetic and observed time series data. We believe the proposed framework helps better delineate the internal structure of complex systems in geoscience where huge amounts of observational datasets exist, and it will also help the modeling community by providing a new way to look at the complexity of real and modeled systems. Runge, Jakob. "Quantifying information transfer and mediation along causal pathways in complex systems." Physical Review E 92.6 (2015): 062829.

The Preferred Movement Path Paradigm: Influence of Running Shoes on Joint Movement.

PubMed

Nigg, Benno M; Vienneau, Jordyn; Smith, Aimée C; Trudeau, Matthieu B; Mohr, Maurice; Nigg, Sandro R

2017-08-01

(A) To quantify differences in lower extremity joint kinematics for groups of runners subjected to different running footwear conditions, and (B) to quantify differences in lower extremity joint kinematics on an individual basis for runners subjected to different running footwear conditions. Three-dimensional ankle and knee joint kinematics were collected for 35 heel-toe runners when wearing three different running shoes and when running barefoot. Absolute mean differences in ankle and knee joint kinematics were computed between running shoe conditions. The percentage of individual runners who displayed differences below a 2°, 3°, and 5° threshold were also calculated. The results indicate that the mean kinematics of the ankle and knee joints were similar between running shoe conditions. Aside from ankle dorsiflexion and knee flexion, the percentage of runners maintaining their movement path between running shoes (i.e., less than 3°) was in the order of magnitude of about 80% to 100%. Many runners showed ankle and knee joint kinematics that differed between a conventional running shoe and barefoot by more than 3°, especially for ankle dorsiflexion and knee flexion. Many runners stay in the same movement path (the preferred movement path) when running in various different footwear conditions. The percentage of runners maintaining their preferred movement path depends on the magnitude of the change introduced by the footwear condition.

An automated integration-free path-integral method based on Kleinert's variational perturbation theory

NASA Astrophysics Data System (ADS)

Wong, Kin-Yiu; Gao, Jiali

2007-12-01

Based on Kleinert's variational perturbation (KP) theory [Path Integrals in Quantum Mechanics, Statistics, Polymer Physics, and Financial Markets, 3rd ed. (World Scientific, Singapore, 2004)], we present an analytic path-integral approach for computing the effective centroid potential. The approach enables the KP theory to be applied to any realistic systems beyond the first-order perturbation (i.e., the original Feynman-Kleinert [Phys. Rev. A 34, 5080 (1986)] variational method). Accurate values are obtained for several systems in which exact quantum results are known. Furthermore, the computed kinetic isotope effects for a series of proton transfer reactions, in which the potential energy surfaces are evaluated by density-functional theory, are in good accordance with experiments. We hope that our method could be used by non-path-integral experts or experimentalists as a "black box" for any given system.

In vitro dissolution kinetic study of theophylline from hydrophilic and hydrophobic matrices.

PubMed

Maswadeh, Hamzah M; Semreen, Mohammad H; Abdulhalim, Abdulatif A

2006-01-01

Oral dosage forms containing 300 mg theophylline in matrix type tablets, were prepared by direct compression method using two kinds of matrices, glycerylbehenate (hydrophobic), and (hydroxypropyl)methyl cellulose (hydrophilic). The in vitro release kinetics of these formulations were studied at pH 6.8 using the USP dissolution apparatus with the paddle assemble. The kinetics of the dissolution process were studied by analyzing the dissolution data using four kinetic equations, the zero-order equation, the first-order equation, the Higuchi square root equation and the Hixson-Crowell cube root law. The analysis of the dissolution kinetic data for the theophylline preparations in this study shows that it follows the first order kinetics and the release process involves erosion / diffusion and an alteration in the surface area and diameter of the matrix system, as well as in the diffusion path length from the matrix drug load during the dissolution process. This relation is best described by the use of both the first-order equation and the Hixson-Crowell cube root law.

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

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

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

DOE PAGES

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

2017-05-17

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

Chloroperoxidase-catalyzed oxidation of 4,6-dimethyldibenzothiophene as dimer complexes: evidence for kinetic cooperativity.

PubMed

Torres, Eduardo; Aburto, Jorge

2005-05-15

A sigmoidal kinetic behavior of chloroperoxidase for the oxidation of 4,6-dimethyldibenzothiophene (4,6-DMDBT) in water-miscible organic solvent is for the first time reported. Kinetics of 4,6-DMDBT oxidation showed a cooperative profile probably due to the capacity of chloroperoxidase to recognize a substrate dimer (pi-pi dimer) in its active site. Experimental evidence is given for dimer formation and its presence in the active site of chloroperoxidase. The kinetic data were adjusted for a binding site able to interact with either monomer or dimer substrates, producing a cooperative model describing a one-site binding of two related species. Determination of kinetics constants by iterative calculations of possible oxidation paths of 4,6-DMDBT suggests that kinetics oxidation of dimer substrate is preferred when compared to monomer oxidation. Steady-state fluorometry of substrate in the absence and presence of chloroperoxidase, described by the spectral center of mass, supports this last conclusion.

Evaluating Status Change of Soil Potassium from Path Model

PubMed Central

He, Wenming; Chen, Fang

2013-01-01

The purpose of this study is to determine critical environmental parameters of soil K availability and to quantify those contributors by using a proposed path model. In this study, plot experiments were designed into different treatments, and soil samples were collected and further analyzed in laboratory to investigate soil properties influence on soil potassium forms (water soluble K, exchangeable K, non-exchangeable K). Furthermore, path analysis based on proposed path model was carried out to evaluate the relationship between potassium forms and soil properties. Research findings were achieved as followings. Firstly, key direct factors were soil S, ratio of sodium-potassium (Na/K), the chemical index of alteration (CIA), Soil Organic Matter in soil solution (SOM), Na and total nitrogen in soil solution (TN), and key indirect factors were Carbonate (CO3), Mg, pH, Na, S, and SOM. Secondly, path model can effectively determine direction and quantities of potassium status changes between Exchangeable potassium (eK), Non-exchangeable potassium (neK) and water-soluble potassium (wsK) under influences of specific environmental parameters. In reversible equilibrium state of , K balance state was inclined to be moved into β and χ directions in treatments of potassium shortage. However in reversible equilibrium of , K balance state was inclined to be moved into θ and λ directions in treatments of water shortage. Results showed that the proposed path model was able to quantitatively disclose moving direction of K status and quantify its equilibrium threshold. It provided a theoretical and practical basis for scientific and effective fertilization in agricultural plants growth. PMID:24204659

Quantifying heterogeneity of lesion uptake in dynamic contrast enhanced MRI for breast cancer diagnosis

NASA Astrophysics Data System (ADS)

Karahaliou, A.; Vassiou, K.; Skiadopoulos, S.; Kanavou, T.; Yiakoumelos, A.; Costaridou, L.

2009-07-01

The current study investigates whether texture features extracted from lesion kinetics feature maps can be used for breast cancer diagnosis. Fifty five women with 57 breast lesions (27 benign, 30 malignant) were subjected to dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) on 1.5T system. A linear-slope model was fitted pixel-wise to a representative lesion slice time series and fitted parameters were used to create three kinetic maps (wash out, time to peak enhancement and peak enhancement). 28 grey level co-occurrence matrices features were extracted from each lesion kinetic map. The ability of texture features per map in discriminating malignant from benign lesions was investigated using a Probabilistic Neural Network classifier. Additional classification was performed by combining classification outputs of most discriminating feature subsets from the three maps, via majority voting. The combined scheme outperformed classification based on individual maps achieving area under Receiver Operating Characteristics curve 0.960±0.029. Results suggest that heterogeneity of breast lesion kinetics, as quantified by texture analysis, may contribute to computer assisted tissue characterization in DCE-MRI.

A biomechanical analysis of upper extremity kinetics in children with cerebral palsy using anterior and posterior walkers.

PubMed

Konop, Katherine A; Strifling, Kelly M B; Wang, Mei; Cao, Kevin; Schwab, Jeffrey P; Eastwood, Daniel; Jackson, Scott; Ackman, Jeffrey D; Harris, Gerald F

2009-10-01

Upper extremity (UE) joint kinetics during aided ambulation is an area of research that is not well characterized in the current literature. Biped UE joints are not anatomically designed to be weight bearing, therefore it is important to quantify UE kinetics during assisted gait. This will help to better understand the biomechanical implications of UE weight bearing, and enable physicians to prescribe more effective methods for treatment and therapy, perhaps minimizing excessive loads and torques. To address this challenge, an UE model that incorporates both kinematics and kinetics has been developed for use with walkers instrumented with load cells. In this study, the UE joint kinetics are calculated for 10 children with cerebral palsy using both anterior and posterior walkers. Three-dimensional joint reaction forces and moments are fully characterized for the wrist, elbow, and shoulder (glenohumeral) joints for both walker types. Statistical analysis methods are used to quantify the differences in forces or moments between the two walker types. Comparisons showed no significant differences in kinetic joint parameters between walker types. Results from a power analysis of the current data are provided which may be useful for planning longer term clinical studies. If risk factors for UE joint pathology can be identified early, perhaps a change in gait training routine, walker prescription, or walker design could prevent further harm.

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

Stress-dependence of kinetic transitions at atomistic defects

NASA Astrophysics Data System (ADS)

Ball, S. L.; Alexander, K. C.; Schuh, C. A.

2018-01-01

The full second-rank activation volume tensors associated with vacancy migration in FCC copper and HCP titanium as well as transition events in the Σ5 (2 1 0) grain boundary in copper are calculated and analyzed. The full tensorial results quantitatively illustrate how the conventional use of an activation volume scalar in atomistic studies of the kinetic processes of complex defects can miss important stress dependencies, in that neither hydrostatic pressure nor deviatoric stress dependencies can be considered alone as dominating the response. The results speak to the importance of anisotropies in the stress-dependence of atomistic kinetics, including crystal structure anisotropy, elastic anisotropy, and defect structure or migration-path anisotropies.

No-scale ripple inflation revisited

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

Li, Tianjun; Li, Zhijin; Nanopoulos, Dimitri V., E-mail: tli@itp.ac.cn, E-mail: lizhijin@physics.tamu.edu, E-mail: dimitri@physics.tamu.edu

We revisit the no-scale ripple inflation model, where no-scale supergravity is modified by an additional term for the inflaton field in the Kähler potential. This term not only breaks one SU(N,1) symmetry explicitly, but also plays an important role for inflation. We generalize the superpotential in the no-scale ripple inflation model slightly. There exists a discrete Z{sub 2} symmetry/parity in the scalar potential in general, which can be preserved or violated by the non-canonical nomalized inflaton kinetic term. Thus, there are three inflation paths: one parity invariant path, and the left and right paths for parity violating scenario. We showmore » that the inflations along the parity invariant path and right path are consistent with the Planck results. However, the gavitino mass for the parity invariant path is so large that the inflation results will be invalid if we consider the inflaton supersymmetry breaking soft mass term. Thus, only the inflation along the right path gives the correct and consistent results. Notably, the tensor-to-scalar ratio in such case can be large, with a value around 0.05, which may be probed by the future Planck experiment.« less

Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

PubMed

Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

2008-01-01

A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

Scanning fluorescence correlation spectroscopy techniques to quantify the kinetics of DNA double strand break repair proteins after γ-irradiation and bleomycin treatment

PubMed Central

Abdisalaam, Salim; Davis, Anthony J.; Chen, David J.; Alexandrakis, George

2014-01-01

A common feature of DNA repair proteins is their mobilization in response to DNA damage. The ability to visualizing and quantifying the kinetics of proteins localizing/dissociating from DNA double strand breaks (DSBs) via immunofluorescence or live cell fluorescence microscopy have been powerful tools in allowing insight into the DNA damage response, but these tools have some limitations. For example, a number of well-established DSB repair factors, in particular those required for non-homologous end joining (NHEJ), do not form discrete foci in response to DSBs induced by ionizing radiation (IR) or radiomimetic drugs, including bleomycin, in living cells. In this report, we show that time-dependent kinetics of the NHEJ factors Ku80 and DNA-dependent protein kinase catalytic subunits (DNA–PKcs) in response to IR and bleomycin can be quantified by Number and Brightness analysis and Raster-scan Image Correlation Spectroscopy. Fluorescent-tagged Ku80 and DNA–PKcs quickly mobilized in response to IR and bleomycin treatments consistent with prior reports using laser-generated DSBs. The response was linearly dependent on IR dose, and blocking NHEJ enhanced immobilization of both Ku80 and DNA–PKcs after DNA damage. These findings support the idea of using Number and Brightness and Raster-scan Image Correlation Spectroscopy as methods to monitor kinetics of DSB repair proteins in living cells under conditions mimicking radiation and chemotherapy treatments. PMID:24137007

How to design PET experiments to study neurochemistry: application to alcoholism.

PubMed

Morris, Evan D; Lucas, Molly V; Petrulli, J Ryan; Cosgrove, Kelly P

2014-03-01

Positron Emission Tomography (PET) (and the related Single Photon Emission Computed Tomography) is a powerful imaging tool with a molecular specificity and sensitivity that are unique among imaging modalities. PET excels in the study of neurochemistry in three ways: 1) It can detect and quantify neuroreceptor molecules; 2) it can detect and quantify changes in neurotransmitters; and 3) it can detect and quantify exogenous drugs delivered to the brain. To carry out any of these applications, the user must harness the power of kinetic modeling. Further, the quality of the information gained is only as good as the soundness of the experimental design. This article reviews the concepts behind the three main uses of PET, the rationale behind kinetic modeling of PET data, and some of the key considerations when planning a PET experiment. Finally, some examples of PET imaging related to the study of alcoholism are discussed and critiqued.

How to Design PET Experiments to Study Neurochemistry: Application to Alcoholism

PubMed Central

Morris, Evan D.; Lucas, Molly V.; Petrulli, J. Ryan; Cosgrove, Kelly P.

2014-01-01

Positron Emission Tomography (PET) (and the related Single Photon Emission Computed Tomography) is a powerful imaging tool with a molecular specificity and sensitivity that are unique among imaging modalities. PET excels in the study of neurochemistry in three ways: 1) It can detect and quantify neuroreceptor molecules; 2) it can detect and quantify changes in neurotransmitters; and 3) it can detect and quantify exogenous drugs delivered to the brain. To carry out any of these applications, the user must harness the power of kinetic modeling. Further, the quality of the information gained is only as good as the soundness of the experimental design. This article reviews the concepts behind the three main uses of PET, the rationale behind kinetic modeling of PET data, and some of the key considerations when planning a PET experiment. Finally, some examples of PET imaging related to the study of alcoholism are discussed and critiqued. PMID:24600335

Plasmonic imaging of protein interactions with single bacterial cells.

PubMed

Syal, Karan; Wang, Wei; Shan, Xiaonan; Wang, Shaopeng; Chen, Hong-Yuan; Tao, Nongjian

2015-01-15

Quantifying the interactions of bacteria with external ligands is fundamental to the understanding of pathogenesis, antibiotic resistance, immune evasion, and mechanism of antimicrobial action. Due to inherent cell-to-cell heterogeneity in a microbial population, each bacterium interacts differently with its environment. This large variability is washed out in bulk assays, and there is a need of techniques that can quantify interactions of bacteria with ligands at the single bacterium level. In this work, we present a label-free and real-time plasmonic imaging technique to measure the binding kinetics of ligand interactions with single bacteria, and perform statistical analysis of the heterogeneity. Using the technique, we have studied interactions of antibodies with single Escherichia coli O157:H7 cells and demonstrated a capability of determining the binding kinetic constants of single live bacteria with ligands, and quantify heterogeneity in a microbial population. Copyright © 2014 Elsevier B.V. All rights reserved.

Biochemical analysis of plant protection afforded by a nonpathogenic endophytic mutant of Colletotrichum magna

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

Redman, R.S.; Rodriguez, R.J.; Clifton, D.R.

1999-02-01

A nonpathogenic mutant of Colletotrichum magna (path-1) was previously shown to protect watermelon (Citrullus lanatus) and cucumber (Cucumis sativus) seedlings from anthracnose disease elicited by wild-type C. magna. Disease protection was observed in stems of path-1-colonized cucurbits but not in cotyledons, indicating that path-1 conferred tissue-specific and/or localized protection. Plant biochemical indicators of a localized and systemic (peroxidase, phenylalanine ammonia-lyase, lignin, and salicylic acid) plant-defense response were investigated in anthracnose-resistant and-susceptible cultivars of cucurbit seedlings exposed to four treatments: (1) water (control), (2) path-1 conidia, (3) wild-type conidia, and (4) challenge conditions (inoculation into path-1 conidia for 48 h andmore » then exposure to wild-type conidia). Collectively, these analyses indicated that disease protection in path-1-colonized plants was correlated with the ability of these plants to mount a defense response more rapidly and to equal or greater levels than plants exposed to wild-type C. magna alone. Watermelon plants colonized with path-1 were also protected against disease caused by Colletotrichum orbiculare and Fusarium oxysporum. A model based on the kinetics of plant-defense activation is presented to explain the mechanism of path-1-conferred disease protection.« less

Biochemical analysis of plant protection afforded by a nonpathogenic endophytic mutant of Colletotrichum magna

USGS Publications Warehouse

Redman, R.S.; Freeman, S.; Clifton, D.R.; Morrel, J.; Brown, G.; Rodriguez, R.J.

1999-01-01

A nonpathogenic mutant of Colletotrichum magna (path-1) was previously shown to protect watermelon (Citrullus lanatus) and cucumber (Cucumis sativus) seedlings from anthracnose disease elicited by wild-type C. magna. Disease protection was observed in stems of path-1-colonized cucurbits but not in cotyledons, indicating that path-1 conferred tissue-specific and/or localized protection. Plant biochemical indicators of a localized and systemic (peroxidase, phenylalanine ammonia-lyase, lignin, and salicylic acid) 'plant-defense' response were investigated in anthracnose-resistant and -susceptible cultivars of cucurbit seedlings exposed to four treatments: (1) water (control), (2) path-1 conidia, (3) wild-type conidia, and (4) challenge conditions (inoculation into path-1 conidia for 48 h and then exposure to wild-type conidia). Collectively, these analyses indicated that disease protection in path-1 colonized plants was correlated with the ability of these plants to mount a defense response more rapidly and to equal or greater levels than plants exposed to wild-type C. magna alone. Watermelon plants colonized with path-1 were also protected against disease caused by Colletotrichum orbiculare and Fusarium oxysporum. A model based on the kinetics of plant-defense activation is presented to explain the mechanism of path-1-conferred disease protection.

Impact of saccharides on the drying kinetics of agarose gels measured by in-situ interferometry

NASA Astrophysics Data System (ADS)

Mao, Bosi; Divoux, Thibaut; Snabre, Patrick

2017-01-01

Agarose gels are viscoelastic soft solids that display a porous microstructure filled with water at 90% w/w or more. Despite an extensive use in food industry and microbiology, little is known about the drying kinetics of such squishy solids, which suffers from a lack of time-resolved local measurements. Moreover, only scattered empirical observations are available on the role of the gel composition on the drying kinetics. Here we study by in-situ interferometry the drying of agarose gels of various compositions cast in Petri dishes. The gel thinning is associated with the displacement of interference fringes that are analyzed using an efficient spatiotemporal filtering method, which allows us to assess local thinning rates as low as 10 nm/s with high accuracy. The gel thinning rate measured at the center of the dish appears as a robust observable to quantify the role of additives on the gel drying kinetics and compare the drying speed of agarose gels loaded with various non-gelling saccharides of increasing molecular weights. Our work shows that saccharides systematically decrease the agarose gel thinning rate up to a factor two, and exemplifies interferometry as a powerful tool to quantify the impact of additives on the drying kinetics of polymer gels.

Exploring the Mechanisms of Differentiation, Dedifferentiation, Reprogramming and Transdifferentiation

PubMed Central

Xu, Li; Zhang, Kun; Wang, Jin

2014-01-01

We explored the underlying mechanisms of differentiation, dedifferentiation, reprogramming and transdifferentiation (cell type switchings) from landscape and flux perspectives. Lineage reprogramming is a new regenerative method to convert a matured cell into another cell including direct transdifferentiation without undergoing a pluripotent cell state and indirect transdifferentiation with an initial dedifferentiation-reversion (reprogramming) to a pluripotent cell state. Each cell type is quantified by a distinct valley on the potential landscape with higher probability. We investigated three driving forces for cell fate decision making: stochastic fluctuations, gene regulation and induction, which can lead to cell type switchings. We showed that under the driving forces the direct transdifferentiation process proceeds from a differentiated cell valley to another differentiated cell valley through either a distinct stable intermediate state or a certain series of unstable indeterminate states. The dedifferentiation process proceeds through a pluripotent cell state. Barrier height and the corresponding escape time from the valley on the landscape can be used to quantify the stability and efficiency of cell type switchings. We also uncovered the mechanisms of the underlying processes by quantifying the dominant biological paths of cell type switchings on the potential landscape. The dynamics of cell type switchings are determined by both landscape gradient and flux. The flux can lead to the deviations of the dominant biological paths for cell type switchings from the naively expected landscape gradient path. As a result, the corresponding dominant paths of cell type switchings are irreversible. We also classified the mechanisms of cell fate development from our landscape theory: super-critical pitchfork bifurcation, sub-critical pitchfork bifurcation, sub-critical pitchfork with two saddle-node bifurcation, and saddle-node bifurcation. Our model showed good agreements with the experiments. It provides a general framework to explore the mechanisms of differentiation, dedifferentiation, reprogramming and transdifferentiation. PMID:25133589

Synthesis and Characterization of Liquid Crystalline Epoxy Resins

DTIC Science & Technology

2014-01-01

Temperature dependence of the four parameters in the Burgers model. ......... 81 Figure 4.7 Dependence of creep compliance on creep time at different...Kinetic parameters for LCERs. ......................................................................... 65 Table 3.4 Kinetic parameters for non-LCERs...curing in a high strength magnetic field. The orientation was quantified by an orientation parameter determined with two-dimensional X-ray diffraction

How Kinetics within the Unfolded State Affects Protein Folding: an Analysis Based on Markov State Models and an Ultra-Long MD Trajectory

PubMed Central

Deng, Nan-jie; Dai, Wei

2013-01-01

Understanding how kinetics in the unfolded state affects protein folding is a fundamentally important yet less well-understood issue. Here we employ three different models to analyze the unfolded landscape and folding kinetics of the miniprotein Trp-cage. The first is a 208 μs explicit solvent molecular dynamics (MD) simulation from D. E. Shaw Research containing tens of folding events. The second is a Markov state model (MSM-MD) constructed from the same ultra-long MD simulation; MSM-MD can be used to generate thousands of folding events. The third is a Markov state model built from temperature replica exchange MD simulations in implicit solvent (MSM-REMD). All the models exhibit multiple folding pathways, and there is a good correspondence between the folding pathways from direct MD and those computed from the MSMs. The unfolded populations interconvert rapidly between extended and collapsed conformations on time scales ≤ 40 ns, compared with the folding time of ≈ 5 μs. The folding rates are independent of where the folding is initiated from within the unfolded ensemble. About 90 % of the unfolded states are sampled within the first 40 μs of the ultra-long MD trajectory, which on average explores ~27 % of the unfolded state ensemble between consecutive folding events. We clustered the folding pathways according to structural similarity into “tubes”, and kinetically partitioned the unfolded state into populations that fold along different tubes. From our analysis of the simulations and a simple kinetic model, we find that when the mixing within the unfolded state is comparable to or faster than folding, the folding waiting times for all the folding tubes are similar and the folding kinetics is essentially single exponential despite the presence of heterogeneous folding paths with non-uniform barriers. When the mixing is much slower than folding, different unfolded populations fold independently leading to non-exponential kinetics. A kinetic partition of the Trp-cage unfolded state is constructed which reveals that different unfolded populations have almost the same probability to fold along any of the multiple folding paths. We are investigating whether the results for the kinetics in the unfolded state of the twenty-residue Trp-cage is representative of larger single domain proteins. PMID:23705683

Capturing the Complexity of Additively Manufactured Microstructures

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

Livescu, Veronica; Bronkhorst, Curt Allan; Vander Wiel, Scott Alan

2016-05-12

The underlying mechanisms and kinetics controlling damage nucleation and growth as a function of material microstructure and loading paths are discussed. These experiments indicate that structural features such as grain boundaries, grain size distribution, grain morphology crystallographic texture are all factors that influence mechanical behavior.

A Detailed Chemical Kinetic Model for TNT

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

Pitz, W J; Westbrook, C K

2005-01-13

A detailed chemical kinetic mechanism for 2,4,6-tri-nitrotoluene (TNT) has been developed to explore problems of explosive performance and soot formation during the destruction of munitions. The TNT mechanism treats only gas-phase reactions. Reactions for the decomposition of TNT and for the consumption of intermediate products formed from TNT are assembled based on information from the literature and on current understanding of aromatic chemistry. Thermodynamic properties of intermediate and radical species are estimated by group additivity. Reaction paths are developed based on similar paths for aromatic hydrocarbons. Reaction-rate constant expressions are estimated from the literature and from analogous reactions where themore » rate constants are available. The detailed reaction mechanism for TNT is added to existing reaction mechanisms for RDX and for hydrocarbons. Computed results show the effect of oxygen concentration on the amount of soot precursors that are formed in the combustion of RDX and TNT mixtures in N{sub 2}/O{sub 2} mixtures.« less

Kinetic Energy of Tornadoes in the United States

PubMed Central

Fricker, Tyler; Elsner, James B.

2015-01-01

Tornadoes can cause catastrophic destruction. Here total kinetic energy (TKE) as a metric of destruction is computed from the fraction of the tornado path experiencing various damage levels and a characteristic wind speed for each level. The fraction of the path is obtained from a model developed for the Nuclear Regulatory Commission that combines theory with empirical data. TKE is validated as a useful metric by comparing it to other indexes and loss indicators. Half of all tornadoes have TKE exceeding 62.1 GJ and a quarter have TKE exceeding 383.2 GJ. One percent of the tornadoes have TKE exceeding 31.9 TJ. April has more energy than May with fewer tornadoes; March has more energy than June with half as many tornadoes. September has the least energy but November and December have the fewest tornadoes. Alabama ranks number one in terms of tornado energy with 2.48 PJ over the period 2007–2013. TKE can be used to help better understand the changing nature of tornado activity. PMID:26132830

Kinetic Energy of Tornadoes in the United States.

PubMed

Fricker, Tyler; Elsner, James B

2015-01-01

Tornadoes can cause catastrophic destruction. Here total kinetic energy (TKE) as a metric of destruction is computed from the fraction of the tornado path experiencing various damage levels and a characteristic wind speed for each level. The fraction of the path is obtained from a model developed for the Nuclear Regulatory Commission that combines theory with empirical data. TKE is validated as a useful metric by comparing it to other indexes and loss indicators. Half of all tornadoes have TKE exceeding 62.1 GJ and a quarter have TKE exceeding 383.2 GJ. One percent of the tornadoes have TKE exceeding 31.9 TJ. April has more energy than May with fewer tornadoes; March has more energy than June with half as many tornadoes. September has the least energy but November and December have the fewest tornadoes. Alabama ranks number one in terms of tornado energy with 2.48 PJ over the period 2007-2013. TKE can be used to help better understand the changing nature of tornado activity.

Kinetic simulations of gas breakdown in the dense plasma focus

DOE PAGES

Bennett, N.; Blasco, M.; Breeding, K.; ...

2017-06-09

We describe the first fully-kinetic, collisional, and electromagnetic simulations of the breakdown phase of a MA-scale dense plasma focus and are shown to agree with measured electrical characteristics, including breakdown time. In the model, avalanche ionization is driven by cathode electron emission and this results in incomplete gas breakdown along the insulator. This reinforces the importance of the conditioning process that creates a metallic layer on the insulator surface. The simulations, nonetheless, help explain the relationship between the gas pressure, the insulator length, and the coaxial gap width. In the past, researchers noted three breakdown patterns related to pressure. Simulationmore » and analytic results show that at low pressures, long ionization path lengths lead to volumetric breakdown, while high pressures lead to breakdown across the relatively small coaxial electrode gap. In an intermediate pressure regime, ionization path lengths are comparable to the insulator length which promotes ideal breakdown along the insulator surface.« less

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

2D Implosion Simulations with a Kinetic Particle Code

NASA Astrophysics Data System (ADS)

Sagert, Irina; Even, Wesley; Strother, Terrance

2017-10-01

Many problems in laboratory and plasma physics are subject to flows that move between the continuum and the kinetic regime. We discuss two-dimensional (2D) implosion simulations that were performed using a Monte Carlo kinetic particle code. The application of kinetic transport theory is motivated, in part, by the occurrence of non-equilibrium effects in inertial confinement fusion (ICF) capsule implosions, which cannot be fully captured by hydrodynamics simulations. Kinetic methods, on the other hand, are able to describe both, continuum and rarefied flows. We perform simple 2D disk implosion simulations using one particle species and compare the results to simulations with the hydrodynamics code RAGE. The impact of the particle mean-free-path on the implosion is also explored. In a second study, we focus on the formation of fluid instabilities from induced perturbations. I.S. acknowledges support through the Director's fellowship from Los Alamos National Laboratory. This research used resources provided by the LANL Institutional Computing Program.

Kinetic analysis of spin current contribution to spectrum of electromagnetic waves in spin-1/2 plasma. I. Dielectric permeability tensor for magnetized plasmas

NASA Astrophysics Data System (ADS)

Andreev, Pavel A.

2017-02-01

The dielectric permeability tensor for spin polarized plasmas is derived in terms of the spin-1/2 quantum kinetic model in six-dimensional phase space. Expressions for the distribution function and spin distribution function are derived in linear approximations on the path of dielectric permeability tensor derivation. The dielectric permeability tensor is derived for the spin-polarized degenerate electron gas. It is also discussed at the finite temperature regime, where the equilibrium distribution function is presented by the spin-polarized Fermi-Dirac distribution. Consideration of the spin-polarized equilibrium states opens possibilities for the kinetic modeling of the thermal spin current contribution in the plasma dynamics.

Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide.

PubMed

Li, Wenjin

2018-02-28

Transition path ensemble consists of reactive trajectories and possesses all the information necessary for the understanding of the mechanism and dynamics of important condensed phase processes. However, quantitative description of the properties of the transition path ensemble is far from being established. Here, with numerical calculations on a model system, the equipartition terms defined in thermal equilibrium were for the first time estimated in the transition path ensemble. It was not surprising to observe that the energy was not equally distributed among all the coordinates. However, the energies distributed on a pair of conjugated coordinates remained equal. Higher energies were observed to be distributed on several coordinates, which are highly coupled to the reaction coordinate, while the rest were almost equally distributed. In addition, the ensemble-averaged energy on each coordinate as a function of time was also quantified. These quantitative analyses on energy distributions provided new insights into the transition path ensemble.

Identifying decohering paths in closed quantum systems

NASA Technical Reports Server (NTRS)

Albrecht, Andreas

1990-01-01

A specific proposal is discussed for how to identify decohering paths in a wavefunction of the universe. The emphasis is on determining the correlations among subsystems and then considering how these correlations evolve. The proposal is similar to earlier ideas of Schroedinger and of Zeh, but in other ways it is closer to the decoherence functional of Griffiths, Omnes, and Gell-Mann and Hartle. There are interesting differences with each of these which are discussed. Once a given coarse-graining is chosen, the candidate paths are fixed in this scheme, and a single well defined number measures the degree of decoherence for each path. The normal probability sum rules are exactly obeyed (instantaneously) by these paths regardless of the level of decoherence. Also briefly discussed is how one might quantify some other aspects of classicality. The important role that concrete calculations play in testing this and other proposals is stressed.

Evaluating the risk of industrial espionage

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

Bott, T.F.

1998-12-31

A methodology for estimating the relative probabilities of different compromise paths for protected information by insider and visitor intelligence collectors has been developed based on an event-tree analysis of the intelligence collection operation. The analyst identifies target information and ultimate users who might attempt to gain that information. The analyst then uses an event tree to develop a set of compromise paths. Probability models are developed for each of the compromise paths that user parameters based on expert judgment or historical data on security violations. The resulting probability estimates indicate the relative likelihood of different compromise paths and provide anmore » input for security resource allocation. Application of the methodology is demonstrated using a national security example. A set of compromise paths and probability models specifically addressing this example espionage problem are developed. The probability models for hard-copy information compromise paths are quantified as an illustration of the results using parametric values representative of historical data available in secure facilities, supplemented where necessary by expert judgment.« less

Kinetic analyses of vasculogenesis inform mechanistic studies

PubMed Central

Winfree, Seth; Chu, Chenghao; Tu, Wanzhu; Blue, Emily K.; Gohn, Cassandra R.; Dunn, Kenneth W.

2017-01-01

Vasculogenesis is a complex process by which endothelial stem and progenitor cells undergo de novo vessel formation. Quantitative assessment of vasculogenesis is a central readout of endothelial progenitor cell functionality. However, current assays lack kinetic measurements. To address this issue, new approaches were developed to quantitatively assess in vitro endothelial colony-forming cell (ECFC) network formation in real time. Eight parameters of network structure were quantified using novel Kinetic Analysis of Vasculogenesis (KAV) software. KAV assessment of structure complexity identified two phases of network formation. This observation guided the development of additional vasculogenic readouts. A tissue cytometry approach was established to quantify the frequency and localization of dividing ECFCs. Additionally, Fiji TrackMate was used to quantify ECFC displacement and speed at the single-cell level during network formation. These novel approaches were then implemented to identify how intrauterine exposure to maternal diabetes mellitus (DM) impairs fetal ECFC vasculogenesis. Fetal ECFCs exposed to maternal DM form fewer initial network structures, which are not stable over time. Correlation analyses demonstrated that ECFC samples with greater division in branches form fewer closed network structures. Additionally, reductions in average ECFC movement over time decrease structural connectivity. Identification of these novel phenotypes utilizing the newly established methodologies provides evidence for the cellular mechanisms contributing to aberrant ECFC vasculogenesis. PMID:28100488

The Oxidation of AlN in Dry and Wet Oxygen

NASA Technical Reports Server (NTRS)

Opila, Elizabeth; Humphrey, Donald; Jacobson, Nathan; Yoshio, Tetsuo; Oda, Kohei

1998-01-01

The oxidation kinetics of AlN containing 3.5 wt% Y2O3 were studied by thermogravimetric analysis in dry oxygen and 10% H2O/balance oxygen at temperatures between 1000 and 1200 C for times between 48 and 100 h. The oxidation kinetics for AlN in dry oxygen were parabolic and of approximately the same magnitude and temperature dependence as other alumina forming materials. In this case, diffusion of oxygen and/or aluminum through the alumina scale is the rate limiting mechanism. The oxidation kinetics for AlN in wet oxygen were nearly linear and much more rapid than rates observed in dry oxygen. Numerous micropores were observed in the alumina formed on AIN in wet oxygen. These pores provide a fast path for oxygen transport. The linear kinetics observed in this case suggest that the interface reaction rate of AlN with wet oxygen is the oxidation rate limiting step.

Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies

PubMed Central

Wang, Zhen; Antoniou, Dimitri; Schwartz, Steven D.; Schramm, Vern L.

2016-01-01

Escherichia coli dihydrofolate reductase (ecDHFR) is used to study fundamental principles of enzyme catalysis. It remains controversial whether fast protein motions are coupled to the hydride transfer catalyzed by ecDHFR. Previous studies with heavy ecDHFR proteins labeled with 13C, 15N, and nonexchangeable 2H reported enzyme mass-dependent hydride transfer kinetics for ecDHFR. Here, we report refined experimental and computational studies to establish that hydride transfer is independent of protein mass. Instead, we found the rate constant for substrate dissociation to be faster for heavy DHFR. Previously reported kinetic differences between light and heavy DHFRs likely arise from kinetic steps other than the chemical step. This study confirms that fast (femtosecond to picosecond) protein motions in ecDHFR are not coupled to hydride transfer and provides an integrative computational and experimental approach to resolve fast dynamics coupled to chemical steps in enzyme catalysis. PMID:26652185

Kinetic Study of the Heck Reaction: An Interdisciplinary Experiment

ERIC Educational Resources Information Center

Gozzi, Christel; Bouzidi, Naoual

2008-01-01

The aim of this experiment is to study and calculate the kinetic constant of a Heck reaction: the arylation of but-3-en-2-ol by iodobenzene catalyzed by palladium acetate in presence of triethylamine in DMF. The reaction leads to a mixture of two ketones. Students use GC analysis to quantify reagents and products of reaction. They control the…

Validated Predictions of Metabolic Energy Consumption for Submaximal Effort Movement

PubMed Central

Tsianos, George A.; MacFadden, Lisa N.

2016-01-01

Physical performance emerges from complex interactions among many physiological systems that are largely driven by the metabolic energy demanded. Quantifying metabolic demand is an essential step for revealing the many mechanisms of physical performance decrement, but accurate predictive models do not exist. The goal of this study was to investigate if a recently developed model of muscle energetics and force could be extended to reproduce the kinematics, kinetics, and metabolic demand of submaximal effort movement. Upright dynamic knee extension against various levels of ergometer load was simulated. Task energetics were estimated by combining the model of muscle contraction with validated models of lower limb musculotendon paths and segment dynamics. A genetic algorithm was used to compute the muscle excitations that reproduced the movement with the lowest energetic cost, which was determined to be an appropriate criterion for this task. Model predictions of oxygen uptake rate (VO2) were well within experimental variability for the range over which the model parameters were confidently known. The model's accurate estimates of metabolic demand make it useful for assessing the likelihood and severity of physical performance decrement for a given task as well as investigating underlying physiologic mechanisms. PMID:27248429

Two betweenness centrality measures based on Randomized Shortest Paths

PubMed Central

Kivimäki, Ilkka; Lebichot, Bertrand; Saramäki, Jari; Saerens, Marco

2016-01-01

This paper introduces two new closely related betweenness centrality measures based on the Randomized Shortest Paths (RSP) framework, which fill a gap between traditional network centrality measures based on shortest paths and more recent methods considering random walks or current flows. The framework defines Boltzmann probability distributions over paths of the network which focus on the shortest paths, but also take into account longer paths depending on an inverse temperature parameter. RSP’s have previously proven to be useful in defining distance measures on networks. In this work we study their utility in quantifying the importance of the nodes of a network. The proposed RSP betweenness centralities combine, in an optimal way, the ideas of using the shortest and purely random paths for analysing the roles of network nodes, avoiding issues involving these two paradigms. We present the derivations of these measures and how they can be computed in an efficient way. In addition, we show with real world examples the potential of the RSP betweenness centralities in identifying interesting nodes of a network that more traditional methods might fail to notice. PMID:26838176

Planning maximally smooth hand movements constrained to nonplanar workspaces.

PubMed

Liebermann, Dario G; Krasovsky, Tal; Berman, Sigal

2008-11-01

The article characterizes hand paths and speed profiles for movements performed in a nonplanar, 2-dimensional workspace (a hemisphere of constant curvature). The authors assessed endpoint kinematics (i.e., paths and speeds) under the minimum-jerk model assumptions and calculated minimal amplitude paths (geodesics) and the corresponding speed profiles. The authors also calculated hand speeds using the 2/3 power law. They then compared modeled results with the empirical observations. In all, 10 participants moved their hands forward and backward from a common starting position toward 3 targets located within a hemispheric workspace of small or large curvature. Comparisons of modeled observed differences using 2-way RM-ANOVAs showed that movement direction had no clear influence on hand kinetics (p < .05). Workspace curvature affected the hand paths, which seldom followed geodesic lines. Constraining the paths to different curvatures did not affect the hand speed profiles. Minimum-jerk speed profiles closely matched the observations and were superior to those predicted by 2/3 power law (p < .001). The authors conclude that speed and path cannot be unambiguously linked under the minimum-jerk assumption when individuals move the hand in a nonplanar 2-dimensional workspace. In such a case, the hands do not follow geodesic paths, but they preserve the speed profile, regardless of the geometric features of the workspace.

Transformation Paths from Cubic to Low-Symmetry Structures in Heusler Ni2MnGa Compound.

PubMed

Zelený, Martin; Straka, Ladislav; Sozinov, Alexei; Heczko, Oleg

2018-05-08

In order to explain the formation of low-temperature phases in stoichiometric Ni 2 MnGa magnetic shape memory alloy, we investigate the phase transformation paths from cubic austenite with Heusler structure to low-symmetry martensitic structures. We used ab initio calculations combined with the generalized solid state nudged elastic band method to determine the minimum energy path and corresponding changes in crystal lattice. The four-, five-, and seven-layered modulated phases of martensite (4O, 10M, and 14M) are built as the relaxed nanotwinned non-modulated (NM) phase. Despite having a total energy larger than the other martensitic phases, the 10M phase will spontaneously form at 0 K, because there is no energy barrier on the path and the energy decreases with a large negative slope. Moreover, a similar negative slope in the beginning of path is found also for the transformation to the 6M premartensite, which appears as a local minimum on the path leading further to 10M martensite. Transformation paths to other structures exhibit more or less significant barriers in the beginning hindering such a transformation from austenite. These findings correspond to experiment and demonstrates that the kinetics of the transformation is decisive for the selection of the particular low-symmetry structure.

Quantitative characterization of mesenchymal stem cell adhesion to the articular cartilage surface.

PubMed

Hung, Ben P; Babalola, Omotunde M; Bonassar, Lawrence J

2013-12-01

There has been great interest in use of mesenchymal stem cell (MSC)-based therapies for cartilage repair. Most recently, treatments involving intra-articular injection of MSCs have shown great promise for cartilage repair and arthritis therapy, which rely on MSC adhesion to cartilage. While there is some information on chondrocyte adhesion to cartilage, there is relatively little known about the kinetics and strength of MSC adhesion to cartilage. The goals of this study were as follows: (1) to quantify the kinetics and strength of adhesion of marrow-derived MSCs to articular cartilage using standard laboratory hardware; (2) to compare this adhesion behavior to that of articular chondrocytes; and (3) to assess the effect of serial monolayer culture on MSC adhesion. First through fourth passage MSCs and primary articular chondrocytes were allowed to adhere to the articular surface of cartilage disks for up to 30 h and the number of adhered cells was recorded to quantify adhesion kinetics. After 30 h, adherent cells were subjected to centrifugal shear to determine adhesion strength, quantified as the shear necessary to detach half the adhered cells (σ50 ). The number of adhered MSCs and adhesion strength increased with passage number and MSCs adhered more strongly than did primary articular chondrocytes. As such, the kinetics and strength of MSC adhesion to cartilage is not dramatically lower than that for articular chondrocytes. This protocol for assessing cell adhesion to cartilage is simple to implement and may represent an important screening tool for assessing the efficacy of cell-based therapies for cartilage repair. Copyright © 2013 Wiley Periodicals, Inc., a Wiley Company.

A Closed Parameterization of DNA–Damage by Charged Particles, as a Function of Energy — A Geometrical Approach

PubMed Central

Van den Heuvel, Frank

2014-01-01

Purpose To present a closed formalism calculating charged particle radiation damage induced in DNA. The formalism is valid for all types of charged particles and due to its closed nature is suited to provide fast conversion of dose to DNA-damage. Methods The induction of double strand breaks in DNA–strings residing in irradiated cells is quantified using a single particle model. This leads to a proposal to use the cumulative Cauchy distribution to express the mix of high and low LET type damage probability generated by a single particle. A microscopic phenomenological Monte Carlo code is used to fit the parameters of the model as a function of kinetic energy related to the damage to a DNA molecule embedded in a cell. The model is applied for four particles: electrons, protons, alpha–particles, and carbon ions. A geometric interpretation of this observation using the impact ionization mean free path as a quantifier, allows extension of the model to very low energies. Results The mathematical expression describes the model adequately using a chi–square test (). This applies to all particle types with an almost perfect fit for protons, while the other particles seem to result in some discrepancies at very low energies. The implementation calculating a strict version of the RBE based on complex damage alone is corroborated by experimental data from the measured RBE. The geometric interpretation generates a unique dimensionless parameter for each type of charged particle. In addition, it predicts a distribution of DNA damage which is different from the current models. PMID:25340636

Diagnosability of Stochastic Chemical Kinetic Systems: A Discrete Event Systems Approach (PREPRINT)

DTIC Science & Technology

2010-01-01

USA. E -mail: thorsley@u.washington.edu. This research is partially supported by the 2006 AFOSR MURI award “High Confidence Design for Distributed...occurrence of the finite sample path ω. These distributions are defined recursively to be π0(x) := π0(x), πωσ(x ′) := ∑ x∈X πω(x)r(x ′,σ | x) e −r(x ′,σ|x... e −rxτ . (2) This probability is this probability that the arrival time of the first event is greater than τ . For finite sample paths with strings

Quantitative Detection of Nucleoside Analogues by Multi-enzyme Biosensors using Time-Resolved Kinetic Measurements.

PubMed

Muthu, Pravin; Lutz, Stefan

2016-04-05

Fast, simple and cost-effective methods for detecting and quantifying pharmaceutical agents in patients are highly sought after to replace equipment and labor-intensive analytical procedures. The development of new diagnostic technology including portable detection devices also enables point-of-care by non-specialists in resource-limited environments. We have focused on the detection and dose monitoring of nucleoside analogues used in viral and cancer therapies. Using deoxyribonucleoside kinases (dNKs) as biosensors, our chemometric model compares observed time-resolved kinetics of unknown analytes to known substrate interactions across multiple enzymes. The resulting dataset can simultaneously identify and quantify multiple nucleosides and nucleoside analogues in complex sample mixtures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic balance deficits in individuals with chronic ankle instability compared to ankle sprain copers 1 year after a first-time lateral ankle sprain injury.

PubMed

Doherty, Cailbhe; Bleakley, Chris; Hertel, Jay; Caulfield, Brian; Ryan, John; Delahunt, Eamonn

2016-04-01

To quantify the dynamic balance deficits that characterise a group with chronic ankle instability compared to lateral ankle sprain copers and non-injured controls using kinematic and kinetic outcomes. Forty-two participants with chronic ankle instability and twenty-eight lateral ankle sprain copers were initially recruited within 2 weeks of sustaining a first-time, acute lateral ankle sprain and required to attend our laboratory 1 year later to complete the current study protocol. An additional group of non-injured individuals were also recruited to act as a control group. All participants completed the anterior, posterior-lateral and posterior-medial reach directions of the star excursion balance test. Sagittal plane kinematics of the lower extremity and associated fractal dimension of the centre of pressure path were also acquired. Participants with chronic ankle instability displayed poorer performance in the anterior, posterior-medial and posterior-lateral reach directions compared with controls bilaterally, and in the posterior-lateral direction compared with lateral ankle sprain copers on their 'involved' limb only. These performance deficits in the posterior-lateral and posterior-medial directions were associated with reduced flexion and dorsiflexion displacements at the hip, knee and ankle at the point of maximum reach, and coincided with reduced complexity of the centre of pressure path. In comparison with lateral ankle sprain copers and controls, participants with chronic ankle instability were characterised by dynamic balance deficits as measured using the SEBT. This was attested to reduced sagittal plane motions at the hip, knee and ankle joints, and reduced capacity of the stance limb to avail of its supporting base. III.

Oxygen self-diffusion mechanisms in monoclinic Zr O2 revealed and quantified by density functional theory, random walk analysis, and kinetic Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Yang, Jing; Youssef, Mostafa; Yildiz, Bilge

2018-01-01

In this work, we quantify oxygen self-diffusion in monoclinic-phase zirconium oxide as a function of temperature and oxygen partial pressure. A migration barrier of each type of oxygen defect was obtained by first-principles calculations. Random walk theory was used to quantify the diffusivities of oxygen interstitials by using the calculated migration barriers. Kinetic Monte Carlo simulations were used to calculate diffusivities of oxygen vacancies by distinguishing the threefold- and fourfold-coordinated lattice oxygen. By combining the equilibrium defect concentrations obtained in our previous work together with the herein calculated diffusivity of each defect species, we present the resulting oxygen self-diffusion coefficients and the corresponding atomistically resolved transport mechanisms. The predicted effective migration barriers and diffusion prefactors are in reasonable agreement with the experimentally reported values. This work provides insights into oxygen diffusion engineering in Zr O2 -related devices and parametrization for continuum transport modeling.

Energy transfer, pressure tensor, and heating of kinetic plasma

NASA Astrophysics Data System (ADS)

Yang, Yan; Matthaeus, William H.; Parashar, Tulasi N.; Haggerty, Colby C.; Roytershteyn, Vadim; Daughton, William; Wan, Minping; Shi, Yipeng; Chen, Shiyi

2017-07-01

Kinetic plasma turbulence cascade spans multiple scales ranging from macroscopic fluid flow to sub-electron scales. Mechanisms that dissipate large scale energy, terminate the inertial range cascade, and convert kinetic energy into heat are hotly debated. Here, we revisit these puzzles using fully kinetic simulation. By performing scale-dependent spatial filtering on the Vlasov equation, we extract information at prescribed scales and introduce several energy transfer functions. This approach allows highly inhomogeneous energy cascade to be quantified as it proceeds down to kinetic scales. The pressure work, - ( P . ∇ ) . u , can trigger a channel of the energy conversion between fluid flow and random motions, which contains a collision-free generalization of the viscous dissipation in collisional fluid. Both the energy transfer and the pressure work are strongly correlated with velocity gradients.

Application of path-integral quantization to indistinguishable particle systems topologically confined by a magnetic field

NASA Astrophysics Data System (ADS)

Jacak, Janusz E.

2018-01-01

We demonstrate an original development of path-integral quantization in the case of a multiply connected configuration space of indistinguishable charged particles on a 2D manifold and exposed to a strong perpendicular magnetic field. The system occurs to be exceptionally homotopy-rich and the structure of the homotopy essentially depends on the magnetic field strength resulting in multiloop trajectories at specific conditions. We have proved, by a generalization of the Bohr-Sommerfeld quantization rule, that the size of a magnetic field flux quantum grows for multiloop orbits like (2 k +1 ) h/c with the number of loops k . Utilizing this property for electrons on the 2D substrate jellium, we have derived upon the path integration a complete FQHE hierarchy in excellent consistence with experiments. The path integral has been next developed to a sum over configurations, displaying various patterns of trajectory homotopies (topological configurations), which in the nonstationary case of quantum kinetics, reproduces some unclear formerly details in the longitudinal resistivity observed in experiments.

Two Meter Flight Path - Time of Flight Positron Annihilation Induced Auger Electron Spectrometer

NASA Astrophysics Data System (ADS)

Mukherjee, S.; Shastry, K.; Maddox, W.; Weiss, A. H.

2008-03-01

Details of the design and construction of a new time of flight positron annihilation induced Auger electron (TOF-PAES) spectrometer are presented. The new spectrometer will be equipped with a 2 meter long ``TOF'' tube that can be biased at a potential different from that of the sample in order to increase or decrease the kinetic energy of the electrons traveling through the tube. The time of flight will be determined from timing signals obtained from the detection of the annihilation gamma (signaling the start of the flight) and detection of the annihilation induced Auger electron at the end of the 2 meter flight path (signaling the end of the flight). The 2 meter long flight path is a factor of two longer than used in previous TOF-PAES systems. The longer flight path can be expected to result in a fractional energy width: delta E/ E that is .5ex1 -.1em/ -.15em.25ex2 as large as the current UTA lab based TOF-PAES spectrometer.

Austenite grain growth kinetics in Al-killed plain carbon steels

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

Militzer, M.; Giumelli, A.; Hawbolt, E.B.

1996-11-01

Austenite grain growth kinetics have been investigated in three Al-killed plain carbon steels. Experimental results have been validated using the statistical grain growth model by Abbruzzese and Luecke, which takes pinning by second-phase particles into account. It is shown that the pinning force is a function of the pre-heat-treatment schedule. Extrapolation to the conditions of a hot-strip mill indicates that grain growth occurs without pinning during conventional processing. Analytical relations are proposed to simulate austenite grain growth for Al-killed plain carbon steels for any thermal path in a hot-strip mill.

Sodium dopants in helium clusters: Structure, equilibrium and submersion kinetics

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

Calvo, F.

Alkali impurities bind to helium nanodroplets very differently depending on their size and charge state, large neutral or charged dopants being wetted by the droplet whereas small neutral impurities prefer to reside aside. Using various computational modeling tools such as quantum Monte Carlo and path-integral molecular dynamics simulations, we have revisited some aspects of the physical chemistry of helium droplets interacting with sodium impurities, including the onset of snowball formation in presence of many-body polarization forces, the transition from non-wetted to wetted behavior in larger sodium clusters, and the kinetics of submersion of small dopants after sudden ionization.

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.

Path Integral Simulation of the H/D Kinetic Isotope Effect in Monoamine Oxidase B Catalyzed Decomposition of Dopamine.

PubMed

Mavri, Janez; Matute, Ricardo A; Chu, Zhen T; Vianello, Robert

2016-04-14

Brain monoamines regulate many centrally mediated body functions, and can cause adverse symptoms when they are out of balance. A starting point to address challenges raised by the increasing burden of brain diseases is to understand, at atomistic level, the catalytic mechanism of an essential amine metabolic enzyme-monoamine oxidase B (MAO B). Recently, we demonstrated that the rate-limiting step of MAO B catalyzed conversion of amines into imines represents the hydride anion transfer from the substrate α-CH2 group to the N5 atom of the flavin cofactor moiety. In this article we simulated for MAO B catalyzed dopamine decomposition the effects of nuclear tunneling by the calculation of the H/D kinetic isotope effect. We applied path integral quantization of the nuclear motion for the methylene group and the N5 atom of the flavin moiety in conjunction with the QM/MM treatment on the empirical valence bond (EVB) level for the rest of the enzyme. The calculated H/D kinetic isotope effect of 12.8 ± 0.3 is in a reasonable agreement with the available experimental data for closely related biogenic amines, which gives strong support for the proposed hydride mechanism. The results are discussed in the context of tunneling in enzyme centers and advent of deuterated drugs into clinical practice.

Dry (CO2) reforming of methane over Pt catalysts studied by DFT and kinetic modeling

NASA Astrophysics Data System (ADS)

Niu, Juntian; Du, Xuesen; Ran, Jingyu; Wang, Ruirui

2016-07-01

Dry reforming of methane (DRM) is a well-studied reaction that is of both scientific and industrial importance. In order to design catalysts that minimize the deactivation and improve the selectivity and activity for a high H2/CO yield, it is necessary to understand the elementary reaction steps involved in activation and conversion of CO2 and CH4. In our present work, a microkinetic model based on density functional theory (DFT) calculations is applied to explore the reaction mechanism for methane dry reforming on Pt catalysts. The adsorption energies of the reactants, intermediates and products, and the activation barriers for the elementary reactions involved in the DRM process are calculated over the Pt(1 1 1) surface. In the process of CH4 direct dissociation, the kinetic results show that CH dissociative adsorption on Pt(1 1 1) surface is the rate-determining step. CH appears to be the most abundant species on the Pt(1 1 1) surface, suggesting that carbon deposition is not easy to form in CH4 dehydrogenation on Pt(1 1 1) surface. In the process of CO2 activation, three possible reaction pathways are considered to contribute to the CO2 decomposition: (I) CO2* + * → CO* + O*; (II) CO2* + H* → COOH* + * → CO* + OH*; (III) CO2* + H* → mono-HCOO* + * → bi-HCOO* + * [CO2* + H* → bi-HCOO* + *] → CHO* + O*. Path I requires process to overcome the activation barrier of 1.809 eV and the forward reaction is calculated to be strongly endothermic by 1.430 eV. In addition, the kinetic results also indicate this process is not easy to proceed on Pt(1 1 1) surface. While the CO2 activation by H adsorbed over the catalyst surface to form COOH intermediate (Path II) is much easier to be carried out with the lower activation barrier of 0.746 eV. The Csbnd O bond scission is the rate-determining step along this pathway and the process needs to overcome the activation barrier of 1.522 eV. Path III reveals the CO2 activation through H adsorbed over the catalyst surface to form HCOO intermediate firstly. This reaction requires a quite high activation barrier and is a strongly endothermic process leading to a very low forward rate constant. In conclusion, Path II is the dominant reaction pathway in CO2 activation. Additionally, there are two pathways of CH oxidation by O: (A) CH* + O* → CHO* + * → CO* + H*; (B) CH* + O* → COH* + * → CO* + H*. Both the activation barriers and kinetic results demonstrate that Path A is the prior reaction pathway. Furthermore, in the two pathways of CH oxidation by OH: (C) CH* + OH* → CHOH* + * → CHO* + H*; (D) CH* + OH* → CHOH* + * → COH* + H*. Path C is easier to proceed. In conclusion, the main reaction pathway in CH oxidation according to the mechanism: CH* + OH* → CHOH* + * → CHO* + H* → CO* + 2H*. These results could provide some useful information for the operation of DRM over Pt catalysts, and are helpful to understand the mechanisms of DRM from the atomic scale.

Cellular Gauge Symmetry and the Li Organization Principle: A Mathematical Addendum. Quantifying energetic dynamics in physical and biological systems through a simple geometric tool and geodetic curves.

PubMed

Yurkin, Alexander; Tozzi, Arturo; Peters, James F; Marijuán, Pedro C

2017-12-01

The present Addendum complements the accompanying paper "Cellular Gauge Symmetry and the Li Organization Principle"; it illustrates a recently-developed geometrical physical model able to assess electronic movements and energetic paths in atomic shells. The model describes a multi-level system of circular, wavy and zigzag paths which can be projected onto a horizontal tape. This model ushers in a visual interpretation of the distribution of atomic electrons' energy levels and the corresponding quantum numbers through rather simple tools, such as compasses, rulers and straightforward calculations. Here we show how this geometrical model, with the due corrections, among them the use of geodetic curves, might be able to describe and quantify the structure and the temporal development of countless physical and biological systems, from Langevin equations for random paths, to symmetry breaks occurring ubiquitously in physical and biological phenomena, to the relationships among different frequencies of EEG electric spikes. Therefore, in our work we explore the possible association of binomial distribution and geodetic curves configuring a uniform approach for the research of natural phenomena, in biology, medicine or the neurosciences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tip-path-plane angle effects on rotor blade-vortex interaction noise levels and directivity

NASA Technical Reports Server (NTRS)

Burley, Casey L.; Martin, Ruth M.

1988-01-01

Acoustic data of a scale model BO-105 main rotor acquired in a large aeroacoustic wind tunnel are presented to investigate the parametric effects of rotor operating conditions on blade-vortex interaction (BVI) impulsive noise. Contours of a BVI noise metric are employed to quantify the effects of rotor advance ratio and tip-path-plane angle on BVI noise directivity and amplitude. Acoustic time history data are presented to illustrate the variations in impulsive characteristics. The directionality, noise levels and impulsive content of both advancing and retreating side BVI are shown to vary significantly with tip-path-plane angle and advance ratio over the range of low and moderate flight speeds considered.

Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.

PubMed

Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J

2014-12-31

RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.

Geochemical Impacts to Groundwater from Geologic Carbon Sequestration: Controls on pH and Inorganic Carbon Concentrations from Reaction Path and Kinetic Modeling

EPA Science Inventory

Geologic carbon sequestration has the potential to cause long-term reductions in global emissions of carbon dioxide to the atmosphere. Safe and effective application of carbon sequestration technology requires an understanding of the potential risks to the quality of underground...

Perceiving and Reenacting Spatiotemporal Characteristics of Walking Sounds

ERIC Educational Resources Information Center

Young, William; Rodger, Matthew; Craig, Cathy M.

2013-01-01

Many studies have examined the processes involved in recognizing types of human action through sound, but little is known about whether the physical characteristics of an action (such as kinetic and kinematic parameters) can be perceived and imitated from sound. Twelve young healthy adults listened to recordings of footsteps on a gravel path taken…

Kinetic Monte Carlo Simulation of Oxygen Diffusion in Ytterbium Disilicate

NASA Technical Reports Server (NTRS)

Good, Brian S.

2015-01-01

Ytterbium disilicate is of interest as a potential environmental barrier coating for aerospace applications, notably for use in next generation jet turbine engines. In such applications, the transport of oxygen and water vapor through these coatings to the ceramic substrate is undesirable if high temperature oxidation is to be avoided. In an effort to understand the diffusion process in these materials, we have performed kinetic Monte Carlo simulations of vacancy-mediated and interstitial oxygen diffusion in Ytterbium disilicate. Oxygen vacancy and interstitial site energies, vacancy and interstitial formation energies, and migration barrier energies were computed using Density Functional Theory. We have found that, in the case of vacancy-mediated diffusion, many potential diffusion paths involve large barrier energies, but some paths have barrier energies smaller than one electron volt. However, computed vacancy formation energies suggest that the intrinsic vacancy concentration is small. In the case of interstitial diffusion, migration barrier energies are typically around one electron volt, but the interstitial defect formation energies are positive, with the result that the disilicate is unlikely to exhibit experience significant oxygen permeability except at very high temperature.

Oxidation kinetics for conversion of U 3O 8 to ε-UO 3 with NO 2

DOE PAGES

Johnson, J. A.; Rawn, C. J.; Spencer, B. B.; ...

2017-04-04

The oxidation kinetics of U 3O 8 powder to ε-UO 3 in an NO 2 environment was measured by in situ x-ray diffraction (XRD). Experiments were performed at temperatures of 195, 210, 235, and 250°C using a custom designed and fabricated sample isolation stage. Data were refined to quantify phase fractions using a newly proposed structure for the ε-UO 3 polymorph. The kinetics data were modeled using a shrinking core approach. A proposed two-step reaction process is presented based on the developed models.

The Use Of Videography For Three-Dimensional Motion Analysis

NASA Astrophysics Data System (ADS)

Hawkins, D. A.; Hawthorne, D. L.; DeLozier, G. S.; Campbell, K. R.; Grabiner, M. D.

1988-02-01

Special video path editing capabilities with custom hardware and software, have been developed for use in conjunction with existing video acquisition hardware and firmware. This system has simplified the task of quantifying the kinematics of human movement. A set of retro-reflective markers are secured to a subject performing a given task (i.e. walking, throwing, swinging a golf club, etc.). Multiple cameras, a video processor, and a computer work station collect video data while the task is performed. Software has been developed to edit video files, create centroid data, and identify marker paths. Multi-camera path files are combined to form a 3D path file using the DLT method of cinematography. A separate program converts the 3D path file into kinematic data by creating a set of local coordinate axes and performing a series of coordinate transformations from one local system to the next. The kinematic data is then displayed for appropriate review and/or comparison.

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.

Effect of reflected and refracted signals on coherent underwater acoustic communication: results from the Kauai experiment (KauaiEx 2003).

PubMed

Rouseff, Daniel; Badiey, Mohsen; Song, Aijun

2009-11-01

The performance of a communications equalizer is quantified in terms of the number of acoustic paths that are treated as usable signal. The analysis uses acoustical and oceanographic data collected off the Hawaiian Island of Kauai. Communication signals were measured on an eight-element vertical array at two different ranges, 1 and 2 km, and processed using an equalizer based on passive time-reversal signal processing. By estimating the Rayleigh parameter, it is shown that all paths reflected by the sea surface at both ranges undergo incoherent scattering. It is demonstrated that some of these incoherently scattered paths are still useful for coherent communications. At range of 1 km, optimal communications performance is achieved when six acoustic paths are retained and all paths with more than one reflection off the sea surface are rejected. Consistent with a model that ignores loss from near-surface bubbles, the performance improves by approximately 1.8 dB when increasing the number of retained paths from four to six. The four-path results though are more stable and require less frequent channel estimation. At range of 2 km, ray refraction is observed and communications performance is optimal when some paths with two sea-surface reflections are retained.

Kinetic modeling of the photocatalytic degradation of clofibric acid in a slurry reactor.

PubMed

Manassero, Agustina; Satuf, María Lucila; Alfano, Orlando Mario

2015-01-01

A kinetic study of the photocatalytic degradation of the pharmaceutical clofibric acid is presented. Experiments were carried out under UV radiation employing titanium dioxide in water suspension. The main reaction intermediates were identified and quantified. Intrinsic expressions to represent the kinetics of clofibric acid and the main intermediates were derived. The modeling of the radiation field in the reactor was carried out by Monte Carlo simulation. Experimental runs were performed by varying the catalyst concentration and the incident radiation. Kinetic parameters were estimated from the experiments by applying a non-linear regression procedure. Good agreement was obtained between model predictions and experimental data, with an error of 5.9 % in the estimations of the primary pollutant concentration.

Graph-based analysis of kinetics on multidimensional potential-energy surfaces.

PubMed

Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y

2009-09-01

The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.

Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link Between Experiments.

PubMed

Cheng, Bingqing; Behler, Jörg; Ceriotti, Michele

2016-06-16

One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell-Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water.

Achieving 3-D Nanoparticle Assembly in Nanocomposite Thin Films via Kinetic Control

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

Huang, Jingyu; Xiao, Yihan; Xu, Ting

Nanocomposite thin films containing well-ordered nanoparticle (NP) assemblies are ideal candidates for the fabrication of metamaterials. Achieving 3-D assembly of NPs in nanocomposite thin films is thermodynamically challenging as the particle size gets similar to that of a single polymer chain. The entropic penalties of polymeric matrix upon NP incorporation leads to NP aggregation on the film surface or within the defects in the film. Controlling the kinetic pathways of assembly process provides an alternative path forward by arresting the system in nonequilibrium states. Here, we report the thin film 3-D hierarchical assembly of 20 nm NPs in supramolecules withmore » a 30 nm periodicity. By mediating the NP diffusion kinetics in the supramolecular matrix, surface aggregation of NPs was suppressed and NPs coassemble with supramolecules to form new 3-D morphologies in thin films. Lastly, the present studies opened a viable route to achieve designer functional composite thin films via kinetic control.« less

Achieving 3-D Nanoparticle Assembly in Nanocomposite Thin Films via Kinetic Control

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

Huang, Jingyu; Xiao, Yihan; Xu, Ting

Nanocomposite thin films containing well-ordered nanoparticle (NP) assemblies are ideal candidates for the fabrication of metamaterials. Achieving 3-D assembly of NPs in nanocomposite thin films is thermodynamically challenging as the particle size gets similar to that of a single polymer chain. The entropic penalties of polymeric matrix upon NP incorporation leads to NP aggregation on the film surface or within the defects in the film. Controlling the kinetic pathways of assembly process provides an alternative path forward by arresting the system in nonequilibrium states. Here, we report the thin film 3-D hierarchical assembly of 20 nm NPs in supramolecules withmore » a 30 nm periodicity. By mediating the NP diffusion kinetics in the supramolecular matrix, surface aggregation of NPs was suppressed and NPs coassemble with supramolecules to form new 3-D morphologies in thin films. The present studies opened a viable route to achieve designer functional composite thin films via kinetic control.« less

Achieving 3-D Nanoparticle Assembly in Nanocomposite Thin Films via Kinetic Control

DOE PAGES

Huang, Jingyu; Xiao, Yihan; Xu, Ting

2017-02-20

Nanocomposite thin films containing well-ordered nanoparticle (NP) assemblies are ideal candidates for the fabrication of metamaterials. Achieving 3-D assembly of NPs in nanocomposite thin films is thermodynamically challenging as the particle size gets similar to that of a single polymer chain. The entropic penalties of polymeric matrix upon NP incorporation leads to NP aggregation on the film surface or within the defects in the film. Controlling the kinetic pathways of assembly process provides an alternative path forward by arresting the system in nonequilibrium states. Here, we report the thin film 3-D hierarchical assembly of 20 nm NPs in supramolecules withmore » a 30 nm periodicity. By mediating the NP diffusion kinetics in the supramolecular matrix, surface aggregation of NPs was suppressed and NPs coassemble with supramolecules to form new 3-D morphologies in thin films. Lastly, the present studies opened a viable route to achieve designer functional composite thin films via kinetic control.« less

Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied

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

Bai, Shirong; Davis, Michael J.; Skodje, Rex T.

2015-11-12

The sensitivity of kinetic observables is analyzed using a newly developed sum over histories representation of chemical kinetics. In the sum over histories representation, the concentrations of the chemical species are decomposed into the sum of probabilities for chemical pathways that follow molecules from reactants to products or intermediates. Unlike static flux methods for reaction path analysis, the sum over histories approach includes the explicit time dependence of the pathway probabilities. Using the sum over histories representation, the sensitivity of an observable with respect to a kinetic parameter such as a rate coefficient is then analyzed in terms of howmore » that parameter affects the chemical pathway probabilities. The method is illustrated for species concentration target functions in H-2 combustion where the rate coefficients are allowed to vary over their associated uncertainty ranges. It is found that large sensitivities are often associated with rate limiting steps along important chemical pathways or by reactions that control the branching of reactive flux« less

Quantifying Traversability of Terrain for a Mobile Robot

NASA Technical Reports Server (NTRS)

Howard, Ayanna; Seraji, Homayoun; Werger, Barry

2005-01-01

A document presents an updated discussion on a method of autonomous navigation for a robotic vehicle navigating across rough terrain. The method involves, among other things, the use of a measure of traversability, denoted the fuzzy traversability index, which embodies the information about the slope and roughness of terrain obtained from analysis of images acquired by cameras mounted on the robot. The improvements presented in the report focus on the use of the fuzzy traversability index to generate a traversability map and a grid map for planning the safest path for the robot. Once grid traversability values have been computed, they are utilized for rejecting unsafe path segments and for computing a traversalcost function for ranking candidate paths, selected by a search algorithm, from a specified initial position to a specified final position. The output of the algorithm is a set of waypoints designating a path having a minimal-traversal cost.

Contributions of Kinetic Energy and Viscous Dissipation to Airway Resistance in Pulmonary Inspiratory and Expiratory Airflows in Successive Symmetric Airway Models With Various Bifurcation Angles.

PubMed

Choi, Sanghun; Choi, Jiwoong; Lin, Ching-Long

2018-01-01

The aim of this study was to investigate and quantify contributions of kinetic energy and viscous dissipation to airway resistance during inspiration and expiration at various flow rates in airway models of different bifurcation angles. We employed symmetric airway models up to the 20th generation with the following five different bifurcation angles at a tracheal flow rate of 20 L/min: 15 deg, 25 deg, 35 deg, 45 deg, and 55 deg. Thus, a total of ten computational fluid dynamics (CFD) simulations for both inspiration and expiration were conducted. Furthermore, we performed additional four simulations with tracheal flow rate values of 10 and 40 L/min for a bifurcation angle of 35 deg to study the effect of flow rate on inspiration and expiration. Using an energy balance equation, we quantified contributions of the pressure drop associated with kinetic energy and viscous dissipation. Kinetic energy was found to be a key variable that explained the differences in airway resistance on inspiration and expiration. The total pressure drop and airway resistance were larger during expiration than inspiration, whereas wall shear stress and viscous dissipation were larger during inspiration than expiration. The dimensional analysis demonstrated that the coefficients of kinetic energy and viscous dissipation were strongly correlated with generation number. In addition, the viscous dissipation coefficient was significantly correlated with bifurcation angle and tracheal flow rate. We performed multiple linear regressions to determine the coefficients of kinetic energy and viscous dissipation, which could be utilized to better estimate the pressure drop in broader ranges of successive bifurcation structures.

Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT

PubMed Central

Bisha, Ina; Rodriguez, Alex; Laio, Alessandro; Magistrato, Alessandra

2014-01-01

Sodium-Galactose Transporter (SGLT) is a secondary active symporter which accumulates sugars into cells by using the electrochemical gradient of Na+ across the membrane. Previous computational studies provided insights into the release process of the two ligands (galactose and sodium ion) into the cytoplasm from the inward-facing conformation of Vibrio parahaemolyticus sodium/galactose transporter (vSGLT). Several aspects of the transport mechanism of this symporter remain to be clarified: (i) a detailed kinetic and thermodynamic characterization of the exit path of the two ligands is still lacking; (ii) contradictory conclusions have been drawn concerning the gating role of Y263; (iii) the role of Na+ in modulating the release path of galactose is not clear. In this work, we use bias-exchange metadynamics simulations to characterize the free energy profile of the galactose and Na+ release processes toward the intracellular side. Surprisingly, we find that the exit of Na+ and galactose is non-concerted as the cooperativity between the two ligands is associated to a transition that is not rate limiting. The dissociation barriers are of the order of 11–12 kcal/mol for both the ion and the substrate, in line with kinetic information concerning this type of transporters. On the basis of these results we propose a branched six-state alternating access mechanism, which may be shared also by other members of the LeuT-fold transporters. PMID:25522004

Atmospheric reaction of Cl + methacrolein: a theoretical study on the mechanism, and pressure- and temperature-dependent rate constants.

PubMed

Sun, Cuihong; Xu, Baoen; Zhang, Shaowen

2014-05-22

Methacrolein is a major degradation product of isoprene, the reaction of methacrolein with Cl atoms may play some roles in the degradation of isoprene where these species are relatively abundant. However, the energetics and kinetics of this reaction, which govern the reaction branching, are still not well understood so far. In the present study, two-dimensional potential energy surfaces were constructed to analyze the minimum energy path of the barrierless addition process between Cl and the C═C double bond of methacrolein, which reveals that the terminal addition intermediate is directly formed from the addition reaction. The terminal addition intermediate can further yield different products among which the reaction paths abstracting the aldehyde hydrogen atom and the methyl hydrogen atom are dominant reaction exits. The minimum reaction path for the direct aldehydic hydrogen atom abstraction is also obtained. The reaction kinetics was calculated by the variational transition state theory in conjunction with the master equation method. From the theoretical model we predicted that the overall rate constant of the Cl + methacrolein reaction at 297 K and atmospheric pressure is koverall = 2.3× 10(-10) cm(3) molecule(-1) s(-1), and the branching ratio of the aldehydic hydrogen abstraction is about 12%. The reaction is pressure dependent at P < 10 Torr with the high pressure limit at about 100 Torr. The calculated results could well account for the experimental observations.

Kinetics of the Decomposition of Hydrogen Peroxide Catalyzed by Ferric Ethylenediaminetetraacetate Complex

PubMed Central

Walling, Cheves; Partch, Richard E.; Weil, Tomas

1975-01-01

Added substrates, acetone and t-butyl alcohol, strongly retard the decomposition of H2O2 brought about by ferric ethylenediaminetetraacetate (EDTA) at pH 8-9.5. Their relative effectiveness and the kinetic form of the retardation are consistent with their interruption of a hydroxyl radical chain that is propagated by HO· attack both upon H2O2 and on complexed and uncomplexed EDTA. Similar retardation is observed with decompositions catalyzed by ferric nitrilotriacetate and hemin, and it is proposed that such redox chains may be quite a general path for transition metal ion catalysis of H2O2 decomposition. PMID:16592209

Ab initio simulation of particle momentum distributions in high-pressure water

NASA Astrophysics Data System (ADS)

Ceriotti, M.

2014-12-01

Applying pressure to water reduces the average oxygen-oxygen distance, and facilitates the delocalisation of protons along the hydrogen bond. This pressure-induced delocalisation is further enhanced by the quantum nature of hydrogen nuclei, which is very significant even well above room temperature. Here we will evaluate the quantum kinetic energy and the particle momentum distribution of hydrogen and oxygen nuclei in water at extreme pressure, using ab initio path integral molecular dynamics. We will show that (transient) dissociation of water molecules induce measurable changes in the kinetic energy hydrogen atoms, although current deep inelastic scattering experiments are probably unable to capture the heterogeneity of the sample.

Energy-range relations for hadrons in nuclear matter

NASA Technical Reports Server (NTRS)

Strugalski, Z.

1985-01-01

Range-energy relations for hadrons in nuclear matter exist similarly to the range-energy relations for charged particles in materials. When hadrons of GeV kinetic energies collide with atomic nuclei massive enough, events occur in which incident hadron is stopped completely inside the target nucleus without causing particle production - without pion production in particular. The stoppings are always accompanied by intensive emission of nucleons with kinetic energy from about 20 up to about 400 MeV. It was shown experimentally that the mean number of the emitted nucleons is a measure of the mean path in nuclear matter in nucleons on which the incident hadrons are stopped.

Sources, paths, and concepts for reduction of noise in the test section of the NASA Langley 4x7m wind tunnel

NASA Technical Reports Server (NTRS)

Hayden, R. E.; Wilby, J. F.

1984-01-01

NASA is investigating the feasibility of modifying the 4x7m Wind Tunnel at the Langley Research Center to make it suitable for a variety of aeroacoustic testing applications, most notably model helicopter rotors. The amount of noise reduction required to meet NASA's goal for test section background noise was determined, the predominant sources and paths causing the background noise were quantified, and trade-off studies between schemes to reduce fan noise at the source and those to attenuate the sound generated in the circuit between the sources and the test section were carried out. An extensive data base is also presented on circuit sources and paths.

Epidemic extinction paths in complex networks

NASA Astrophysics Data System (ADS)

Hindes, Jason; Schwartz, Ira B.

2017-05-01

We study the extinction of long-lived epidemics on finite complex networks induced by intrinsic noise. Applying analytical techniques to the stochastic susceptible-infected-susceptible model, we predict the distribution of large fluctuations, the most probable or optimal path through a network that leads to a disease-free state from an endemic state, and the average extinction time in general configurations. Our predictions agree with Monte Carlo simulations on several networks, including synthetic weighted and degree-distributed networks with degree correlations, and an empirical high school contact network. In addition, our approach quantifies characteristic scaling patterns for the optimal path and distribution of large fluctuations, both near and away from the epidemic threshold, in networks with heterogeneous eigenvector centrality and degree distributions.

Epidemic extinction paths in complex networks.

PubMed

Hindes, Jason; Schwartz, Ira B

2017-05-01

We study the extinction of long-lived epidemics on finite complex networks induced by intrinsic noise. Applying analytical techniques to the stochastic susceptible-infected-susceptible model, we predict the distribution of large fluctuations, the most probable or optimal path through a network that leads to a disease-free state from an endemic state, and the average extinction time in general configurations. Our predictions agree with Monte Carlo simulations on several networks, including synthetic weighted and degree-distributed networks with degree correlations, and an empirical high school contact network. In addition, our approach quantifies characteristic scaling patterns for the optimal path and distribution of large fluctuations, both near and away from the epidemic threshold, in networks with heterogeneous eigenvector centrality and degree distributions.

A scaling law for random walks on networks

PubMed Central

Perkins, Theodore J.; Foxall, Eric; Glass, Leon; Edwards, Roderick

2014-01-01

The dynamics of many natural and artificial systems are well described as random walks on a network: the stochastic behaviour of molecules, traffic patterns on the internet, fluctuations in stock prices and so on. The vast literature on random walks provides many tools for computing properties such as steady-state probabilities or expected hitting times. Previously, however, there has been no general theory describing the distribution of possible paths followed by a random walk. Here, we show that for any random walk on a finite network, there are precisely three mutually exclusive possibilities for the form of the path distribution: finite, stretched exponential and power law. The form of the distribution depends only on the structure of the network, while the stepping probabilities control the parameters of the distribution. We use our theory to explain path distributions in domains such as sports, music, nonlinear dynamics and stochastic chemical kinetics. PMID:25311870

Predicting diffusion paths and interface motion in gamma/gamma + beta, Ni-Cr-Al diffusion couples

NASA Technical Reports Server (NTRS)

Nesbitt, J. A.; Heckel, R. W.

1987-01-01

A simplified model has been developed to predict Beta recession and diffusion paths in ternary gamma/gamma + beta diffusion couples (gamma:fcc, beta: NiAl structure). The model was tested by predicting beta recession and diffusion paths for four gamma/gamma + beta, Ni-Cr-Al couples annealed for 100 hours at 1200 C. The model predicted beta recession within 20 percent of that measured for each of the couples. The model also predicted shifts in the concentration of the gamma phase at the gamma/gamma + beta interface within 2 at. pct Al and 6 at. pct Cr of that measured in each of the couples. A qualitative explanation based on simple kinetic and mass balance arguments has been given which demonstrates the necessity for diffusion in the two-phase region of certain gamma/gamma + beta, Ni-Cr-Al couples.

A scaling law for random walks on networks

NASA Astrophysics Data System (ADS)

Perkins, Theodore J.; Foxall, Eric; Glass, Leon; Edwards, Roderick

2014-10-01

The dynamics of many natural and artificial systems are well described as random walks on a network: the stochastic behaviour of molecules, traffic patterns on the internet, fluctuations in stock prices and so on. The vast literature on random walks provides many tools for computing properties such as steady-state probabilities or expected hitting times. Previously, however, there has been no general theory describing the distribution of possible paths followed by a random walk. Here, we show that for any random walk on a finite network, there are precisely three mutually exclusive possibilities for the form of the path distribution: finite, stretched exponential and power law. The form of the distribution depends only on the structure of the network, while the stepping probabilities control the parameters of the distribution. We use our theory to explain path distributions in domains such as sports, music, nonlinear dynamics and stochastic chemical kinetics.

A scaling law for random walks on networks.

PubMed

Perkins, Theodore J; Foxall, Eric; Glass, Leon; Edwards, Roderick

2014-10-14

The dynamics of many natural and artificial systems are well described as random walks on a network: the stochastic behaviour of molecules, traffic patterns on the internet, fluctuations in stock prices and so on. The vast literature on random walks provides many tools for computing properties such as steady-state probabilities or expected hitting times. Previously, however, there has been no general theory describing the distribution of possible paths followed by a random walk. Here, we show that for any random walk on a finite network, there are precisely three mutually exclusive possibilities for the form of the path distribution: finite, stretched exponential and power law. The form of the distribution depends only on the structure of the network, while the stepping probabilities control the parameters of the distribution. We use our theory to explain path distributions in domains such as sports, music, nonlinear dynamics and stochastic chemical kinetics.

Quantifying edge significance on maintaining global connectivity

PubMed Central

Qian, Yuhua; Li, Yebin; Zhang, Min; Ma, Guoshuai; Lu, Furong

2017-01-01

Global connectivity is a quite important issue for networks. The failures of some key edges may lead to breakdown of the whole system. How to find them will provide a better understanding on system robustness. Based on topological information, we propose an approach named LE (link entropy) to quantify the edge significance on maintaining global connectivity. Then we compare the LE with the other six acknowledged indices on the edge significance: the edge betweenness centrality, degree product, bridgeness, diffusion importance, topological overlap and k-path edge centrality. Experimental results show that the LE approach outperforms in quantifying edge significance on maintaining global connectivity. PMID:28349923

Mean Free Path in Soccer and Gases

ERIC Educational Resources Information Center

Luzuriaga, J.

2010-01-01

The trajectories of the molecules in an ideal gas and of the ball in a soccer game are compared. The great difference between these motions and some similarities are discussed. This example could be suitable for discussing many concepts in kinetic theory in a way that can be pictured by students for getting a more intuitive understanding. It could…

Effect of small and large animal skull bone on photoacoustic signal

NASA Astrophysics Data System (ADS)

Xu, Qiuyun; Volinski, Bridget; Hariri, Ali; Fatima, Afreen; Nasiriavanaki, Mohammadreza

2017-03-01

Photoacoustic imaging (PAI) has proved to be a promising non-invasive technique for diagnosis, prognosis and treatment monitoring of neurological disorders in small and large animals. Skull bone effects both light illumination and ultrasound propagation. Hence, the PA signal is largely affected. This study aims to quantify and compare the attenuation of PA signal due to the skull obstacle in the light illumination path, in the ultrasound propagation path, or in both. The effect of mouse, rat, and mesocephalic dog skull bones, ex-vivo, is quantitatively studied.

Kinetic modeling of antimony(III) oxidation and sorption in soils.

PubMed

Cai, Yongbing; Mi, Yuting; Zhang, Hua

2016-10-05

Kinetic batch and saturated column experiments were performed to study the oxidation, adsorption and transport of Sb(III) in two soils with contrasting properties. Kinetic and column experiment results clearly demonstrated the extensive oxidation of Sb(III) in soils, and this can in return influence the adsorption and transport of Sb. Both sorption capacity and kinetic oxidation rate were much higher in calcareous Huanjiang soil than in acid red Yingtan soil. The results indicate that soil serve as a catalyst in promoting oxidation of Sb(III) even under anaerobic conditions. A PHREEQC model with kinetic formulations was developed to simulate the oxidation, sorption and transport of Sb(III) in soils. The model successfully described Sb(III) oxidation and sorption data in kinetic batch experiment. It was less successful in simulating the reactive transport of Sb(III) in soil columns. Additional processes such as colloid facilitated transport need to be quantified and considered in the model. Copyright © 2016 Elsevier B.V. All rights reserved.

The influence of speed and grade on wheelchair propulsion hand pattern.

PubMed

Slowik, Jonathan S; Requejo, Philip S; Mulroy, Sara J; Neptune, Richard R

2015-11-01

The hand pattern used during manual wheelchair propulsion (i.e., full-cycle hand path) can provide insight into an individual's propulsion technique. However, previous analyses of hand patterns have been limited by their focus on a single propulsion condition and reliance on subjective qualitative characterization methods. The purpose of this study was to develop a set of objective quantitative parameters to characterize hand patterns and determine the influence of propulsion speed and grade of incline on the patterns preferred by manual wheelchair users. Kinematic and kinetic data were collected from 170 experienced manual wheelchair users on an ergometer during three conditions: level propulsion at their self-selected speed, level propulsion at their fastest comfortable speed and graded propulsion (8%) at their level self-selected speed. Hand patterns were quantified using a set of objective parameters, and differences across conditions were identified. Increased propulsion speed resulted in a shift away from under-rim hand patterns. Increased grade of incline resulted in the hand remaining near the handrim throughout the cycle. Manual wheelchair users change their hand pattern based on task-specific constraints and goals. Further work is needed to investigate how differences between hand patterns influence upper extremity demand and potentially lead to the development of overuse injuries and pain. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microfluidic flow cytometer for quantifying photobleaching of fluorescent proteins in cells

PubMed Central

Lubbeck, Jennifer L.; Dean, Kevin M.; Ma, Hairong; Palmer, Amy E.; Jimenez, Ralph

2012-01-01

Traditional flow cytometers are capable of rapid cellular assays on the basis of fluorescence intensity and light scatter. Microfluidic flow cytometers have largely followed the same path of technological development as their traditional counterparts, however the significantly smaller transport distance and resulting lower cell speeds in microchannels provides for the opportunity to detect novel spectroscopic signatures based on multiple, non-temporally-coincident excitation beams. Here, we characterize the design and operation of a cytometer with a 3-beam, probe/bleach/probe geometry, employing HeLa suspension cells expressing fluorescent proteins. The data collection rate exceeds 20 cells/s under a range of beam intensities (5 kW – 179 kW/cm2). The measured percent photobleaching (ratio of fluorescence intensities excited by the first and third beams: Sbeam3/Sbeam1) partially resolves a mixture of four red fluorescent proteins in mixed samples. Photokinetic simulations are presented and demonstrate that the percent photobleaching reflects a combination of the reversible and irreversible photobleaching kinetics. By introducing a photobleaching optical signature, which complements traditional fluorescence intensity-based detection, this method adds another dimension to multi-channel fluorescence cytometry, and provides a means for flow-cytometry-based screening of directed libraries of fluorescent protein photobleaching. PMID:22424298

The Influence of Speed and Grade on Wheelchair Propulsion Hand Pattern

PubMed Central

Slowik, Jonathan S.; Requejo, Philip S.; Mulroy, Sara J.; Neptune, Richard R.

2015-01-01

Background The hand pattern used during manual wheelchair propulsion (i.e., full-cycle hand path) can provide insight into an individual's propulsion technique. However, previous analyses of hand patterns have been limited by their focus on a single propulsion condition and reliance on subjective qualitative characterization methods. The purpose of this study was to develop a set of objective quantitative parameters to characterize hand patterns and determine the influence of propulsion speed and grade of incline on the patterns preferred by manual wheelchair users. Methods Kinematic and kinetic data were collected from 170 experienced manual wheelchair users on an ergometer during three conditions: level propulsion at their self-selected speed, level propulsion at their fastest comfortable speed, and graded propulsion (8%) at their level self-selected speed. Hand patterns were quantified using a set of objective parameters and differences across conditions were identified. Findings Increased propulsion speed resulted in a shift away from under-rim hand patterns. Increased grade of incline resulted in the hand remaining near the handrim throughout the cycle. Interpretation Manual wheelchair users change their hand pattern based on task-specific constraints and goals. Further work is needed to investigate how differences between hand patterns influence upper extremity demand and potentially lead to the development of overuse injuries and pain. PMID:26228706

Operational Performance Risk Assessment in Support of A Supervisory Control System

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

Denning, Richard S.; Muhlheim, Michael David; Cetiner, Sacit M.

Supervisory control system (SCS) is developed for multi-unit advanced small modular reactors to minimize human interventions in both normal and abnormal operations. In SCS, control action decisions made based on probabilistic risk assessment approach via Event Trees/Fault Trees. Although traditional PRA tools are implemented, their scope is extended to normal operations and application is reversed; success of non-safety related system instead failure of safety systems this extended PRA approach called as operational performance risk assessment (OPRA). OPRA helps to identify success paths, combination of control actions for transients and to quantify these success paths to provide possible actions without activatingmore » plant protection system. In this paper, a case study of the OPRA in supervisory control system is demonstrated within the context of the ALMR PRISM design, specifically power conversion system. The scenario investigated involved a condition that the feed water control valve is observed to be drifting to the closed position. Alternative plant configurations were identified via OPRA that would allow the plant to continue to operate at full or reduced power. Dynamic analyses were performed with a thermal-hydraulic model of the ALMR PRISM system using Modelica to evaluate remained safety margins. Successful recovery paths for the selected scenario are identified and quantified via SCS.« less

Surface Area, and Oxidation Effects on Nitridation Kinetics of Silicon Powder Compacts

NASA Technical Reports Server (NTRS)

Bhatt, R. T.; Palczer, A. R.

1998-01-01

Commercially available silicon powders were wet-attrition-milled from 2 to 48 hr to achieve surface areas (SA's) ranging from 1.3 to 70 sq m/g. The surface area effects on the nitridation kinetics of silicon powder compacts were determined at 1250 or 1350 C for 4 hr. In addition, the influence of nitridation environment, and preoxidation on nitridation kinetics of a silicon powder of high surface area (approximately equals 63 sq m/g) was investigated. As the surface area increased, so did the percentage nitridation after 4 hr in N2 at 1250 or 1350 C. Silicon powders of high surface area (greater than 40 sq m/g) can be nitrided to greater than 70% at 1250 C in 4 hr. The nitridation kinetics of the high-surface-area powder compacts were significantly delayed by preoxidation treatment. Conversely, the nitridation environment had no significant influence on the nitridation kinetics of the same powder. Impurities present in the starting powder, and those accumulated during attrition milling, appeared to react with the silica layer on the surface of silicon particles to form a molten silicate layer, which provided a path for rapid diffusion of nitrogen and enhanced the nitridation kinetics of high surface area silicon powder.

Whole body creatine and protein kinetics in healthy men and women: effects of creatine and amino acid supplementation.

PubMed

Kalhan, Satish C; Gruca, Lourdes; Marczewski, Susan; Bennett, Carole; Kummitha, China

2016-03-01

Creatine kinetics were measured in young healthy subjects, eight males and seven females, age 20-30 years, after an overnight fast on creatine-free diet. Whole body turnover of glycine and its appearance in creatine was quantified using [1-(13)C] glycine and the rate of protein turnover was quantified using L-ring [(2)H5] phenylalanine. The creatine pool size was estimated by the dilution of a bolus [C(2)H3] creatine. Studies were repeated following a five days supplement creatine 21 g.day(-1) and following supplement amino acids 14.3 g day(-1). Creatine caused a ten-fold increase in the plasma concentration of creatine and a 50 % decrease in the concentration of guanidinoacetic acid. Plasma amino acids profile showed a significant decrease in glycine, glutamine, and taurine and a significant increase in citrulline, valine, lysine, and cysteine. There was a significant decrease in the rate of appearance of glycine, suggesting a decrease in de-novo synthesis (p = 0.006). The fractional and absolute rate of synthesis of creatine was significantly decreased by supplemental creatine. Amino acid supplement had no impact on any of the parameters. This is the first detailed analysis of creatine kinetics and the effects of creatine supplement in healthy young men and women. These methods can be applied for the analysis of creatine kinetics in different physiological states.

The Synergy Between Total Scattering and Advanced Simulation Techniques: Quantifying Geopolymer Gel Evolution

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

White, Claire; Bloomer, Breaunnah E.; Provis, John L.

2012-05-16

With the ever increasing demands for technologically advanced structural materials, together with emerging environmental consciousness due to climate change, geopolymer cement is fast becoming a viable alternative to traditional cements due to proven mechanical engineering characteristics and the reduction in CO2 emitted (approximately 80% less CO2 emitted compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of the molecular changes responsible for nanostructural evolution during the geopolymerization process. Here, in-situ total scattering measurements in the form of X-ray pair distribution function (PDF) analysis are used to quantify the extent of reaction of metakaolin/slag alkali-activated geopolymer binders, includingmore » the effects of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerization reaction. Restricting quantification of the kinetics to the initial ten hours of reaction does not enable elucidation of the true extent of the reaction, but using X-ray PDF data obtained after 128 days of reaction enables more accurate determination of the initial extent of reaction. The synergies between the in-situ X-ray PDF data and simulations conducted by multiscale density functional theory-based coarse-grained Monte Carlo analysis are outlined, particularly with regard to the potential for the X-ray data to provide a time scale for kinetic analysis of the extent of reaction obtained from the multiscale simulation methodology.« less

Fuzzy Performance between Surface Fitting and Energy Distribution in Turbulence Runner

PubMed Central

Liang, Zhongwei; Liu, Xiaochu; Ye, Bangyan; Brauwer, Richard Kars

2012-01-01

Because the application of surface fitting algorithms exerts a considerable fuzzy influence on the mathematical features of kinetic energy distribution, their relation mechanism in different external conditional parameters must be quantitatively analyzed. Through determining the kinetic energy value of each selected representative position coordinate point by calculating kinetic energy parameters, several typical algorithms of complicated surface fitting are applied for constructing microkinetic energy distribution surface models in the objective turbulence runner with those obtained kinetic energy values. On the base of calculating the newly proposed mathematical features, we construct fuzzy evaluation data sequence and present a new three-dimensional fuzzy quantitative evaluation method; then the value change tendencies of kinetic energy distribution surface features can be clearly quantified, and the fuzzy performance mechanism discipline between the performance results of surface fitting algorithms, the spatial features of turbulence kinetic energy distribution surface, and their respective environmental parameter conditions can be quantitatively analyzed in detail, which results in the acquirement of final conclusions concerning the inherent turbulence kinetic energy distribution performance mechanism and its mathematical relation. A further turbulence energy quantitative study can be ensured. PMID:23213287

Simple measures of channel habitat complexity predict transient hydraulic storage in streams

EPA Science Inventory

Stream thalweg depth profiles (along path of greatest channel depth) and woody debris tallies have recently become components of routine field procedures for quantifying physical habitat in national stream monitoring efforts. Mean residual depth, standard deviation of thalweg dep...

Characterization Test Procedures for Intersection Collision Avoidance Systems Based on Vehicle-to-Vehicle Communications

DOT National Transportation Integrated Search

2015-12-01

Characterization test procedures have been developed to quantify the performance of intersection collision avoidance (ICA) systems based on vehicle-to-vehicle communications. These systems warn the driver of an imminent crossing-path collision at a r...

The Path of Carbon in Photosynthesis XIII. pH Effects in C{sup 14}O{sub 2} Fixation by Scenedesmus

DOE R&D Accomplishments Database

Ouellet, C.; Benson, A. A.

1951-10-23

The rates of photosynthesis and dark fixation of C{sup 14}O{sub 2} in Scenedesmus have been compared in dilute phosphate buffers of 1.6 to 11.4 pH; determination of C{sup 14} incorporation into the various products shows enhancement of uptake in an acid medium into sucrose, polysaccharides, alanine and serine, in an alkaline medium into malic asparctic acids. kinetic experiments at extreme pH values suggest that several paths are available for CO{sub 2} assimilation. A tentative correlation of the results with the pH optima of some enzymes and resultant effects upon concentrations of intermediates is presented.

Gait Strategy in Patients with Ehlers-Danlos Syndrome Hypermobility Type: A Kinematic and Kinetic Evaluation Using 3D Gait Analysis

ERIC Educational Resources Information Center

Galli, Manuela; Cimolin, Veronica; Rigoldi, Chiara; Castori, Marco; Celletti, Claudia; Albertini, Giorgio; Camerota, Filippo

2011-01-01

The aim of this study was to quantify the gait patterns of adults with joint hypermobility syndrome/Ehlers-Danlos syndrome (JHS/EDS-HT) hypermobility type, using Gait Analysis. We quantified the gait strategy in 12 JHS/EDS-HT adults individuals (age: 43.08 + 6.78 years) compared to 20 healthy controls (age: 37.23 plus or minus 8.91 years), in…

Kinetic and mechanistic reactivity. Isoprene impact on ozone levels in an urban area near Tijuca Forest, Rio de Janeiro.

PubMed

da Silva, Cleyton Martins; da Silva, Luane Lima; Corrêa, Sergio Machado; Arbilla, Graciela

2016-12-01

Volatile organic compounds (VOCs) play a central role in atmospheric chemistry. In this work, the kinetic and mechanistic reactivities of VOCs are analyzed, and the contribution of the organic compounds emitted by anthropogenic and natural sources is estimated. VOCs react with hydroxyl radicals and other photochemical oxidants, such as ozone and nitrate radicals, which cause the conversion of NO to NO 2 in various potential reaction paths, including photolysis, to form oxygen atoms, which generate ozone. The kinetic reactivity was evaluated based on the reaction coefficients for hydroxyl radicals with VOCs. The mechanistic reactivity was estimated using a detailed mechanism and the incremental reactivity scale that Carter proposed. Different scenarios were proposed and discussed, and a minimum set of compounds, which may describe the tropospheric reactivity in the studied area, was determined. The role of isoprene was analyzed in terms of its contribution to ozone formation.

Quantifying time-of-flight-resolved optical field dynamics in turbid media with interferometric near-infrared spectroscopy (iNIRS) (Conference Presentation)

NASA Astrophysics Data System (ADS)

Borycki, Dawid; Kholiqov, Oybek; Zhou, Wenjun; Srinivasan, Vivek J.

2017-03-01

Sensing and imaging methods based on the dynamic scattering of coherent light, including laser speckle, laser Doppler, and diffuse correlation spectroscopy quantify scatterer motion using light intensity (speckle) fluctuations. The underlying optical field autocorrelation (OFA), rather than being measured directly, is typically inferred from the intensity autocorrelation (IA) through the Siegert relationship, by assuming that the scattered field obeys Gaussian statistics. In this work, we demonstrate interferometric near-infrared spectroscopy (iNIRS) for measurement of time-of-flight (TOF) resolved field and intensity autocorrelations in fluid tissue phantoms and in vivo. In phantoms, we find a breakdown of the Siegert relationship for short times-of-flight due to a contribution from static paths whose optical field does not decorrelate over experimental time scales, and demonstrate that eliminating such paths by polarization gating restores the validity of the Siegert relationship. Inspired by these results, we developed a method, called correlation gating, for separating the OFA into static and dynamic components. Correlation gating enables more precise quantification of tissue dynamics. To prove this, we show that iNIRS and correlation gating can be applied to measure cerebral hemodynamics of the nude mouse in vivo using dynamically scattered (ergodic) paths and not static (non-ergodic) paths, which may not be impacted by blood. More generally, correlation gating, in conjunction with TOF resolution, enables more precise separation of diffuse and non-diffusive contributions to OFA than is possible with TOF resolution alone. Finally, we show that direct measurements of OFA are statistically more efficient than indirect measurements based on IA.

The Solidification of Multicomponent Alloys

PubMed Central

Boettinger, William J.

2017-01-01

Various topics taken from the author’s research portfolio that involve multicomponent alloy solidification are reviewed. Topics include: ternary eutectic solidification and Scheil-Gulliver paths in ternary systems. A case study of the solidification of commercial 2219 aluminum alloy is described. Also described are modifications of the Scheil-Gulliver analysis to treat dendrite tip kinetics and solid diffusion for multicomponent alloys. PMID:28819348

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

Stereoscopic display technologies, interaction paradigms, and rendering approaches for neurosurgical visualization

NASA Astrophysics Data System (ADS)

Cooperstock, Jeremy R.; Wang, Guangyu

2009-02-01

We conducted a comparative study of different stereoscopic display modalities (head-mounted display, polarized projection, and multiview lenticular display) to evaluate their efficacy in supporting manipulation and understanding of 3D content, specifically, in the context of neurosurgical visualization. Our study was intended to quantify the differences in resulting task performance between these choices of display technology. The experimental configuration involved a segmented brain vasculature and a simulated tumor. Subjects were asked to manipulate the vasculature and a pen-like virtual probe in order to define a vessel-free path from cortical surface to the targeted tumor. Because of the anatomical complexity, defining such a path can be a challenging task. To evaluate the system, we quantified performance differences under three different stereoscopic viewing conditions. Our results indicate that, on average, participants achieved best performance using polarized projection, and worst with the multiview lenticular display. These quantitative measurements were further reinforced by the subjects' responses to our post-test questionnaire regarding personal preferences.

Frequency-dependent seismic attenuation in the eastern United States as observed from the 2011 central Virginia earthquake and aftershock sequence

USGS Publications Warehouse

McNamara, Daniel E.; Gee, Lind; Benz, Harley M.; Chapman, Martin

2014-01-01

Ground shaking due to earthquakes in the eastern United States (EUS) is felt at significantly greater distances than in the western United States (WUS) and for some earthquakes it has been shown to display a strong preferential direction. Shaking intensity variation can be due to propagation path effects, source directivity, and/or site amplification. In this paper, we use S and Lg waves recorded from the 2011 central Virginia earthquake and aftershock sequence, in the Central Virginia Seismic Zone, to quantify attenuation as frequency‐dependent Q(f). In support of observations based on shaking intensity, we observe high Q values in the EUS relative to previous studies in the WUS with especially efficient propagation along the structural trend of the Appalachian mountains. Our analysis of Q(f) quantifies the path effects of the northeast‐trending felt distribution previously inferred from the U.S. Geological Survey (USGS) “Did You Feel It” data, historic intensity data, and the asymmetrical distribution of rockfalls and landslides.

Probabilistic parameter estimation in a 2-step chemical kinetics model for n-dodecane jet autoignition

NASA Astrophysics Data System (ADS)

Hakim, Layal; Lacaze, Guilhem; Khalil, Mohammad; Sargsyan, Khachik; Najm, Habib; Oefelein, Joseph

2018-05-01

This paper demonstrates the development of a simple chemical kinetics model designed for autoignition of n-dodecane in air using Bayesian inference with a model-error representation. The model error, i.e. intrinsic discrepancy from a high-fidelity benchmark model, is represented by allowing additional variability in selected parameters. Subsequently, we quantify predictive uncertainties in the results of autoignition simulations of homogeneous reactors at realistic diesel engine conditions. We demonstrate that these predictive error bars capture model error as well. The uncertainty propagation is performed using non-intrusive spectral projection that can also be used in principle with larger scale computations, such as large eddy simulation. While the present calibration is performed to match a skeletal mechanism, it can be done with equal success using experimental data only (e.g. shock-tube measurements). Since our method captures the error associated with structural model simplifications, we believe that the optimised model could then lead to better qualified predictions of autoignition delay time in high-fidelity large eddy simulations than the existing detailed mechanisms. This methodology provides a way to reduce the cost of reaction kinetics in simulations systematically, while quantifying the accuracy of predictions of important target quantities.

Deterministic Approach to the Kinetic Theory of Gases

NASA Astrophysics Data System (ADS)

Beck, József

2010-02-01

In the so-called Bernoulli model of the kinetic theory of gases, where (1) the particles are dimensionless points, (2) they are contained in a cube container, (3) no attractive or exterior forces are acting on them, (4) there is no collision between the particles, (5) the collision against the walls of the container are according to the law of elastic reflection, we deduce from Newtonian mechanics two local probabilistic laws: a Poisson limit law and a central limit theorem. We also prove some global law of large numbers, justifying that "density" and "pressure" are constant. Finally, as a byproduct of our research, we prove the surprising super-uniformity of the typical billiard path in a square.

Single-exponential activation behavior behind the super-Arrhenius relaxations in glass-forming liquids.

PubMed

Wang, Lianwen; Li, Jiangong; Fecht, Hans-Jörg

2010-11-17

The reported relaxation time for several typical glass-forming liquids was analyzed by using a kinetic model for liquids which invoked a new kind of atomic cooperativity--thermodynamic cooperativity. The broadly studied 'cooperative length' was recognized as the kinetic cooperativity. Both cooperativities were conveniently quantified from the measured relaxation data. A single-exponential activation behavior was uncovered behind the super-Arrhenius relaxations for the liquids investigated. Hence the mesostructure of these liquids and the atomic mechanism of the glass transition became clearer.

Quantification of joint inflammation in rheumatoid arthritis by time-resolved diffuse optical spectroscopy and tracer kinetic modeling

NASA Astrophysics Data System (ADS)

Ioussoufovitch, Seva; Morrison, Laura B.; Lee, Ting-Yim; St. Lawrence, Keith; Diop, Mamadou

2015-03-01

Rheumatoid arthritis (RA) is characterized by chronic synovial inflammation, which can cause progressive joint damage and disability. Diffuse optical spectroscopy (DOS) and imaging have the potential to become potent monitoring tools for RA. We devised a method that combined time-resolved DOS and tracer kinetics modeling to rapidly and reliably quantify blood flow in the joint. Preliminary results obtained from two animals show that the technique can detect joint inflammation as early as 5 days after onset.

Effects of Bacterial Siderophore and Biofilm Synthesis on Silicate Mineral Dissolution Kinetics: Results from Experiments with Targeted Mutants

NASA Astrophysics Data System (ADS)

Van Den Berghe, M. D.; West, A. J.; Nealson, K. H.

2018-05-01

This project aims to characterize and quantify the specific microbial mechanisms and metabolic pathways responsible for silicate mineral dissolution and micronutrient acquisition directly from mineral phases.

Kinetic Plasma and Turbulent Mix Studies using DT Plastic-shell Implosions with Shell-thickness and Pressure Variations

NASA Astrophysics Data System (ADS)

Kim, Y.; Herrmann, H. W.; Hoffman, N. M.; Schmitt, M. J.; Bradley, P. A.; Kagan, G.; Gales, S.; Horsfield, C. J.; Rubery, M.; Leatherland, A.; Gatu Johnson, M.; Glebov, V.; Seka, W.; Marshall, F.; Stoeckl, C.; Church, J.

2014-10-01

Kinetic plasma and turbulent mix effects on inertial confinement fusion have been studied using a series of DT-filled plastic-shell implosions at the OMEGA laser facility. Plastic capsules of 4 different shell thicknesses (7.4, 15, 20, 29 micron) were shot at 2 different fill pressures in order to vary the ion mean free path compared to the size of fuel region (i.e., Knudsen number). We varied the empirical Knudsen number by a factor of 25. Measurements were obtained from the burn-averaged ion temperature and fuel areal density. Preliminary results indicate that as the empirical Knudsen number increases, fusion performances (e.g., neutron yield) increasingly deviate from hydrodynamic simulations unless turbulent mix and ion kinetic terms (e.g., enhanced ion diffusion, viscosity, thermal conduction, as well as Knudsen-layer fusion reactivity reduction) are considered. We are developing two separate simulations: one is a reduced-ion-kinetics model and the other is turbulent mix model. Two simulation results will be compared with the experimental observables.

Si1-yCy/Si(001) gas-source molecular beam epitaxy from Si2H6 and CH3SiH3: Surface reaction paths and growth kinetics

NASA Astrophysics Data System (ADS)

Foo, Y. L.; Bratland, K. A.; Cho, B.; Desjardins, P.; Greene, J. E.

2003-04-01

In situ surface probes and postdeposition analyses were used to follow surface reaction paths and growth kinetics of Si1-yCy alloys grown on Si(001) by gas-source molecular-beam epitaxy from Si2H6/CH3SiH3 mixtures as a function of C concentration y (0-2.6 at %) and temperature Ts (500-600 °C). High-resolution x-ray diffraction reciprocal lattice maps show that all layers are in tension and fully coherent with their substrates. Film growth rates R decrease with both y and Ts, and the rate of decrease in R as a function of y increases rapidly with Ts. In situ isotopically tagged D2 temperature-programmed desorption (TPD) measurements reveal that C segregation during steady-state Si1-yCy(001) growth results in charge transfer from Si surface dangling bonds to second-layer C atoms, which have a higher electronegativity than Si. From the TPD results, we obtain the coverage θSi*(y,Ts) of Si* surface sites with C backbonds as well as H2 desorption energies Ed from both Si and Si* surface sites. θSi* increases with increasing y and Ts in the kinetically limited segregation regime while Ed decreases from 2.52 eV for H2 desorption from Si surface sites with Si back bonds to 2.22 eV from Si* surface sites. This leads to an increase in the H2 desorption rate, and hence should yield higher film deposition rates, with increasing y and/or Ts during Si1-yCy(001) growth. The effect, however, is more than offset by the decrease in Si2H6 reactive sticking probabilities at Si* surface sites. Film growth rates R(Ts,JSi2H6,JCH3SiH3) calculated using a simple transition-state kinetic model, together with measured kinetic parameters, were found to be in excellent agreement with the experimental data.

Establishing the kinetics of ballistic-to-diffusive transition using directional statistics

NASA Astrophysics Data System (ADS)

Liu, Pai; Heinson, William R.; Sumlin, Benjamin J.; Shen, Kuan-Yu; Chakrabarty, Rajan K.

2018-04-01

We establish the kinetics of ballistic-to-diffusive (BD) transition observed in two-dimensional random walk using directional statistics. Directional correlation is parameterized using the walker's turning angle distribution, which follows the commonly adopted wrapped Cauchy distribution (WCD) function. During the BD transition, the concentration factor (ρ) governing the WCD shape is observed to decrease from its initial value. We next analytically derive the relationship between effective ρ and time, which essentially quantifies the BD transition rate. The prediction of our kinetic expression agrees well with the empirical datasets obtained from correlated random walk simulation. We further connect our formulation with the conventionally used scaling relationship between the walker's mean-square displacement and time.

Quantifying the Electrocatalytic Turnover of Vitamin B12-Mediated Dehalogenation on Single Soft Nanoparticles.

PubMed

Cheng, Wei; Compton, Richard G

2016-02-12

We report the electrocatalytic dehalogenation of trichloroethylene (TCE) by single soft nanoparticles in the form of Vitamin B12 -containing droplets. We quantify the turnover number of the catalytic reaction at the single soft nanoparticle level. The kinetic data shows that the binding of TCE with the electro-reduced vitamin in the Co(I) oxidation state is chemically reversible. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Artificial intelligence-assisted occupational lung disease diagnosis.

PubMed

Harber, P; McCoy, J M; Howard, K; Greer, D; Luo, J

1991-08-01

An artificial intelligence expert-based system for facilitating the clinical recognition of occupational and environmental factors in lung disease has been developed in a pilot fashion. It utilizes a knowledge representation scheme to capture relevant clinical knowledge into structures about specific objects (jobs, diseases, etc) and pairwise relations between objects. Quantifiers describe both the closeness of association and risk, as well as the degree of belief in the validity of a fact. An independent inference engine utilizes the knowledge, combining likelihoods and uncertainties to achieve estimates of likelihood factors for specific paths from work to illness. The system creates a series of "paths," linking work activities to disease outcomes. One path links a single period of work to a single possible disease outcome. In a preliminary trial, the number of "paths" from job to possible disease averaged 18 per subject in a general population and averaged 25 per subject in an asthmatic population. Artificial intelligence methods hold promise in the future to facilitate diagnosis in pulmonary and occupational medicine.

JSEM: A Framework for Identifying and Evaluating Indicators.

ERIC Educational Resources Information Center

Hyman, Jeffrey B.; Leibowitz, Scott G.

2001-01-01

Presents an approach to identifying and evaluating combinations of indicators when the mathematical relationships between the indicators and an endpoint may not be quantified, a limitation common to many ecological assessments. Uses the framework of Structural Equation Modeling (SEM), which combines path analysis with measurement model, to…

Gait asymmetry: composite scores for mechanical analyses of sprint running.

PubMed

Exell, T A; Gittoes, M J R; Irwin, G; Kerwin, D G

2012-04-05

Gait asymmetry analyses are beneficial from clinical, coaching and technology perspectives. Quantifying overall athlete asymmetry would be useful in allowing comparisons between participants, or between asymmetry and other factors, such as sprint running performance. The aim of this study was to develop composite kinematic and kinetic asymmetry scores to quantify athlete asymmetry during maximal speed sprint running. Eight male sprint trained athletes (age 22±5 years, mass 74.0±8.7 kg and stature 1.79±0.07 m) participated in this study. Synchronised sagittal plane kinematic and kinetic data were collected via a CODA motion analysis system, synchronised to two Kistler force plates. Bilateral, lower limb data were collected during the maximal velocity phase of sprint running (velocity=9.05±0.37 ms(-1)). Kinematic and kinetic composite asymmetry scores were developed using the previously established symmetry angle for discrete variables associated with successful sprint performance and comparisons of continuous joint power data. Unlike previous studies quantifying gait asymmetry, the scores incorporated intra-limb variability by excluding variables from the composite scores that did not display significantly larger (p<0.05) asymmetry than intra-limb variability. The variables that contributed to the composite scores and the magnitude of asymmetry observed for each measure varied on an individual participant basis. The new composite scores indicated the inter-participant differences that exist in asymmetry during sprint running and may serve to allow comparisons between overall athlete asymmetry with other important factors such as performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

Epithelial apoptosis in mechanistically distinct methods of injury in the murine small intestine

PubMed Central

Vyas, Dinesh; Robertson, Charles M; Stromberg, Paul E; Martin, James R.; Dunne, W. Michael; Houchen, Courtney W; Barrett, Terrence A; Ayala, Alfred; Perl, Mario; Buchman, Timothy G; Coopersmith, Craig M

2007-01-01

Gut epithelial apoptosis is involved in the pathophysiology of multiple diseases. This study characterized intestinal apoptosis in three mechanistically distinct injuries with different kinetics of cell death. FVB/N mice were subjected to gamma radiation, Pseudomonas aeruginosa pneumonia or injection of monoclonal anti-CD3 antibody and sacrificed 4, 12, or 24 hours post-injury (n=10/time point). Apoptosis was quantified in the jejunum by hematoxylin and eosin (H&E), active caspase-3, terminal deoxynucleotidyl transferase dUTP-mediated nick end labeling (TUNEL), in situ oligoligation reaction (ISOL,) cytokeratin 18, and annexin V staining. Reproducible results were obtained only for H&E, active caspase-3, TUNEL and ISOL, which were quantified and compared against each other for each injury at each time point. Kinetics of injury were different with early apoptosis highest following radiation, late apoptosis highest following anti CD3, and more consistent levels following pneumonia. ISOL was the most consistent stain and was always statistically indistinguishable from at least 2 stains. In contrast, active caspase-3 demonstrated lower levels of apoptosis, while the TUNEL assay had higher levels of apoptosis in the most severely injured intestine regardless of mechanism of injury. H&E was a statistical outlier more commonly than any other stain. This suggests that regardless of mechanism or kinetics of injury, ISOL correlates to other quantification methods of detecting gut epithelial apoptosis more than any other method studied and compares favorably to other commonly accepted techniques of quantifying apoptosis in a large intestinal cross sectional by balancing sensitivity and specificity across a range of times and levels of death. PMID:17357092

Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

PubMed

Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J

2013-02-28

A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.

Interactions of information transfer along separable causal paths

NASA Astrophysics Data System (ADS)

Jiang, Peishi; Kumar, Praveen

2018-04-01

Complex systems arise as a result of interdependences between multiple variables, whose causal interactions can be visualized in a time-series graph. Transfer entropy and information partitioning approaches have been used to characterize such dependences. However, these approaches capture net information transfer occurring through a multitude of pathways involved in the interaction and as a result mask our ability to discern the causal interaction within a subgraph of interest through specific pathways. We build on recent developments of momentary information transfer along causal paths proposed by Runge [Phys. Rev. E 92, 062829 (2015), 10.1103/PhysRevE.92.062829] to develop a framework for quantifying information partitioning along separable causal paths. Momentary information transfer along causal paths captures the amount of information transfer between any two variables lagged at two specific points in time. Our approach expands this concept to characterize the causal interaction in terms of synergistic, unique, and redundant information transfer through separable causal paths. Through a graphical model, we analyze the impact of the separable and nonseparable causal paths and the causality structure embedded in the graph as well as the noise effect on information partitioning by using synthetic data generated from two coupled logistic equation models. Our approach can provide a valuable reference for an autonomous information partitioning along separable causal paths which form a causal subgraph influencing a target.

Brain-computer interface control along instructed paths

NASA Astrophysics Data System (ADS)

Sadtler, P. T.; Ryu, S. I.; Tyler-Kabara, E. C.; Yu, B. M.; Batista, A. P.

2015-02-01

Objective. Brain-computer interfaces (BCIs) are being developed to assist paralyzed people and amputees by translating neural activity into movements of a computer cursor or prosthetic limb. Here we introduce a novel BCI task paradigm, intended to help accelerate improvements to BCI systems. Through this task, we can push the performance limits of BCI systems, we can quantify more accurately how well a BCI system captures the user’s intent, and we can increase the richness of the BCI movement repertoire. Approach. We have implemented an instructed path task, wherein the user must drive a cursor along a visible path. The instructed path task provides a versatile framework to increase the difficulty of the task and thereby push the limits of performance. Relative to traditional point-to-point tasks, the instructed path task allows more thorough analysis of decoding performance and greater richness of movement kinematics. Main results. We demonstrate that monkeys are able to perform the instructed path task in a closed-loop BCI setting. We further investigate how the performance under BCI control compares to native arm control, whether users can decrease their movement variability in the face of a more demanding task, and how the kinematic richness is enhanced in this task. Significance. The use of the instructed path task has the potential to accelerate the development of BCI systems and their clinical translation.

Automatic Quantification of Radiographic Wrist Joint Space Width of Patients With Rheumatoid Arthritis.

PubMed

Huo, Yinghe; Vincken, Koen L; van der Heijde, Desiree; de Hair, Maria J H; Lafeber, Floris P; Viergever, Max A

2017-11-01

Objective: Wrist joint space narrowing is a main radiographic outcome of rheumatoid arthritis (RA). Yet, automatic radiographic wrist joint space width (JSW) quantification for RA patients has not been widely investigated. The aim of this paper is to present an automatic method to quantify the JSW of three wrist joints that are least affected by bone overlapping and are frequently involved in RA. These joints are located around the scaphoid bone, viz. the multangular-navicular, capitate-navicular-lunate, and radiocarpal joints. Methods: The joint space around the scaphoid bone is detected by using consecutive searches of separate path segments, where each segment location aids in constraining the subsequent one. For joint margin delineation, first the boundary not affected by X-ray projection is extracted, followed by a backtrace process to obtain the actual joint margin. The accuracy of the quantified JSW is evaluated by comparison with the manually obtained ground truth. Results: Two of the 50 radiographs used for evaluation of the method did not yield a correct path through all three wrist joints. The delineated joint margins of the remaining 48 radiographs were used for JSW quantification. It was found that 90% of the joints had a JSW deviating less than 20% from the mean JSW of manual indications, with the mean JSW error less than 10%. Conclusion: The proposed method is able to automatically quantify the JSW of radiographic wrist joints reliably. The proposed method may aid clinical researchers to study the progression of wrist joint damage in RA studies. Objective: Wrist joint space narrowing is a main radiographic outcome of rheumatoid arthritis (RA). Yet, automatic radiographic wrist joint space width (JSW) quantification for RA patients has not been widely investigated. The aim of this paper is to present an automatic method to quantify the JSW of three wrist joints that are least affected by bone overlapping and are frequently involved in RA. These joints are located around the scaphoid bone, viz. the multangular-navicular, capitate-navicular-lunate, and radiocarpal joints. Methods: The joint space around the scaphoid bone is detected by using consecutive searches of separate path segments, where each segment location aids in constraining the subsequent one. For joint margin delineation, first the boundary not affected by X-ray projection is extracted, followed by a backtrace process to obtain the actual joint margin. The accuracy of the quantified JSW is evaluated by comparison with the manually obtained ground truth. Results: Two of the 50 radiographs used for evaluation of the method did not yield a correct path through all three wrist joints. The delineated joint margins of the remaining 48 radiographs were used for JSW quantification. It was found that 90% of the joints had a JSW deviating less than 20% from the mean JSW of manual indications, with the mean JSW error less than 10%. Conclusion: The proposed method is able to automatically quantify the JSW of radiographic wrist joints reliably. The proposed method may aid clinical researchers to study the progression of wrist joint damage in RA studies.

Epithelial invasion outcompetes hypha development during Candida albicans infection as revealed by an image-based systems biology approach.

PubMed

Mech, Franziska; Wilson, Duncan; Lehnert, Teresa; Hube, Bernhard; Thilo Figge, Marc

2014-02-01

Candida albicans is the most common opportunistic fungal pathogen of the human mucosal flora, frequently causing infections. The fungus is responsible for invasive infections in immunocompromised patients that can lead to sepsis. The yeast to hypha transition and invasion of host-tissue represent major determinants in the switch from benign colonizer to invasive pathogen. A comprehensive understanding of the infection process requires analyses at the quantitative level. Utilizing fluorescence microscopy with differential staining, we obtained images of C. albicans undergoing epithelial invasion during a time course of 6 h. An image-based systems biology approach, combining image analysis and mathematical modeling, was applied to quantify the kinetics of hyphae development, hyphal elongation, and epithelial invasion. The automated image analysis facilitates high-throughput screening and provided quantities that allow for the time-resolved characterization of the morphological and invasive state of fungal cells. The interpretation of these data was supported by two mathematical models, a kinetic growth model and a kinetic transition model, that were developed using differential equations. The kinetic growth model describes the increase in hyphal length and revealed that hyphae undergo mass invasion of epithelial cells following primary hypha formation. We also provide evidence that epithelial cells stimulate the production of secondary hyphae by C. albicans. Based on the kinetic transition model, the route of invasion was quantified in the state space of non-invasive and invasive fungal cells depending on their number of hyphae. This analysis revealed that the initiation of hyphae formation represents an ultimate commitment to invasive growth and suggests that in vivo, the yeast to hypha transition must be under exquisitely tight negative regulation to avoid the transition from commensal to pathogen invading the epithelium. © 2013 International Society for Advancement of Cytometry.

Decay of Solar Wind Turbulence behind Interplanetary Shocks

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

Pitňa, Alexander; Šafránková, Jana; Němeček, Zdeněk

We investigate the decay of magnetic and kinetic energies behind IP shocks with motivation to find a relaxation time when downstream turbulence reaches a usual solar wind value. We start with a case study that introduces computation techniques and quantifies a contribution of kinetic fluctuations to the general energy balance. This part of the study is based on high-time (31 ms) resolution plasma data provided by the Spektr-R spacecraft. On the other hand, a statistical part is based on 92 s Wind plasma and magnetic data and its results confirm theoretically established decay laws for kinetic and magnetic energies. Wemore » observe the power-law behavior of the energy decay profiles and we estimated the power-law exponents of both kinetic and magnetic energy decay rates as −1.2. We found that the decay of MHD turbulence does not start immediately after the IP shock ramp and we suggest that the proper decay of turbulence begins when a contribution of the kinetic processes becomes negligible. We support this suggestion with a detailed analysis of the decay of turbulence at the kinetic scale.« less

Kinetic Measurements Reveal Enhanced Protein-Protein Interactions at Intercellular Junctions

PubMed Central

Shashikanth, Nitesh; Kisting, Meridith A.; Leckband, Deborah E.

2016-01-01

The binding properties of adhesion proteins are typically quantified from measurements with soluble fragments, under conditions that differ radically from the confined microenvironment of membrane bound proteins in adhesion zones. Using classical cadherin as a model adhesion protein, we tested the postulate that confinement within quasi two-dimensional intercellular gaps exposes weak protein interactions that are not detected in solution binding assays. Micropipette-based measurements of cadherin-mediated, cell-cell binding kinetics identified a unique kinetic signature that reflects both adhesive (trans) bonds between cadherins on opposing cells and lateral (cis) interactions between cadherins on the same cell. In solution, proposed lateral interactions were not detected, even at high cadherin concentrations. Mutations postulated to disrupt lateral cadherin association altered the kinetic signatures, but did not affect the adhesive (trans) binding affinity. Perturbed kinetics further coincided with altered cadherin distributions at junctions, wound healing dynamics, and paracellular permeability. Intercellular binding kinetics thus revealed cadherin interactions that occur within confined, intermembrane gaps but not in solution. Findings further demonstrate the impact of these revealed interactions on the organization and function of intercellular junctions. PMID:27009566

Velocity persistence of Brownian particles generated in a glow discharge

NASA Astrophysics Data System (ADS)

Hurd, Alan J.; Ho, Pauline

1989-06-01

Quasielastic light scattering from Brownian particles in the rarefied environment of a glow discharge exhibits Gaussianlike intensity correlation functions owing to the long mean free paths of the particles. The shape of the correlation function depends on the particles' average thermal velocity and friction coefficient, which can be related to aggregate mass and structure, and indicates a crossover from kinetic to hydrodynamic behavior.

Anomalous fast diffusion in Cu-NiFe nanolaminates.

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

Jankowski, Alan F.

2017-09-01

For this work, the decomposition of the one-dimensional composition wave in Cu-NiFe nanolaminate structures is examined using x-ray diffraction to assess the kinetics of phase decomposition. The anomalously high diffusivity value found for long-term aging at room temperature is attributed to the inherent nanostructure that features paths for short-circuit diffusion in nanolaminates as attributed to interlayer grain boundaries.

Interfacial reactions between metal and gallium arsenide

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

Lin, J.C.; Schulz, K.J.; Hsieh, K.C.

1989-10-01

The phase formation sequence for GaAs/metal ternary diffusion couples is discussed. The diffusion path concept is introduced and is used with the phase diagram to understand interfacial reactions between GaAs and metal. The correlation between growth kinetics and interface morphology is discussed. Studies of bulk and thin film couples in two systems, GaAs/Pd and GaAs/Pt, are given to illustrate these concepts.

Quantitative studies of kinetic effects in direct- and indirect-drive Inertial Confinement Fusion implosions

NASA Astrophysics Data System (ADS)

Rinderknecht, Hans

2013-10-01

A comprehensive set of experiments using shock-driven implosions has been conducted to quantitatively study kinetic effects by exploring deviations from hydrodynamic behavior in plasmas relevant to inertial confinement fusion (ICF). Two types of targets were imploded at OMEGA to create ~10 keV, ~1022 cm-3 plasmas with conditions comparable to the incipient hotspot in ignition designs: thin-glass targets filled with mixtures of D2 and 3He gas; and thin deuterated-plastic shells filled with 3He. In the thin-glass experiments, the gas pressure was varied from 1 to 25 atm to scan the ion-mean-free path in the plasma at shock burn. The observed nuclear yields and temperatures deviated more strongly from hydrodynamic predictions as the ion-mean-free path increased to the order of the plasma size. This result provides the first direct experimental evidence how kinetic effects impact yields and ion temperature. The ratio of D to 3He was also varied while maintaining the fuel mass density. As the D fraction was reduced, the DD and D3He fusion products displayed an anomalous yield reduction. Separation of the D and 3He ion species across the strong (Mach ~10) shock-front will be discussed as the likely cause of this result. Finally, thin-CD shells filled with 3He produced significantly more D3He-protons when imploded than is explained by hydrodynamic mix models. This result suggests a kinetic form of mix dominates at the strongly-shocked shell-gas interface. This work was performed in collaboration with C. Li, M. Rosenberg, A. Zylstra, H. Sio, M. Gatu Johnson, F. Séguin, J. Frenje, and R. Petrasso (MIT), V. Glebov, C. Stoeckl, J. Delettrez, and C. Sangster (LLE), J. Pino, P. Amendt, C. Bellei, and S. Wilks (LLNL), G. Kagan, N. Hoffmann and K. Molvig (LANL), and A. Nikroo (GA) and was supported in part by the NLUF, FSC/UR, U.S. DOE, LLNL and LLE.

MODIFIED PATH METHODOLOGY FOR OBTAINING INTERVAL-SCALED POSTURAL ASSESSMENTS OF FARMWORKERS.

PubMed

Garrison, Emma B; Dropkin, Jonathan; Russell, Rebecca; Jenkins, Paul

2018-01-29

Agricultural workers perform tasks that frequently require awkward and extreme postures that are associated with musculoskeletal disorders (MSDs). The PATH (Posture, Activity, Tools, Handling) system currently provides a sound methodology for quantifying workers' exposure to these awkward postures on an ordinal scale of measurement, which places restrictions on the choice of analytic methods. This study reports a modification of the PATH methodology that instead captures these postures as degrees of flexion, an interval-scaled measurement. Rather than making live observations in the field, as in PATH, the postural assessments were performed on photographs using ImageJ photo analysis software. Capturing the postures in photographs permitted more careful measurement of the degrees of flexion. The current PATH methodology requires that the observer in the field be trained in the use of PATH, whereas the single photographer used in this modification requires only sufficient training to maintain the proper camera angle. Ultimately, these interval-scale measurements could be combined with other quantitative measures, such as those produced by electromyograms (EMGs), to provide more sophisticated estimates of future risk for MSDs. Further, these data can provide a baseline from which the effects of interventions designed to reduce hazardous postures can be calculated with greater precision. Copyright© by the American Society of Agricultural Engineers.

Whole Body Creatine and Protein Kinetics in Healthy Men and Women: Effects of creatine and amino acid supplementation

PubMed Central

Kalhan, Satish C; Gruca, Lourdes; Marczewski, Susan; Bennett, Carole; Kummitha, China

2015-01-01

Creatine kinetics were measured in young healthy subjects, eight males and seven females, age 20–30 years, after an overnight fast on creatine free diet. Whole body turnover of glycine and its appearance in creatine was quantified using [1-13C] glycine and the rate of protein turnover was quantified using L-ring [2H5] phenylalanine. The creatine pool size was estimated by the dilution of a bolus [C2H3] creatine. Studies were repeated following a five days supplement creatine 21g.day−1 and following supplement amino acids 14.3 g.day−1. Creatine caused a ten folds increase in the plasma concentration of creatine and a 50% decrease in the concentration of guanidinoacetic acid. Plasma amino acids profile showed a significant decrease in glycine, glutamine and taurine and a significant increase in citrulline, valine, lysine and cysteine. There was a significant decrease in the rate of appearance of glycine, suggesting a decrease in de-novo synthesis (p=0.006). The fractional and absolute rate of synthesis of creatine was significantly decreased by supplemental creatine. Amino acid supplement had no impact on any of the parameters. Creatine supplement caused a significant decrease in the rate of synthesis of creatine. This is the first detailed analysis of creatine kinetics and the effects of creatine supplement in healthy young men and women. These methods can be applied for the analysis of creatine kinetics in different physiological states. PMID:26480831

A low-cost Mr compatible ergometer to assess post-exercise phosphocreatine recovery kinetics.

PubMed

Naimon, Niels D; Walczyk, Jerzy; Babb, James S; Khegai, Oleksandr; Che, Xuejiao; Alon, Leeor; Regatte, Ravinder R; Brown, Ryan; Parasoglou, Prodromos

2017-06-01

To develop a low-cost pedal ergometer compatible with ultrahigh (7 T) field MR systems to reliably quantify metabolic parameters in human lower leg muscle using phosphorus magnetic resonance spectroscopy. We constructed an MR compatible ergometer using commercially available materials and elastic bands that provide resistance to movement. We recruited ten healthy subjects (eight men and two women, mean age ± standard deviation: 32.8 ± 6.0 years, BMI: 24.1 ± 3.9 kg/m 2 ). All subjects were scanned on a 7 T whole-body magnet. Each subject was scanned on two visits and performed a 90 s plantar flexion exercise at 40% maximum voluntary contraction during each scan. During the first visit, each subject performed the exercise twice in order for us to estimate the intra-exam repeatability, and once during the second visit in order to estimate the inter-exam repeatability of the time constant of phosphocreatine recovery kinetics. We assessed the intra and inter-exam reliability in terms of the within-subject coefficient of variation (CV). We acquired reliable measurements of PCr recovery kinetics with an intra- and inter-exam CV of 7.9% and 5.7%, respectively. We constructed a low-cost pedal ergometer compatible with ultrahigh (7 T) field MR systems, which allowed us to quantify reliably PCr recovery kinetics in lower leg muscle using 31 P-MRS.

Quantifying Nanoparticle Internalization Using a High Throughput Internalization Assay.

PubMed

Mann, Sarah K; Czuba, Ewa; Selby, Laura I; Such, Georgina K; Johnston, Angus P R

2016-10-01

The internalization of nanoparticles into cells is critical for effective nanoparticle mediated drug delivery. To investigate the kinetics and mechanism of internalization of nanoparticles into cells we have developed a DNA molecular sensor, termed the Specific Hybridization Internalization Probe - SHIP. Self-assembling polymeric 'pHlexi' nanoparticles were functionalized with a Fluorescent Internalization Probe (FIP) and the interactions with two different cell lines (3T3 and CEM cells) were studied. The kinetics of internalization were quantified and chemical inhibitors that inhibited energy dependent endocytosis (sodium azide), dynamin dependent endocytosis (Dyngo-4a) and macropinocytosis (5-(N-ethyl-N-isopropyl) amiloride (EIPA)) were used to study the mechanism of internalization. Nanoparticle internalization kinetics were significantly faster in 3T3 cells than CEM cells. We have shown that ~90% of the nanoparticles associated with 3T3 cells were internalized, compared to only 20% of the nanoparticles associated with CEM cells. Nanoparticle uptake was via a dynamin-dependent pathway, and the nanoparticles were trafficked to lysosomal compartments once internalized. SHIP is able to distinguish between nanoparticles that are associated on the outer cell membrane from nanoparticles that are internalized. This study demonstrates the assay can be used to probe the kinetics of nanoparticle internalization and the mechanisms by which the nanoparticles are taken up by cells. This information is fundamental for engineering more effective nanoparticle delivery systems. The SHIP assay is a simple and a high-throughput technique that could have wide application in therapeutic delivery research.

Thermally Stable Ni-rich Austenite Formed Utilizing Multistep Intercritical Heat Treatment in a Low-Carbon 10 Wt Pct Ni Martensitic Steel

NASA Astrophysics Data System (ADS)

Jain, Divya; Isheim, Dieter; Zhang, Xian J.; Ghosh, Gautam; Seidman, David N.

2017-08-01

Austenite reversion and its thermal stability attained during the transformation is key to enhanced toughness and blast resistance in transformation-induced-plasticity martensitic steels. We demonstrate that the thermal stability of Ni-stabilized austenite and kinetics of the transformation can be controlled by forming Ni-rich regions in proximity of pre-existing (retained) austenite. Atom probe tomography (APT) in conjunction with thermodynamic and kinetic modeling elucidates the role of Ni-rich regions in enhancing growth kinetics of thermally stable austenite, formed utilizing a multistep intercritical ( Quench- Lamellarization- Tempering (QLT)-type) heat treatment for a low-carbon 10 wt pct Ni steel. Direct evidence of austenite formation is provided by dilatometry, and the volume fraction is quantified by synchrotron X-ray diffraction. The results indicate the growth of nm-thick austenite layers during the second intercritical tempering treatment (T-step) at 863 K (590 °C), with austenite retained from first intercritical treatment (L-step) at 923 K (650 °C) acting as a nucleation template. For the first time, the thermal stability of austenite is quantified with respect to its compositional evolution during the multistep intercritical treatment of these steels. Austenite compositions measured by APT are used in combination with the thermodynamic and kinetic approach formulated by Ghosh and Olson to assess thermal stability and predict the martensite-start temperature. This approach is particularly useful as empirical relations cannot be extrapolated for the highly Ni-enriched austenite investigated in the present study.

Stable isotope tracer dilution for quantifying very low-density lipoprotein-triacylglycerol kinetics in man.

PubMed

Sidossis, Labros S; Magkos, Faidon; Mittendorfer, Bettina; Wolfe, Robert R

2004-08-01

A number of approaches have been employed in the past to measure very low-density lipoprotein (VLDL) triacylglycerol (TG) kinetics in humans in vivo, varying in the selection of tracer and mode of administration. All, however, make use of labeled TG precursors and more or less complicated mathematical models to derive the kinetic parameters of interest. The aim of the present study was to develop a conceptually straightforward method, based on the traditional tracer infusion technique, for quantifying VLDL-TG production rates in man using stable isotopes. Our approach involves ingestion of [U-13C3]glycerol to endogenously label the glycerol in VLDL-TG, plasmapheresis, isolation of the newly 13C-labeled VLDL from plasma, and administration within the next 2-3 days via a primed constant autologous reinfusion. This procedure produces enough tracer for a priming dose plus 2-3 h of infusion. In the physiological conditions examined (basal and hyperglycemic states, fat- and carbohydrate-rich diets), with almost 3-fold ranging VLDL-TG pool sizes, a steady state in plasma VLDL-TG glycerol tracer-to-tracee ratio was readily achieved within 2 h. Consequently, calculations are made according to the isotope dilution principle, thus avoiding assumptions implicit in more complicated models. The stable isotope VLDL-TG tracer dilution method offers an alternative and reliable tool for the determination of endogenous VLDL-TG kinetics in man under a variety of metabolic states. Copyright 2003 Elsevier Ltd.

A Kinetic Model Describing Injury-Burden in Team Sports.

PubMed

Fuller, Colin W

2017-12-01

Injuries in team sports are normally characterised by the incidence, severity, and location and type of injuries sustained: these measures, however, do not provide an insight into the variable injury-burden experienced during a season. Injury burden varies according to the team's match and training loads, the rate at which injuries are sustained and the time taken for these injuries to resolve. At the present time, this time-based variation of injury burden has not been modelled. To develop a kinetic model describing the time-based injury burden experienced by teams in elite team sports and to demonstrate the model's utility. Rates of injury were quantified using a large eight-season database of rugby injuries (5253) and exposure (60,085 player-match-hours) in English professional rugby. Rates of recovery from injury were quantified using time-to-recovery analysis of the injuries. The kinetic model proposed for predicting a team's time-based injury burden is based on a composite rate equation developed from the incidence of injury, a first-order rate of recovery from injury and the team's playing load. The utility of the model was demonstrated by examining common scenarios encountered in elite rugby. The kinetic model developed describes and predicts the variable injury-burden arising from match play during a season of rugby union based on the incidence of match injuries, the rate of recovery from injury and the playing load. The model is equally applicable to other team sports and other scenarios.

A common-path phase-shift interferometry surface plasmon imaging system

NASA Astrophysics Data System (ADS)

Su, Y.-T.; Chen, Shean-Jen; Yeh, T.-L.

2005-03-01

A biosensing imaging system is proposed based on the integration of surface plasmon resonance (SPR) and common-path phase-shift interferometry (PSI) techniques to measure the two-dimensional spatial phase variation caused by biomolecular interactions upon a sensing chip. The SPR phase imaging system can offer high resolution and high-throughout screening capabilities to analyze microarray biomolecular interaction without the need for additional labeling. With the long-term stability advantage of the common-path PSI technique even with external disturbances such as mechanical vibration, buffer flow noise, and laser unstable issue, the system can match the demand of real-time kinetic study for biomolecular interaction analysis (BIA). The SPR-PSI imaging system has achieved a detection limit of 2×10-7 refraction index change, a long-term phase stability of 2.5x10-4π rms over four hours, and a spatial phase resolution of 10-3 π with a lateral resolution of 100μm.

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

Kinetic Studies of Imidazoles in Tropospheric Aqueous-Phase Chemistry: Photochemistry of Imidazole-2-carboxaldehyde and Oxidation Reaction with Hydroxyl Radicals

NASA Astrophysics Data System (ADS)

Felber, T.; Otto, T.; Herrmann, H.

2017-12-01

The formation of imidazoles via the reaction of dicarbonyls with nitrogen containing compounds in the atmosphere and their potential to act as photosensitizers possibly initiating secondary organic aerosol (SOA) growth is a field of increasing activity. A recent field study quantified and qualified imidazoles in ambient aerosol samples from Europe and China. However, kinetic data and mechanisms of particle-phase reactions involving imidazoles are still scarce. In this study, kinetic measurements were investigated using laser flash photolysis-laser long path absorption (LFP-LLPA). Quenching rate constants for the reactions of the excited triplet state of imidazole-2-carboxaldehyde (IC) with bromide anion (kq = (1.6 ± 0.3) × 107 L mol-1 s-1), oxygen (kq = (2.5 ± 0.07) × 109 L mol-1 s-1), and formic acid (kq = (8.8 ± 0.5) × 109 L mol-1 s-1) are determined. IC is efficiently quenched by oxygen and formic acid. Furthermore, the quenching reaction of IC with isopropanol is investigated and compared to the reaction with formic acid to propose a preliminary mechanism of photosensitized reactions of IC with organic compounds. It is suggested that an electron transfer occurs, as it is the case for inorganics. Furthermore, rate constants of hydroxyl (OH) radical oxidation reactions with different imidazoles were determined. Following rate constants are obtained at a temperature of 298 K: k(imidazole-2-carboxaldehyde) = (3.3 ± 1.3) × 109 L mol-1 s-1, k(1-methylimidazolium hydrogen sulfate) = (2.7 ± 0.2) × 109 L mol-1 s-1, k(2-methylimidazole) = (5.4 ± 0.2) × 109 L mol-1 s-1, k(4(5)-methylimidazole) = (5.1 ± 0.3) × 109 L mol-1 s-1, k(1-ethylimidazole) = (3.0 ± 0.3) × 109 L mol-1 s-1, k(2-ethylimidazole) = (5.0 ± 0.2) × 109 L mol-1 s-1. The OH radical reaction rate constants of imidazoles are in the same range as for non-heteroaromatic compounds. Therefore, imidazoles can be expected to exist just for a limited time in the atmosphere (τ = 16 - 29 hours) after their formation. The received kinetic data will be added into model studies to evaluate the importance of aqueous-phase chemistry of imidazoles for atmospheric processes as well as the impact of photosensitized reactions on atmospheric particles possibly contributing to SOA formation.

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.

Measuring edge-of-field water quality: Where we have been and the path forward

USDA-ARS?s Scientific Manuscript database

Heightened pressure to demonstrate the resource benefits of conservation practices and continued high-profile water quality impairments and concerns are increasing the need to quantify edge-of-field water quality. With this in mind, this manuscript summarizes previous developments in edge-of-field ...

Application of a Transient Storage Zone Model o Soil Pipeflow Tracer Injection Experiments

USDA-ARS?s Scientific Manuscript database

Soil pipes, defined here as discrete preferential flow paths generally parallel to the slope, are important subsurface flow pathways that play a role in many soil erosion phenomena. However, limited research has been performed on quantifying and characterizing their flow and transport characteristic...

Soil pipe flow tracer experiments: 2. Application of a transient storage zone model

USDA-ARS?s Scientific Manuscript database

Soil pipes, defined here as discrete preferential flow paths generally parallel to the slope, are important subsurface flow pathways that play a role in many soil erosion phenomena. However, limited research has been performed on quantifying and characterizing their flow and transport characteristic...

Towards Quantifying Programmable Logic Controller Resilience Against Intentional Exploits

DTIC Science & Technology

2012-03-22

may improve the SCADA system’s resilience against DoS and man-in-the-middle ( MITM ) attacks. DoS attacks may be mitigated by using the redundant...paths available on the network links. MITM attacks may be mitigated by the data integrity checks associated with the middleware. Figure 4 illustrates

Kinetic analysis of a monoclonal therapeutic antibody and its single-chain homolog by surface plasmon resonance.

PubMed

Patel, Rekha; Andrien, Bruce A

2010-01-01

Monoclonal antibodies (mAbs) and antibody fragments have become an emerging class of therapeutics since 1986. Their versatility enables them to be engineered for optimal efficiency and decreased immunogenicity, and the path to market has been set by recent regulatory approvals. One of the initial criteria for success of any protein or antibody therapeutic is to understand its binding characteristics to the target antigen. Surface plasmon resonance (SPR) has been widely used and is an important tool for ligand-antigen binding characterization. In this work, the binding kinetics of a recombinant mAb and its single-chain antibody homolog, single-chain variable fragment (scFv), was analyzed by SPR. These two proteins target the same antigen. The binding kinetics of the mAb (bivalent antibody) and scFv (monovalent scFv) for this antigen was analyzed along with an assessment of the thermodynamics of the binding interactions. Alternative binding configurations were investigated to evaluate potential experimental bias because theoretically experimental binding configuration should have no impact on binding kinetics. Self-association binding kinetics in the proteins' respective formulation solutions and antigen epitope mapping were also evaluated. Functional characterization of monoclonal and single-chain antibodies has become just as important as structural characterization in the biotechnology field.

Maximum proton kinetic energy and patient-generated neutron fluence considerations in proton beam arc delivery radiation therapy.

PubMed

Sengbusch, E; Pérez-Andújar, A; DeLuca, P M; Mackie, T R

2009-02-01

Several compact proton accelerator systems for use in proton therapy have recently been proposed. Of paramount importance to the development of such an accelerator system is the maximum kinetic energy of protons, immediately prior to entry into the patient, that must be reached by the treatment system. The commonly used value for the maximum kinetic energy required for a medical proton accelerator is 250 MeV, but it has not been demonstrated that this energy is indeed necessary to treat all or most patients eligible for proton therapy. This article quantifies the maximum kinetic energy of protons, immediately prior to entry into the patient, necessary to treat a given percentage of patients with rotational proton therapy, and examines the impact of this energy threshold on the cost and feasibility of a compact, gantry-mounted proton accelerator treatment system. One hundred randomized treatment plans from patients treated with IMRT were analyzed. The maximum radiological pathlength from the surface of the patient to the distal edge of the treatment volume was obtained for 180 degrees continuous arc proton therapy and for 180 degrees split arc proton therapy (two 90 degrees arcs) using CT# profiles from the Pinnacle (Philips Medical Systems, Madison, WI) treatment planning system. In each case, the maximum kinetic energy of protons, immediately prior to entry into the patient, that would be necessary to treat the patient was calculated using proton range tables for various media. In addition, Monte Carlo simulations were performed to quantify neutron production in a water phantom representing a patient as a function of the maximum proton kinetic energy achievable by a proton treatment system. Protons with a kinetic energy of 240 MeV, immediately prior to entry into the patient, were needed to treat 100% of patients in this study. However, it was shown that 90% of patients could be treated at 198 MeV, and 95% of patients could be treated at 207 MeV. Decreasing the proton kinetic energy from 250 to 200 MeV decreases the total neutron energy fluence produced by stopping a monoenergetic pencil beam in a water phantom by a factor of 2.3. It is possible to significantly lower the requirements on the maximum kinetic energy of a compact proton accelerator if the ability to treat a small percentage of patients with rotational therapy is sacrificed. This decrease in maximum kinetic energy, along with the corresponding decrease in neutron production, could lower the cost and ease the engineering constraints on a compact proton accelerator treatment facility.

SensiPath: computer-aided design of sensing-enabling metabolic pathways.

PubMed

Delépine, Baudoin; Libis, Vincent; Carbonell, Pablo; Faulon, Jean-Loup

2016-07-08

Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Effect of Slag Composition on the Crystallization Kinetics of Synthetic CaO-SiO2-Al2O3-MgO Slags

NASA Astrophysics Data System (ADS)

Esfahani, Shaghayegh; Barati, Mansoor

2018-04-01

The crystallization kinetics of CaO-SiO2-Al2O3-MgO (CSAM) slags was studied with the aid of single hot thermocouple technique (SHTT). Kinetic parameters such as the Avrami exponent ( n), rate coefficient ( K), and effective activation energy of crystallization ( E A ) were obtained by kinetic analysis of data obtained from in situ observation of glassy to crystalline transformation and image analysis. Also, the dependence of nucleation and growth rates of crystalline phases were quantified as a function of time, temperature, and slag basicity. Together with the observations of crystallization front, they facilitated establishing the dominant mechanisms of crystallization. In an attempt to predict crystallization rate under non-isothermal conditions, a mathematical model was developed that employs the rate data of isothermal transformation. The model was validated by reproducing an experimental continuous cooling transformation diagram purely from isothermal data.

Self-adaptive enhanced sampling in the energy and trajectory spaces: accelerated thermodynamics and kinetic calculations.

PubMed

Gao, Yi Qin

2008-04-07

Here, we introduce a simple self-adaptive computational method to enhance the sampling in energy, configuration, and trajectory spaces. The method makes use of two strategies. It first uses a non-Boltzmann distribution method to enhance the sampling in the phase space, in particular, in the configuration space. The application of this method leads to a broad energy distribution in a large energy range and a quickly converged sampling of molecular configurations. In the second stage of simulations, the configuration space of the system is divided into a number of small regions according to preselected collective coordinates. An enhanced sampling of reactive transition paths is then performed in a self-adaptive fashion to accelerate kinetics calculations.

Determination of in vivo RNA kinetics using RATE-seq.

PubMed

Neymotin, Benjamin; Athanasiadou, Rodoniki; Gresham, David

2014-10-01

The abundance of a transcript is determined by its rate of synthesis and its rate of degradation; however, global methods for quantifying RNA abundance cannot distinguish variation in these two processes. Here, we introduce RNA approach to equilibrium sequencing (RATE-seq), which uses in vivo metabolic labeling of RNA and approach to equilibrium kinetics, to determine absolute RNA degradation and synthesis rates. RATE-seq does not disturb cellular physiology, uses straightforward normalization with exogenous spike-ins, and can be readily adapted for studies in most organisms. We demonstrate the use of RATE-seq to estimate genome-wide kinetic parameters for coding and noncoding transcripts in Saccharomyces cerevisiae. © 2014 Neymotin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Antibody escape kinetics of equine infectious anemia virus infection of horses.

PubMed

Schwartz, Elissa J; Nanda, Seema; Mealey, Robert H

2015-07-01

Lentivirus escape from neutralizing antibodies (NAbs) is not well understood. In this work, we quantified antibody escape of a lentivirus, using antibody escape data from horses infected with equine infectious anemia virus. We calculated antibody blocking rates of wild-type virus, fitness costs of mutant virus, and growth rates of both viruses. These quantitative kinetic estimates of antibody escape are important for understanding lentiviral control by antibody neutralization and in developing NAb-eliciting vaccine strategies. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Real-time monitoring of enzyme activity in a mesoporous silicon double layer

PubMed Central

Orosco, Manuel M.; Pacholski, Claudia; Sailor, Michael J.

2009-01-01

A double layer mesoporous silicon with different pore sizes functions as a nano-reactor that can isolate, filter and quantify the kinetics of enzyme reactions in real-time by optical reflectivity. This tiny reactor may be used to rapidly characterize a variety of isolated enzymes in a label-free manner. Activity of certain protease enzymes is often an indicator of disease states such as cancer1,2, stroke2, and neurodegeneracy3, and thus, there is a need for rapid assays that can characterize the kinetics and substrate specificity of enzymatic reactions. Nanostructured membranes can efficiently separate biomolecules4 but coupling a sensitive detection method remains difficult. Here we report a single mesoporous nano-reactor that can isolate and quantify in real-time the reaction products of proteases. The reactor consists of two layers of porous films electrochemically prepared from crystalline silicon. The upper layer with large pore sizes traps the protease enzymes and acts as the reactor while the lower layer with smaller pore sizes excludes the large proteins and captures the reaction products. Infiltration of the digested fragments into the lower layer produces a measurable change in optical reflectivity and this allows label-free quantification of enzyme kinetics in real-time within a volume of approximately 5 nanoliters. PMID:19350037

Quantification of Protein-Induced Membrane Remodeling Kinetics In Vitro with Lipid Multilayer Gratings

PubMed Central

Lowry, Troy W.; Hariri, Hanaa; Prommapan, Plengchart; Kusi-Appiah, Aubrey; Vafai, Nicholas; Bienkiewicz, Ewa A.; Van Winkle, David H.; Stagg, Scott M.

2016-01-01

The dynamic self-organization of lipids in biological systems is a highly regulated process that enables the compartmentalization of living systems at micro- and nanoscopic scales. Consequently, quantitative methods for assaying the kinetics of supramolecular remodeling such as vesicle formation from planar lipid bilayers or multilayers are needed to understand cellular self-organization. Here, a new nanotechnology-based method for quantitative measurements of lipid–protein interactions is presented and its suitability for quantifying the membrane binding, inflation, and budding activity of the membrane-remodeling protein Sar1 is demonstrated. Lipid multilayer gratings are printed onto surfaces using nanointaglio and exposed to Sar1, resulting in the inflation of lipid multilayers into unilamellar structures, which can be observed in a label-free manner by monitoring the diffracted light. Local variations in lipid multilayer volume on the surface is used to vary substrate availability in a microarray format. A quantitative model is developed that allows quantification of binding affinity (KD) and kinetics (kon and koff). Importantly, this assay is uniquely capable of quantifying membrane remodeling. Upon Sar1-induced inflation of single bilayers from surface supported multilayers, the semicylindrical grating lines are observed to remodel into semispherical buds when a critical radius of curvature is reached. PMID:26649649

Suitability of [18F]altanserin and PET to determine 5-HT2A receptor availability in the rat brain: in vivo and in vitro validation of invasive and non-invasive kinetic models.

PubMed

Kroll, Tina; Elmenhorst, David; Matusch, Andreas; Wedekind, Franziska; Weisshaupt, Angela; Beer, Simone; Bauer, Andreas

2013-08-01

While the selective 5-hydroxytryptamine type 2a receptor (5-HT2AR) radiotracer [18F]altanserin is well established in humans, the present study evaluated its suitability for quantifying cerebral 5-HT2ARs with positron emission tomography (PET) in albino rats. Ten Sprague Dawley rats underwent 180 min PET scans with arterial blood sampling. Reference tissue methods were evaluated on the basis of invasive kinetic models with metabolite-corrected arterial input functions. In vivo 5-HT2AR quantification with PET was validated by in vitro autoradiographic saturation experiments in the same animals. Overall brain uptake of [18F]altanserin was reliably quantified by invasive and non-invasive models with the cerebellum as reference region shown by linear correlation of outcome parameters. Unlike in humans, no lipophilic metabolites occurred so that brain activity derived solely from parent compound. PET data correlated very well with in vitro autoradiographic data of the same animals. [18F]Altanserin PET is a reliable tool for in vivo quantification of 5-HT2AR availability in albino rats. Models based on both blood input and reference tissue describe radiotracer kinetics adequately. Low cerebral tracer uptake might, however, cause restrictions in experimental usage.

Total Kinetic Energy and Fragment Mass Distribution of Neutron-Induced Fission of U-233

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

Higgins, Daniel James; Schmitt, Kyle Thomas; Mosby, Shea Morgan

Properties of fission in U-233 were studied at the Los Alamos Neutron Science Center (LANSCE) at incident neutron energies from thermal to 40 MeV at both the Lujan Neutron Scattering Center flight path 12 and at WNR flight path 90-Left from Dec 2016 to Jan 2017. Fission fragments are observed in coincidence using a twin ionization chamber with Frisch grids. The average total kinetic energy (TKE) released from fission and fragment mass distributions are calculated from observations of energy deposited in the detector and conservation of mass and momentum. Accurate experimental measurements of these parameters are necessary to better understandmore » the fission process and obtain data necessary for calculating criticality. The average TKE released from fission has been well characterized for several isotopes at thermal neutron energy, however, few measurements have been made at fast neutron energies. This experiment expands on previous successful experiments using an ionization chamber to measure TKE and fragment mass distributions of U-235, U-238, and Pu-239. This experiment requires the full spectrum of neutron energies and can therefore only be performed at a small number of facilities in the world. The required full neutron energy spectrum is obtained by combining measurements from WNR 90L and Lujan FP12 at LANSCE.« less

Error Reduction Methods for Integrated-path Differential-absorption Lidar Measurements

NASA Technical Reports Server (NTRS)

Chen, Jeffrey R.; Numata, Kenji; Wu, Stewart T.

2012-01-01

We report new modeling and error reduction methods for differential-absorption optical-depth (DAOD) measurements of atmospheric constituents using direct-detection integrated-path differential-absorption lidars. Errors from laser frequency noise are quantified in terms of the line center fluctuation and spectral line shape of the laser pulses, revealing relationships verified experimentally. A significant DAOD bias is removed by introducing a correction factor. Errors from surface height and reflectance variations can be reduced to tolerable levels by incorporating altimetry knowledge and "log after averaging", or by pointing the laser and receiver to a fixed surface spot during each wavelength cycle to shorten the time of "averaging before log".

Method and an apparatus to control the lateral motion of a long metal bar being formed by a mechanical process such as rolling or drawing

DOEpatents

Chang, Tzyy-Shuh; Huang, Hsun-Hau; Lin, Chang-Hung

2007-10-02

An adjustable guide, includes two or more mechanisms each having a rotatable retaining element containing a retaining groove with a variable radius in its perimeter surface. The grooves form a guidance path to control the lateral, i.e. non-axial, motion of a long bar moving along a longitudinal axis during a production process.The diameter of the guidance path varies according to the variable radii of the grooves. The guidance path increases in size at a predetermined rate, from a point of origin to an end point on the retaining groove. Rotating the retaining elements causes the diameter of the retaining grooves to change so that the size of the guidance path can be changed to match the diameter of the bar being rolled, size of the guidance path can be changed to fit the diameter of a new bar rolled without having to exchange the guide for a different sized guide, reduce fiction between the bar and the guide, a media, such as compressed air, can be injected between the retaining elements via orifices.Each retaining element is attached to a mounting apparatus. The mounting apparatus can be fixed or flexible. The flexible mounting apparatus includes one or more springs and one or more shock absorbers. A force neutral position of the flexible mounting apparatus is designed to be located on the predetermined ideal bar path line. The flexible mounting apparatus dissipates kinetic energy from the bar thereby reducing the bar's lateral motion relative to the ideal bar path line.The damping ratio of the mounting apparatus can be adjustable to alter the product's vibration mode to enable better control of the bar's lateral motion.

The precipitation of gypsum, celestine, and barite and coprecipitation of radium during seawater evaporation

NASA Astrophysics Data System (ADS)

Rosenberg, Yoav Oved; Sade, Ziv; Ganor, Jiwchar

2018-07-01

While the precipitation paths of the major ions (i.e., Ca2+, Na+, K+, Cl- and SO42-) during seawater evaporation have been extensively studied, the precipitation of minor solutes from evaporated seawater was not thoroughly studied. The present study aims to achieve a quantitative understanding of Sr2+, Ba2+ and Ra2+ removal from evaporated seawater, by exploring in-situ evaporation of seawater in a series of ponds of a salt plant. Seawater samples, at various degrees of evaporation, were collected and analyzed for their solute concentrations. Mass balance and thermodynamic calculations were performed for each sample, revealing that the evaporated seawater remained oversaturated with respect to the three sulphate minerals: gypsum, celestine and barite, for a considerable period before precipitation commenced. In view of this observation, the results are discussed within the framework of the classical nucleation theory. It is hypothesized that the precipitation of these minerals is kinetically hindered by surface area starvation which, in turn, causes the nucleation of these minerals to be the rate determining step. The removal of Ra commences in concordance with the precipitation of Sr and Ba, suggesting that Ra removal is controlled by the formation of a solid solution. Although a ternary solid solution of RaxBaySr1-x-ySO4 actually precipitates, the removal of Ra was modeled by the precipitation of a binary solid solution of RaxBa1-xSO4. Using empirical law from the literature, the removal of Ra could be modeled fairly well. The model suggests that the removal of Ra in evaporated seawater is hindered in comparison to low ionic strength solutions. This inhibition is a result of: 1. The high ionic strength (up to 10.8 mol kg-1); and 2. Precipitation kinetics that may be quantified by the degree of supersaturation with respect to end-member barite in the evaporated seawater (up to 51).

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

A model for the kinetics of a solar-pumped long path laser experiment

NASA Technical Reports Server (NTRS)

Stock, L. V.; Wilson, J. W.; Deyoung, R. J.

1986-01-01

A kinetic model for a solar-simulator pumped iodine laser system is developed and compared to an experiment in which the solar simulator output is dispersed over a large active volume (150 cu cm) with low simulator light intensity (approx. 200 solar constants). A trace foreign gas which quenches the upper level is introduced into the model. Furthermore, a constant representing optical absorption of the stimulated emission is introduced, in addition to a constant representing the scattering at each of the mirrors, via the optical cavity time constant. The non-uniform heating of the gas is treated as well as the pressure change as a function of time within the cavity. With these new phenomena introduced into the kinetic model, a best reasonable fit to the experimental data is found by adjusting the reaction rate coefficients within the range of known uncertainty by numerical methods giving a new bound within this range of uncertainty. The experimental parameters modeled are the lasing time, laser pulse energy, and time to laser threshold.

Monte Carlo simulation for kinetic chemotaxis model: An application to the traveling population wave

NASA Astrophysics Data System (ADS)

Yasuda, Shugo

2017-02-01

A Monte Carlo simulation of chemotactic bacteria is developed on the basis of the kinetic model and is applied to a one-dimensional traveling population wave in a microchannel. In this simulation, the Monte Carlo method, which calculates the run-and-tumble motions of bacteria, is coupled with a finite volume method to calculate the macroscopic transport of the chemical cues in the environment. The simulation method can successfully reproduce the traveling population wave of bacteria that was observed experimentally and reveal the microscopic dynamics of bacterium coupled with the macroscopic transports of the chemical cues and bacteria population density. The results obtained by the Monte Carlo method are also compared with the asymptotic solution derived from the kinetic chemotaxis equation in the continuum limit, where the Knudsen number, which is defined by the ratio of the mean free path of bacterium to the characteristic length of the system, vanishes. The validity of the Monte Carlo method in the asymptotic behaviors for small Knudsen numbers is numerically verified.

Analysis of atmospheric flow over a surface protrusion using the turbulence kinetic energy equation with reference to aeronautical operating systems

NASA Technical Reports Server (NTRS)

Frost, W.; Harper, W. L.

1975-01-01

Flow over surface obstructions can produce significantly large wind shears such that adverse flying conditions can occur for aeronautical systems (helicopters, STOL vehicles, etc.). Atmospheric flow fields resulting from a semi-elliptical surface obstruction in an otherwise horizontally homogeneous statistically stationary flow are modelled with the boundary-layer/Boussinesq-approximation of the governing equation of fluid mechanics. The turbulence kinetic energy equation is used to determine the dissipative effects of turbulent shear on the mean flow. Iso-lines of turbulence kinetic energy and turbulence intensity are plotted in the plane of the flow and highlight regions of high turbulence intensity in the stagnation zone and sharp gradients in intensity along the transition from adverse to favourable pressure gradient. Discussion of the effects of the disturbed wind field in CTOL and STOL aircraft flight path and obstruction clearance standards is given. The results indicate that closer inspection of these presently recommended standards as influenced by wind over irregular terrains is required.

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

An empirical typology of hospital nurses' individual learning paths.

PubMed

Poell, Rob F; Van der Krogt, Ferd J

2014-03-01

A relatively new theoretical concept is proposed in this paper, namely, the individual learning path. Learning paths are created by individual employees and comprise a set of learning-relevant activities that are both coherent as a whole and meaningful to them. To explore the empirical basis of this theoretical concept. A qualitative study involving semi-structured interviews. Two academic medical centers (university hospitals) and two general hospitals in the Netherlands. A total of 89 nurses were involved in the study. Semi-structured interviews were analyzed qualitatively; cluster analysis was then performed on quantified data from the interviews. Four types of learning path emerged, namely, the formal-external, self-directed, social-emotional, and information-oriented learning paths. The relatively new theoretical concept of an individual learning path can be observed in practice and a number of different learning-path types can be distinguished. Nurses were found to create their own learning paths, that is, select a theme that is relevant primarily to themselves, conduct a variety of learning activities around this theme, participate in social contexts that might help them, and mobilize learning facilities provided by their organization. These activities go way beyond the notion of employees as self-directed learners merely in a didactic sense (establishing learning goals, choosing the right learning activities for these goals, evaluating to what extent their goals have been met as a result). The findings can be interpreted as evidence of employees acting strategically when it comes to their professional development. Providers of continuing professional education/development need to take this into account. Copyright © 2013 Elsevier Ltd. All rights reserved.

Coupled long term simulation of reach scale water and heat fluxes across the river groundwater interface and hyporheic temperature dynamics

NASA Astrophysics Data System (ADS)

Munz, Matthias; Oswald, Sascha E.; Schmidt, Christian

2017-04-01

Flow pattern and seasonal as well as diurnal temperature variations control ecological and biogeochemical conditions in hyporheic sediments. In particular, hyporheic temperatures have a great impact on many microbial processes. In this study we used 3-D coupled water flow and heat transport simulations applying the HydroGeoSphere code in combination with high frequent observations of hydraulic heads and temperatures for quantifying reach scale water and heat flux across the river groundwater interface and hyporheic temperature dynamics of a lowland gravel-bed river. The magnitude and dynamics of simulated temperatures matched the observed with an average mean absolute error of 0.7 °C and an average Nash Sutcliffe Efficiency of 0.87. Our results highlight that the average temperature in the hyporheic zone follows the temperature in the river which is characterized by distinct seasonal and daily temperature cycles. Individual hyporheic flow path temperature substantially varies around the average hyporheic temperature. Hyporheic flow path temperature was found to strongly depend on the flow path residence time and the temperature gradient between river and groundwater; that is, in winter the average flow path temperature of long flow paths is potentially higher compared to short flow paths. Based on the simulation results we derived a general empirical relationship, estimating the influence of hyporheic flow path residence time on hyporheic flow path temperature. Furthermore we used an empirical temperature relationship between effective temperature and respiration rate to estimate the influence of hyporheic flow path residence time and temperature on hyporheic oxygen consumption. This study highlights the relation between complex hyporheic temperature patterns, hyporheic residence times and their implications on temperature sensitive biogeochemical processes.

Mixing and reactions in multiphase flow through porous media

NASA Astrophysics Data System (ADS)

Jimenez-Martinez, J.; Le Borgne, T.; Meheust, Y.; Porter, M. L.; De Anna, P.; Hyman, J.; Tabuteau, H.; Turuban, R.; Carey, J. W.; Viswanathan, H. S.

2016-12-01

The understanding and quantification of flow and transport processes in multiphase systems remains a grand scientific and engineering challenge in natural and industrial systems (e.g., soils and vadose zone, CO2 sequestration, unconventional oil and gas extraction, enhanced oil recovery). Beyond the kinetic of the chemical reactions, mixing processes in porous media play a key role in controlling both fluid-fluid and fluid-solid reactions. However, conventional continuum-scale models and theories oversimplify and/or ignore many important pore-scale processes. Multiphase flows, with the creation of highly heterogeneous fluid velocity fields (i.e., low velocities regions or stagnation zones, and high velocity regions or preferential paths), makes conservative and reactive transport more complex. We present recent multi-scale experimental developments and theoretical approaches to quantify transport, mixing, and reaction and their coupling with multiphase flows. We discuss our main findings: i) the sustained concentration gradients and enhanced reactivity in a two-phase system for a continuous injection, and the comparison with a pulse line injection; ii) the enhanced mixing by a third mobile-immiscible phase; and iii) the role that capillary forces play in the localization of the fluid-solid reactions. These experimental results are for highly-idealized geometries, however, the proposed models are related to basic porous media and unsaturated flow properties, and could be tested on more complex systems.

Interannual Variation of Surface Circulation in the Japan/East Sea due to External Forcings and Intrinsic Variability

NASA Astrophysics Data System (ADS)

Choi, Byoung-Ju; Cho, Seong Hun; Jung, Hee Seok; Lee, Sang-Ho; Byun, Do-Seong; Kwon, Kyungman

2018-03-01

The interannual variation of surface ocean currents can be as large as seasonal variation in the Japan/East Sea (JES). To identify the major factors that cause such interannual variability of surface ocean circulation in the JES, surface circulation was simulated from 1998 to 2009 using a three-dimensional model. Contributions of atmospheric forcing (ATM), open boundary data (OBC), and intrinsic variability (ITV) of the surface flow in the JES on the interannual variability of surface ocean circulation were separately examined using numerical simulations. Variability in surface circulation was quantified in terms of variance in sea surface height, 100-m depth water temperature, and surface currents. ITV was found to be the dominant factor that induced interannual variabilities of surface circulation, the main path of the East Korea Warm Current (EKWC), and surface kinetic energy on a time scale of 2-4 years. OBC and ATM were secondary factors contributing to the interannual variation of surface circulation. Interannual variation of ATM changed the separation latitude of EKWC and increased the variability of surface circulation in the Ulleung Basin. Interannual variation of OBC enhanced low-frequency changes in surface circulation and eddies in the Yamato Basin. It also modulated basin-wide uniform oscillations of sea level. This study suggests that precise estimation of initial conditions using data assimilation is essential for long-term prediction of surface circulation in the JES.

Energy Optimal Path Planning: Integrating Coastal Ocean Modelling with Optimal Control

NASA Astrophysics Data System (ADS)

Subramani, D. N.; Haley, P. J., Jr.; Lermusiaux, P. F. J.

2016-02-01

A stochastic optimization methodology is formulated for computing energy-optimal paths from among time-optimal paths of autonomous vehicles navigating in a dynamic flow field. To set up the energy optimization, the relative vehicle speed and headings are considered to be stochastic, and new stochastic Dynamically Orthogonal (DO) level-set equations that govern their stochastic time-optimal reachability fronts are derived. Their solution provides the distribution of time-optimal reachability fronts and corresponding distribution of time-optimal paths. An optimization is then performed on the vehicle's energy-time joint distribution to select the energy-optimal paths for each arrival time, among all stochastic time-optimal paths for that arrival time. The accuracy and efficiency of the DO level-set equations for solving the governing stochastic level-set reachability fronts are quantitatively assessed, including comparisons with independent semi-analytical solutions. Energy-optimal missions are studied in wind-driven barotropic quasi-geostrophic double-gyre circulations, and in realistic data-assimilative re-analyses of multiscale coastal ocean flows. The latter re-analyses are obtained from multi-resolution 2-way nested primitive-equation simulations of tidal-to-mesoscale dynamics in the Middle Atlantic Bight and Shelbreak Front region. The effects of tidal currents, strong wind events, coastal jets, and shelfbreak fronts on the energy-optimal paths are illustrated and quantified. Results showcase the opportunities for longer-duration missions that intelligently utilize the ocean environment to save energy, rigorously integrating ocean forecasting with optimal control of autonomous vehicles.

Perilymph Kinetics of FITC-Dextran Reveals Homeostasis Dominated by the Cochlear Aqueduct and Cerebrospinal Fluid.

PubMed

Salt, A N; Gill, R M; Hartsock, J J

2015-06-01

Understanding how drugs are distributed in perilymph following local applications is important as local drug therapies are increasingly used to treat disorders of the inner ear. The potential contribution of cerebrospinal fluid (CSF) entry to perilymph homeostasis has been controversial for over half a century, largely due to artifactual contamination of collected perilymph samples with CSF. Measures of perilymph flow and of drug distribution following round window niche applications have both suggested a slow, apically directed flow occurs along scala tympani (ST) in the normal, sealed cochlea. In the present study, we have used fluorescein isothiocyanate-dextran as a marker to study perilymph kinetics in guinea pigs. Dextran is lost from perilymph more slowly than other substances so far quantified. Dextran solutions were injected from pipettes sealed into the lateral semicircular canal (SCC), the cochlear apex, or the basal turn of ST. After varying delays, sequential perilymph samples were taken from the cochlear apex or lateral SCC, allowing dextran distribution along the perilymphatic spaces to be quantified. Variability was low and findings were consistent with the injection procedure driving volume flow towards the cochlear aqueduct, and with volume flow during perilymph sampling driven by CSF entry at the aqueduct. The decline of dextran with time in the period between injection and sampling was consistent with both a slow volume influx of CSF (~30 nL/min) entering the basal turn of ST at the cochlear aqueduct and a CSF-perilymph exchange driven by pressure-driven fluid oscillation across the cochlear aqueduct. Sample data also allowed contributions of other processes, such as communications with adjacent compartments, to be quantified. The study demonstrates that drug kinetics in the basal turn of ST is complex and is influenced by a considerable number of interacting processes.

Effect of tillage on macropore flow and phosphorus transport to tile drains

USDA-ARS?s Scientific Manuscript database

Elevated phosphorus (P) concentrations in subsurface drainage water are thought to be the result of P bypassing the soil matrix via macropore flow. The objectives of this study were to quantify event water delivery to tile drains via macropore flow paths during storm events and to determine the effe...

The Semantic Distance Task: Quantifying Semantic Distance with Semantic Network Path Length

ERIC Educational Resources Information Center

Kenett, Yoed N.; Levi, Effi; Anaki, David; Faust, Miriam

2017-01-01

Semantic distance is a determining factor in cognitive processes, such as semantic priming, operating upon semantic memory. The main computational approach to compute semantic distance is through latent semantic analysis (LSA). However, objections have been raised against this approach, mainly in its failure at predicting semantic priming. We…

Intelligent Engine Systems: HPT Clearance Control

NASA Technical Reports Server (NTRS)

2008-01-01

The Advanced Thermally Actuated Clearance Control System underwent several studies. Improved flow path isolation quantified what can be gained by making the HPT case nearly adiabatic. The best method of heat transfer was established, and finally two different borrowed air cooling circuits were evaluated to be used for the HPT Active Clearance Control System.

Validation of a simple distributed sediment delivery approach in selected sub-basins of the River Inn catchment area

NASA Astrophysics Data System (ADS)

Reid, Lucas; Kittlaus, Steffen; Scherer, Ulrike

2015-04-01

For large areas without highly detailed data the empirical Universal Soil Loss Equation (USLE) is widely used to quantify soil loss. The problem though is usually the quantification of actual sediment influx into the rivers. As the USLE provides long-term mean soil loss rates, it is often combined with spatially lumped models to estimate the sediment delivery ratio (SDR). But it gets difficult with spatially lumped approaches in large catchment areas where the geographical properties have a wide variance. In this study we developed a simple but spatially distributed approach to quantify the sediment delivery ratio by considering the characteristics of the flow paths in the catchments. The sediment delivery ratio was determined using an empirical approach considering the slope, morphology and land use properties along the flow path as an estimation of travel time of the eroded particles. The model was tested against suspended solids measurements in selected sub-basins of the River Inn catchment area in Germany and Austria, ranging from the high alpine south to the Molasse basin in the northern part.

Assay of Calcium Transients and Synapses in Rat Hippocampal Neurons by Kinetic Image Cytometry and High-Content Analysis: An In Vitro Model System for Postchemotherapy Cognitive Impairment.

PubMed

McDonough, Patrick M; Prigozhina, Natalie L; Basa, Ranor C B; Price, Jeffrey H

2017-07-01

Postchemotherapy cognitive impairment (PCCI) is commonly exhibited by cancer patients treated with a variety of chemotherapeutic agents, including the endocrine disruptor tamoxifen (TAM). The etiology of PCCI is poorly understood. Our goal was to develop high-throughput assay methods to test the effects of chemicals on neuronal function applicable to PCCI. Rat hippocampal neurons (RHNs) were plated in 96- or 384-well dishes and exposed to test compounds (forskolin [FSK], 17β-estradiol [ES]), TAM or fulvestrant [FUL], aka ICI 182,780) for 6-14 days. Kinetic Image Cytometry™ (KIC™) methods were developed to quantify spontaneously occurring intracellular calcium transients representing the activity of the neurons, and high-content analysis (HCA) methods were developed to quantify the expression, colocalization, and puncta formed by synaptic proteins (postsynaptic density protein-95 [PSD-95] and presynaptic protein Synapsin-1 [Syn-1]). As quantified by KIC, FSK increased the occurrence and synchronization of the calcium transients indicating stimulatory effects on RHN activity, whereas TAM had inhibitory effects. As quantified by HCA, FSK also increased PSD-95 puncta and PSD-95:Syn-1 colocalization, whereas ES increased the puncta of both PSD-95 and Syn-1 with little effect on colocalization. The estrogen receptor antagonist FUL also increased PSD-95 puncta. In contrast, TAM reduced Syn-1 and PSD-95:Syn-1 colocalization, consistent with its inhibitory effects on the calcium transients. Thus TAM reduced activity and synapse formation by the RHNs, which may relate to the ability of this agent to cause PCCI. The results illustrate that KIC and HCA can be used to quantify neurotoxic and neuroprotective effects of chemicals in RHNs to investigate mechanisms and potential therapeutics for PCCI.

Exact and Approximate Probabilistic Symbolic Execution

NASA Technical Reports Server (NTRS)

Luckow, Kasper; Pasareanu, Corina S.; Dwyer, Matthew B.; Filieri, Antonio; Visser, Willem

2014-01-01

Probabilistic software analysis seeks to quantify the likelihood of reaching a target event under uncertain environments. Recent approaches compute probabilities of execution paths using symbolic execution, but do not support nondeterminism. Nondeterminism arises naturally when no suitable probabilistic model can capture a program behavior, e.g., for multithreading or distributed systems. In this work, we propose a technique, based on symbolic execution, to synthesize schedulers that resolve nondeterminism to maximize the probability of reaching a target event. To scale to large systems, we also introduce approximate algorithms to search for good schedulers, speeding up established random sampling and reinforcement learning results through the quantification of path probabilities based on symbolic execution. We implemented the techniques in Symbolic PathFinder and evaluated them on nondeterministic Java programs. We show that our algorithms significantly improve upon a state-of- the-art statistical model checking algorithm, originally developed for Markov Decision Processes.

Thermochemical and Kinetics of Hydrazine Dehydrogenation by an Oxygen Atom in Hydrazine-Rich Systems: A Dimer Model.

PubMed

Spada, Rene F K; Ferrão, Luiz F A; Roberto-Neto, Orlando; Lischka, Hans; Machado, Francisco B C

2015-12-24

The kinetics of the reaction of N2H4 with oxygen depends sensitively on the initial conditions used. In oxygen-rich systems, the rate constant shows a conventional positive temperature dependence, while in hydrazine-rich setups the dependence is negative in certain temperature ranges. In this study, a theoretical model is presented that adequately reproduces the experimental results trend and values for hydrazine-rich environment, consisting of the hydrogen abstraction from the hydrazine (N2H4) dimer by an oxygen atom. The thermochemical properties of the reaction were computed using two quantum chemical approaches, the coupled cluster theory with single, double, and noniterative triple excitations (CCSD(T)) and the M06-2X DFT approach with the aug-cc-pVTZ and the maug-cc-pVTZ basis sets, respectively. The kinetic data were calculated with the improved canonical variational theory (ICVT) using a dual-level methodology to build the reaction path. The tunneling effects were considered by means of the small curvature tunneling (SCT) approximation. Potential wells on both sides of the reaction ((N2H4)2 + O → N2H4···N2H3 + OH) were determined. A reaction path with a negative activation energy was found leading, in the temperature range of 250-423 K, to a negative dependence of the rate constant on the temperature, which is in good agreement with the experimental measurements. Therefore, the consideration of the hydrazine dimer model provides significantly improved agreement with the experimental data and should be included in the mechanism of the global N2H4 combustion process, as it can be particularly important in hydrazine-rich systems.

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.

Conceptual plural information is used to guide early parsing decisions: Evidence from garden-path sentences with reciprocal verbs.

PubMed

Patson, Nikole D; Ferreira, Fernanda

2009-05-01

In three eyetracking studies, we investigated the role of conceptual plurality in initial parsing decisions in temporarily ambiguous sentences with reciprocal verbs (e.g., While the lovers kissed the baby played alone). We varied the subject of the first clause using three types of plural noun phrases: conjoined noun phrases (the bride and the groom), plural definite descriptions (the lovers), and numerically quantified noun phrases (the two lovers). We found no evidence for garden-path effects when the subject was conjoined (Ferreira & McClure, 1997), but traditional garden-path effects were found with the other plural noun phrases. In addition, we tested plural anaphors that had a plural antecedent present in the discourse. We found that when the antecedent was conjoined, garden-path effects were absent compared to cases in which the antecedent was a plural definite description. Our results indicate that the parser is sensitive to the conceptual representation of a plural constituent. In particular, it appears that a Complex Reference Object (Moxey et al., 2004) automatically activates a reciprocal reading of a reciprocal verb.

Explore Stochastic Instabilities of Periodic Points by Transition Path Theory

NASA Astrophysics Data System (ADS)

Cao, Yu; Lin, Ling; Zhou, Xiang

2016-06-01

We consider the noise-induced transitions from a linearly stable periodic orbit consisting of T periodic points in randomly perturbed discrete logistic map. Traditional large deviation theory and asymptotic analysis at small noise limit cannot distinguish the quantitative difference in noise-induced stochastic instabilities among the T periodic points. To attack this problem, we generalize the transition path theory to the discrete-time continuous-space stochastic process. In our first criterion to quantify the relative instability among T periodic points, we use the distribution of the last passage location related to the transitions from the whole periodic orbit to a prescribed disjoint set. This distribution is related to individual contributions to the transition rate from each periodic points. The second criterion is based on the competency of the transition paths associated with each periodic point. Both criteria utilize the reactive probability current in the transition path theory. Our numerical results for the logistic map reveal the transition mechanism of escaping from the stable periodic orbit and identify which periodic point is more prone to lose stability so as to make successful transitions under random perturbations.

Chemical Reaction Engineering: Current Status and Future Directions.

ERIC Educational Resources Information Center

Dudukovic, M. P.

1987-01-01

Describes Chemical Reaction Engineering (CRE) as the discipline that quantifies the interplay of transport phenomena and kinetics in relating reactor performance to operating conditions and input variables. Addresses the current status of CRE in both academic and industrial settings and outlines future trends. (TW)

REFINED PBPK MODEL OF AGGREGATE EXPOSURE TO METHYL TERTIARY-BUTYL ETHER

EPA Science Inventory

Aggregate (multiple pathway) exposures to methyl tertiary-butyl ether (MTBE) in air and water occur via dermal, inhalation, and oral routes. Previously, physiologically-based pharmacokinetic (PBPK) models have been used to quantify the kinetic behavior of MTBE and its primary met...

Quantifying How Observations Inform a Numerical Reanalysis of Hawaii

NASA Astrophysics Data System (ADS)

Powell, B. S.

2017-11-01

When assimilating observations into a model via state-estimation, it is possible to quantify how each observation changes the modeled estimate of a chosen oceanic metric. Using an existing 2 year reanalysis of Hawaii that includes more than 31 million observations from satellites, ships, SeaGliders, and autonomous floats, I assess which observations most improve the estimates of the transport and eddy kinetic energy. When the SeaGliders were in the water, they comprised less than 2.5% of the data, but accounted for 23% of the transport adjustment. Because the model physics constrains advanced state-estimation, the prescribed covariances are propagated in time to identify observation-model covariance. I find that observations that constrain the isopycnal tilt across the transport section provide the greatest impact in the analysis. In the case of eddy kinetic energy, observations that constrain the surface-driven upper ocean have more impact. This information can help to identify optimal sampling strategies to improve both state-estimates and forecasts.

A Simple Parameterization of Mixing of Passive Scalars in Turbulent Flows

NASA Astrophysics Data System (ADS)

Nithianantham, Ajithshanthar; Venayagamoorthy, Karan

2015-11-01

A practical model for quantifying the turbulent diascalar diffusivity is proposed as Ks = 1 . 1γ'LTk 1 / 2 , where LT is defined as the Thorpe length scale, k is the turbulent kinetic energy and γ' is one-half of the mechanical to scalar time scale ratio, which was shown by previous researchers to be approximately 0 . 7 . The novelty of the proposed model lies in the use of LT, which is a widely used length scale in stably stratified flows (almost exclusively used in oceanography), for quantifying turbulent mixing in unstratified flows. LT can be readily obtained in the field using a Conductivity, Temperature and Depth (CTD) profiler. The turbulent kinetic energy is mostly contained in the large scales of the flow field and hence can be measured in the field or modeled in numerical simulations. Comparisons using DNS data show remarkably good agreement between the predicted and exact diffusivities. Office of Naval Research and National Science Foundation.

A calibrated Monte Carlo approach to quantify the impacts of misorientation and different driving forces on texture development

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

Liangzhe Zhang; Anthony D. Rollett; Timothy Bartel

2012-02-01

A calibrated Monte Carlo (cMC) approach, which quantifies grain boundary kinetics within a generic setting, is presented. The influence of misorientation is captured by adding a scaling coefficient in the spin flipping probability equation, while the contribution of different driving forces is weighted using a partition function. The calibration process relies on the established parametric links between Monte Carlo (MC) and sharp-interface models. The cMC algorithm quantifies microstructural evolution under complex thermomechanical environments and remedies some of the difficulties associated with conventional MC models. After validation, the cMC approach is applied to quantify the texture development of polycrystalline materials withmore » influences of misorientation and inhomogeneous bulk energy across grain boundaries. The results are in good agreement with theory and experiments.« less

A simple distributed sediment delivery approach for rural catchments

NASA Astrophysics Data System (ADS)

Reid, Lucas; Scherer, Ulrike

2014-05-01

The transfer of sediments from source areas to surface waters is a complex process. In process based erosion models sediment input is thus quantified by representing all relevant sub processes such as detachment, transport and deposition of sediment particles along the flow path to the river. A successful application of these models requires, however, a large amount of spatially highly resolved data on physical catchment characteristics, which is only available for a few, well examined small catchments. For the lack of appropriate models, the empirical Universal Soil Loss Equation (USLE) is widely applied to quantify the sediment production in meso to large scale basins. As the USLE provides long-term mean soil loss rates, it is often combined with spatially lumped models to estimate the sediment delivery ratio (SDR). In these models, the SDR is related to data on morphological characteristics of the catchment such as average local relief, drainage density, proportion of depressions or soil texture. Some approaches include the relative distance between sediment source areas and the river channels. However, several studies showed that spatially lumped parameters describing the morphological characteristics are only of limited value to represent the factors of influence on sediment transport at the catchment scale. Sediment delivery is controlled by the location of the sediment source areas in the catchment and the morphology along the flow path to the surface water bodies. This complex interaction of spatially varied physiographic characteristics cannot be adequately represented by lumped morphological parameters. The objective of this study is to develop a simple but spatially distributed approach to quantify the sediment delivery ratio by considering the characteristics of the flow paths in a catchment. We selected a small catchment located in in an intensively cultivated loess region in Southwest Germany as study area for the development of the SDR approach. The flow pathways were extracted in a geographic information system. Then the sediment delivery ratio for each source area was determined using an empirical approach considering the slope, morphology and land use properties along the flow path. As a benchmark for the calibration of the model parameters we used results of a detailed process based erosion model available for the study area. Afterwards the approach was tested in larger catchments located in the same loess region.

A Joint Model for the Kinetics of CTC Count and PSA Concentration During Treatment in Metastatic Castration-Resistant Prostate Cancer*

PubMed Central

Wilbaux, M; Tod, M; De Bono, J; Lorente, D; Mateo, J; Freyer, G; You, B; Hénin, E

2015-01-01

Assessment of treatment efficacy in metastatic castration-resistant prostate cancer (mCRPC) is limited by frequent nonmeasurable bone metastases. The count of circulating tumor cells (CTCs) is a promising surrogate marker that may replace the widely used prostate-specific antigen (PSA). The purpose of this study was to quantify the dynamic relationships between the longitudinal kinetics of these markers during treatment in patients with mCRPC. Data from 223 patients with mCRPC treated by chemotherapy and/or hormonotherapy were analyzed for up to 6 months of treatment. A semimechanistic model was built, combining the following several pharmacometric advanced features: (1) Kinetic-Pharmacodynamic (K-PD) compartments for treatments (chemotherapy and hormonotherapy); (2) a latent variable linking both marker kinetics; (3) modeling of CTC kinetics with a cell lifespan model; and (4) a negative binomial distribution for the CTC random sampling. Linked with survival, this model would potentially be useful for predicting treatment efficacy during drug development or for therapeutic adjustment in treated patients. PMID:26225253

Kinetics of Schottky defect formation and annihilation in single crystal TlBr.

PubMed

Bishop, Sean R; Tuller, Harry L; Kuhn, Melanie; Ciampi, Guido; Higgins, William; Shah, Kanai S

2013-07-28

The kinetics for Schottky defect (Tl and Br vacancy pair) formation and annihilation in ionically conducting TlBr are characterized through a temperature induced conductivity relaxation technique. Near room temperature, defect generation-annihilation was found to take on the order of hours before equilibrium was reached after a step change in temperature, and that mechanical damage imparted on the sample rapidly increases this rate. The rate limiting step to Schottky defect formation-annihilation is identified as being the migration of lower mobility Tl (versus Br), with an estimate for source-sink density derived from calculated diffusion lengths. This study represents one of the first investigations of Schottky defect generation-annihilation kinetics and demonstrates its utility in quantifying detrimental mechanical damage in radiation detector materials.

Kinetic modeling in PET imaging of hypoxia

PubMed Central

Li, Fan; Joergensen, Jesper T; Hansen, Anders E; Kjaer, Andreas

2014-01-01

Tumor hypoxia is associated with increased therapeutic resistance leading to poor treatment outcome. Therefore the ability to detect and quantify intratumoral oxygenation could play an important role in future individual personalized treatment strategies. Positron Emission Tomography (PET) can be used for non-invasive mapping of tissue oxygenation in vivo and several hypoxia specific PET tracers have been developed. Evaluation of PET data in the clinic is commonly based on visual assessment together with semiquantitative measurements e.g. standard uptake value (SUV). However, dynamic PET contains additional valuable information on the temporal changes in tracer distribution. Kinetic modeling can be used to extract relevant pharmacokinetic parameters of tracer behavior in vivo that reflects relevant physiological processes. In this paper, we review the potential contribution of kinetic analysis for PET imaging of hypoxia. PMID:25250200

Accelerated path integral methods for atomistic simulations at ultra-low temperatures

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

Uhl, Felix, E-mail: felix.uhl@rub.de; Marx, Dominik; Ceriotti, Michele

2016-08-07

Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated pathmore » integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH{sub 5}{sup +}. We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH{sub 4} to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.« less

Kinetics of the BrO + NO2 Association Reaction. Temperature and Pressure Dependence in the Falloff Regime

NASA Technical Reports Server (NTRS)

Thron, R. P.; Daykin, E. P.; Wine, P.H.

1997-01-01

A laser flash photolysis-long path absorption technique has been employed to study the kinetics of the reaction BrO + NO2 + M yields (k1) products as a function of temperature (248-346 K), pressure (16-800 torr), and buffer gas identity (N2,CF4) The reaction is found to be in the falloff regime between third and second-order over the entire range of conditions investigated This is the first study where temperature-dependent measurements of k1(P,T) have been reported at pressures greater than 12 torr; hence, our results help constrain choices of k1(P,T) for use in models of lower stratospheric BrO(x) chemistry. Approximate falloff parameters in a convenient form for atmospheric modeling are derived.

Sound wave resonances in micro-electro-mechanical systems devices vibrating at high frequencies according to the kinetic theory of gases

NASA Astrophysics Data System (ADS)

Desvillettes, Laurent; Lorenzani, Silvia

2012-09-01

The mechanism leading to gas damping in micro-electro-mechanical systems (MEMS) devices vibrating at high frequencies is investigated by using the linearized Boltzmann equation based on simplified kinetic models and diffuse reflection boundary conditions. Above a certain frequency of oscillation, the sound waves propagating through the gas are trapped in the gaps between the moving elements and the fixed boundaries of the microdevice. In particular, we found a scaling law, valid for all Knudsen numbers Kn (defined as the ratio between the gas mean free path and a characteristic length of the gas flow), that predicts a resonant response of the system. This response enables a minimization of the damping force exerted by the gas on the oscillating wall of the microdevice.

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.

Filtering analysis of a direct numerical simulation of the turbulent Rayleigh-Benard problem

NASA Technical Reports Server (NTRS)

Eidson, T. M.; Hussaini, M. Y.; Zang, T. A.

1990-01-01

A filtering analysis of a turbulent flow was developed which provides details of the path of the kinetic energy of the flow from its creation via thermal production to its dissipation. A low-pass spatial filter is used to split the velocity and the temperature field into a filtered component (composed mainly of scales larger than a specific size, nominally the filter width) and a fluctuation component (scales smaller than a specific size). Variables derived from these fields can fall into one of the above two ranges or be composed of a mixture of scales dominated by scales near the specific size. The filter is used to split the kinetic energy equation into three equations corresponding to the three scale ranges described above. The data from a direct simulation of the Rayleigh-Benard problem for conditions where the flow is turbulent are used to calculate the individual terms in the three kinetic energy equations. This is done for a range of filter widths. These results are used to study the spatial location and the scale range of the thermal energy production, the cascading of kinetic energy, the diffusion of kinetic energy, and the energy dissipation. These results are used to evaluate two subgrid models typically used in large-eddy simulations of turbulence. Subgrid models attempt to model the energy below the filter width that is removed by a low-pass filter.

Ion-kinetic simulations of D- 3He gas-filled inertial confinement fusion target implosions with moderate to large Knudsen number

DOE PAGES

Larroche, O.; Rinderknecht, H. G.; Rosenberg, M. J.; ...

2016-01-06

Experiments designed to investigate the transition to non-collisional behavior in D 3He-gas inertial confinement fusion target implosions display increasingly large discrepancies with respect to simulations by standard hydrodynamics codes as the expected ion mean-free-paths λ c increase with respect to the target radius R (i.e., when the Knudsen number N K = λ c/R grows). To take properly into account large N K's, multi-ion-species Vlasov-Fokker-Planck computations of the inner gas in the capsules have been performed, for two different values of N K, one moderate and one large. The results, including nuclear yield, reactivity-weighted ion temperatures, nuclear emissivities, and surfacemore » brightness, have been compared with the experimental data and with the results of hydrodynamical simulations, some of which include an ad hocmodeling of kinetic effects. The experimental results are quite accurately rendered by the kinetic calculations in the smaller-N K case, much better than by the hydrodynamical calculations. The kinetic effects at play in this case are thus correctly understood. However, in the higher-N K case, the agreement is much worse. Furthermore, the remaining discrepancies are shown to arise from kinetic phenomena (e.g., inter-species diffusion) occurring at the gas-pusher interface, which should be investigated in the future work.« less

Diversified Control Paths: A Significant Way Disease Genes Perturb the Human Regulatory Network

PubMed Central

Wang, Bingbo; Gao, Lin; Zhang, Qingfang; Li, Aimin; Deng, Yue; Guo, Xingli

2015-01-01

Background The complexity of biological systems motivates us to use the underlying networks to provide deep understanding of disease etiology and the human diseases are viewed as perturbations of dynamic properties of networks. Control theory that deals with dynamic systems has been successfully used to capture systems-level knowledge in large amount of quantitative biological interactions. But from the perspective of system control, the ways by which multiple genetic factors jointly perturb a disease phenotype still remain. Results In this work, we combine tools from control theory and network science to address the diversified control paths in complex networks. Then the ways by which the disease genes perturb biological systems are identified and quantified by the control paths in a human regulatory network. Furthermore, as an application, prioritization of candidate genes is presented by use of control path analysis and gene ontology annotation for definition of similarities. We use leave-one-out cross-validation to evaluate the ability of finding the gene-disease relationship. Results have shown compatible performance with previous sophisticated works, especially in directed systems. Conclusions Our results inspire a deeper understanding of molecular mechanisms that drive pathological processes. Diversified control paths offer a basis for integrated intervention techniques which will ultimately lead to the development of novel therapeutic strategies. PMID:26284649

Statistical Symbolic Execution with Informed Sampling

NASA Technical Reports Server (NTRS)

Filieri, Antonio; Pasareanu, Corina S.; Visser, Willem; Geldenhuys, Jaco

2014-01-01

Symbolic execution techniques have been proposed recently for the probabilistic analysis of programs. These techniques seek to quantify the likelihood of reaching program events of interest, e.g., assert violations. They have many promising applications but have scalability issues due to high computational demand. To address this challenge, we propose a statistical symbolic execution technique that performs Monte Carlo sampling of the symbolic program paths and uses the obtained information for Bayesian estimation and hypothesis testing with respect to the probability of reaching the target events. To speed up the convergence of the statistical analysis, we propose Informed Sampling, an iterative symbolic execution that first explores the paths that have high statistical significance, prunes them from the state space and guides the execution towards less likely paths. The technique combines Bayesian estimation with a partial exact analysis for the pruned paths leading to provably improved convergence of the statistical analysis. We have implemented statistical symbolic execution with in- formed sampling in the Symbolic PathFinder tool. We show experimentally that the informed sampling obtains more precise results and converges faster than a purely statistical analysis and may also be more efficient than an exact symbolic analysis. When the latter does not terminate symbolic execution with informed sampling can give meaningful results under the same time and memory limits.

Objective assessment of gait in xylazine-induced ataxic horses.

PubMed

Nout-Lomas, Y S; Page, K M; Kang, H G; Aanstoos, M E; Greene, H M

2017-05-01

There is poor agreement between observers of equine neurological gait abnormalities using the modified Mayhew grading scale. To stimulate a dose-dependent ataxia in horses through xylazine administration and identify quantifiable relevant gait parameters. Balanced, randomised, 2-way crossover design. Eight horses were assessed before and after administration of xylazine (low dose and high dose). Gait analyses performed before and after xylazine administration included: 1) kinematic data collected on an equine high-speed treadmill (flat and 10% decline) and from accelerometers placed on head and sacrum; and 2) kinetic data collected on a force plate. All horses developed dose-dependent ataxia. Horses developed a dose-dependent increased stride time, stride length, and time of contact (P<0.0001), and a decreased stride frequency (P<0.0002) after administration of xylazine. Although pelvic acceleration increased in the mediolateral direction (P<0.05) in horses walked on the treadmill, this movement decreased when walking over ground after administration of xylazine (P<0.05). Furthermore, centre of pressure and path length indices changed significantly in horses following administration of xylazine (P<0.05). This study examined one breed of horse (Arabian), all of similar height and weight. Accelerometers were attached to skin, not bone; no correction was made for artefacts from skin displacement. The sedative drug effect is of certain duration, limiting the data collection period. Administration of xylazine induced a dose-dependent ataxia in horses and resulted in significant changes of gait parameters, pelvic accelerations, and stabilographic variables, some of which changed in a dose-dependent fashion. Some of the altered gait parameters in this model were probably a result of overall slowing down of the stride cycle secondary to the sedative effect. Continued efforts to discover and evaluate quantifiable gait parameters that are susceptible to change following development of clinical neurological disease in horses is warranted. © 2016 EVJ Ltd.

Determining soil erosion from roads in coastal plain of Alabama

Treesearch

McFero Grace; W.J. Elliot

2008-01-01

This paper reports soil losses and observed sediment deposition for 16 randomly selected forest road sections in the National Forests of Alabama. Visible sediment deposition zones were tracked along the stormwater flow path to the most remote location as a means of quantifying soil loss from road sections. Volumes of sediment in deposition zones were determined by...

Free Volume of the Hard Spheres Gas

ERIC Educational Resources Information Center

Shutler, P. M. E.; Martinez, J. C.; Springham, S. V.

2007-01-01

The Enskog factor [chi] plays a central role in the theory of dense gases, quantifying how the finite size of molecules causes many physical quantities, such as the equation of state, the mean free path, and the diffusion coefficient, to deviate from those of an ideal gas. We suggest an intuitive but rigorous derivation of this fact by showing how…

Quantifying and Testing Indirect Effects in Simple Mediation Models when the Constituent Paths Are Nonlinear

ERIC Educational Resources Information Center

Hayes, Andrew F.; Preacher, Kristopher J.

2010-01-01

Most treatments of indirect effects and mediation in the statistical methods literature and the corresponding methods used by behavioral scientists have assumed linear relationships between variables in the causal system. Here we describe and extend a method first introduced by Stolzenberg (1980) for estimating indirect effects in models of…

Analyzing and interpreting genome data at the network level with ConsensusPathDB.

PubMed

Herwig, Ralf; Hardt, Christopher; Lienhard, Matthias; Kamburov, Atanas

2016-10-01

ConsensusPathDB consists of a comprehensive collection of human (as well as mouse and yeast) molecular interaction data integrated from 32 different public repositories and a web interface featuring a set of computational methods and visualization tools to explore these data. This protocol describes the use of ConsensusPathDB (http://consensuspathdb.org) with respect to the functional and network-based characterization of biomolecules (genes, proteins and metabolites) that are submitted to the system either as a priority list or together with associated experimental data such as RNA-seq. The tool reports interaction network modules, biochemical pathways and functional information that are significantly enriched by the user's input, applying computational methods for statistical over-representation, enrichment and graph analysis. The results of this protocol can be observed within a few minutes, even with genome-wide data. The resulting network associations can be used to interpret high-throughput data mechanistically, to characterize and prioritize biomarkers, to integrate different omics levels, to design follow-up functional assay experiments and to generate topology for kinetic models at different scales.

Statistical analysis of dynamic fibrils observed from NST/BBSO observations

NASA Astrophysics Data System (ADS)

Gopalan Priya, Thambaje; Su, Jiang-Tao; Chen, Jie; Deng, Yuan-Yong; Prasad Choudhury, Debi

2018-02-01

We present the results obtained from the analysis of dynamic fibrils in NOAA active region (AR) 12132, using high resolution Hα observations from the New Solar Telescope operating at Big Bear Solar Observatory. The dynamic fibrils are seen to be moving up and down, and most of these dynamic fibrils are periodic and have a jet-like appearance. We found from our observations that the fibrils follow almost perfect parabolic paths in many cases. A statistical analysis on the properties of the parabolic paths showing an analysis on deceleration, maximum velocity, duration and kinetic energy of these fibrils is presented here. We found the average maximum velocity to be around 15 kms‑1 and mean deceleration to be around 100 ms‑2. The observed deceleration appears to be a fraction of gravity of the Sun and is not compatible with the path of ballistic motion due to gravity of the Sun. We found a positive correlation between deceleration and maximum velocity. This correlation is consistent with simulations done earlier on magnetoacoustic shock waves propagating upward.

Effects of Alloyed Metal on the Catalysis Activity of Pt for Ethanol Partial Oxidation: Adsorption and Dehydrogenation on Pt3M (M=Pt, Ru, Sn, Re, Rh, and Pd)

PubMed Central

Xu, Zhen-Feng; Wang, Yixuan

2011-01-01

The adsorption and dehydrogenation reactions of ethanol over bimetallic clusters, Pt3M (M = Pt, Ru, Sn, Re, Rh, and Pd), have been extensively investigated with density functional theory. Both the α-hydrogen and hydroxyl adsorptions on Pt as well as on the alloyed transition metal M sites of PtM were considered as initial reaction steps. The adsorptions of ethanol on Pt and M sites of some PtM via the α-hydrogen were well established. Although the α-hydrogen adsorption on Pt site is weaker than the hydroxyl, the potential energy profiles show that the dehydrogenation via the α-hydrogen path has much lower energy barrier than that via the hydroxyl path. Generally for the α-hydrogen path the adsorption is a rate-determining-step because of rather low dehydrogenation barrier for the α-hydrogen adsorption complex (thermodynamic control), while the hydroxyl path is determined by its dehydrogenation step (kinetic control). The effects of alloyed metal on the catalysis activity of Pt for ethanol partial oxidation, including adsorption energy, energy barrier, electronic structure, and eventually rate constant were discussed. Among all of the alloyed metals only Sn enhances the rate constant of the dehydrogenation via the α-hydrogen path on the Pt site of Pt3Sn as compared with Pt alone, which interprets why the PtSn is the most active to the oxidation of ethanol. PMID:22102920

PathScore: a web tool for identifying altered pathways in cancer data.

PubMed

Gaffney, Stephen G; Townsend, Jeffrey P

2016-12-01

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects. Web application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at: github.com/sggaffney/pathscore with a GPLv3 license. stephen.gaffney@yale.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Demonstration of a rapidly-swept external cavity quantum cascade laser for rapid and sensitive quantification of chemical mixtures

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

Brumfield, Brian E.; Taubman, Matthew S.; Phillips, Mark C.

2016-02-13

A rapidly-swept external cavity quantum cascade laser (ECQCL) system for fast open-path quantification of multiple chemicals and mixtures is presented. The ECQCL system is swept over its entire tuning range (>100 cm-1) at frequencies up to 200 Hz. At 200 Hz the wavelength tuning rate and spectral resolution are 2x104 cm-1/sec and < 0.2 cm-1, respectively. The capability of the current system to quantify changes in chemical concentrations on millesecond timescales is demonstrated at atmospheric pressure using an open-path multi-pass cell. The detection limits for chemicals ranged from ppb to ppm levels depending on the absorption cross-section.

Avalanche ecology and large magnitude avalanche events: Glacier National Park, Montana, USA

USGS Publications Warehouse

Fagre, Daniel B.; Peitzsch, Erich H.

2010-01-01

Large magnitude snow avalanches play an important role ecologically in terms of wildlife habitat, vegetation diversity, and sediment transport within a watershed. Ecological effects from these infrequent avalanches can last for decades. Understanding the frequency of such large magnitude avalanches is also critical to avalanche forecasting for the Going-to-the-Sun Road (GTSR). In January 2009, a large magnitude avalanche cycle occurred in and around Glacier National Park, Montana. The study site is the Little Granite avalanche path located along the GTSR. The study is designed to quantify change in vegetative cover immediately after a large magnitude event and document ecological response over a multi-year period. GPS field mapping was completed to determine the redefined perimeter of the avalanche path. Vegetation was inventoried using modified U.S. Forest Service Forest Inventory and Analysis plots, cross sections were taken from over 100 dead trees throughout the avalanche path, and an avalanche chronology was developed. Initial results indicate that the perimeter of this path was expanded by 30%. The avalanche travelled approximately 1200 vertical meters and 3 linear kilometers. Stands of large conifers as old as 150 years were decimated by the avalanche, causing a shift in dominant vegetation types in many parts of the avalanche path. Woody debris is a major ground cover up to 3 m in depth on lower portions of the avalanche path and will likely affect tree regrowth. Monitoring and measuring the post-avalanche vegetation recovery of this particular avalanche path provides a unique dataset for determining the ecological role of avalanches in mountain landscapes.

Optimization of High-Throughput Sequencing Kinetics for determining enzymatic rate constants of thousands of RNA substrates

PubMed Central

Niland, Courtney N.; Jankowsky, Eckhard; Harris, Michael E.

2016-01-01

Quantification of the specificity of RNA binding proteins and RNA processing enzymes is essential to understanding their fundamental roles in biological processes. High Throughput Sequencing Kinetics (HTS-Kin) uses high throughput sequencing and internal competition kinetics to simultaneously monitor the processing rate constants of thousands of substrates by RNA processing enzymes. This technique has provided unprecedented insight into the substrate specificity of the tRNA processing endonuclease ribonuclease P. Here, we investigate the accuracy and robustness of measurements associated with each step of the HTS-Kin procedure. We examine the effect of substrate concentration on the observed rate constant, determine the optimal kinetic parameters, and provide guidelines for reducing error in amplification of the substrate population. Importantly, we find that high-throughput sequencing, and experimental reproducibility contribute their own sources of error, and these are the main sources of imprecision in the quantified results when otherwise optimized guidelines are followed. PMID:27296633

Quantifying second generation ethanol inhibition: Design of Experiments approach and kinetic model development.

PubMed

Schneiderman, Steven J; Johnson, Roger W; Menkhaus, Todd J; Gilcrease, Patrick C

2015-03-01

While softwoods represent a potential feedstock for second generation ethanol production, compounds present in their hydrolysates can inhibit fermentation. In this study, a novel Design of Experiments (DoE) approach was used to identify significant inhibitory effects on Saccharomyces cerevisiae D5A for the purpose of guiding kinetic model development. Although acetic acid, furfural and 5-hydroxymethyl furfural (HMF) were present at potentially inhibitory levels, initial factorial experiments only identified ethanol as a significant rate inhibitor. It was hypothesized that high ethanol levels masked the effects of other inhibitors, and a subsequent factorial design without ethanol found significant effects for all other compounds. When these non-ethanol effects were accounted for in the kinetic model, R¯(2) was significantly improved over an ethanol-inhibition only model (R¯(2)=0.80 vs. 0.76). In conclusion, when ethanol masking effects are removed, DoE is a valuable tool to identify significant non-ethanol inhibitors and guide kinetic model development. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cross-laboratory comparative study of the impact of experimental and regression methodologies on salmonella thermal inactivation parameters in ground beef

USDA-ARS?s Scientific Manuscript database

Isothermal inactivation studies are commonly used to quantify thermal inactivation kinetics of bacteria. Meta-analyses and comparisons utilizing results from multiple sources have revealed large variations in reported inactivation parameters for Salmonella, even in similar food materials. Different ...

Differential scanning calorimetry study and computer modeling of β ⇒ α phase transformation in a Ti-6Al-4V alloy

NASA Astrophysics Data System (ADS)

Malinov, S.; Guo, Z.; Sha, W.; Wilson, A.

2001-04-01

The relationship between heat-treatment parameters and microstructure in titanium alloys has so far been mainly studied empirically, using characterization techniques such as microscopy. Calculation and modeling of the kinetics of phase transformation have not yet been widely used for these alloys. Differential scanning calorimetry (DSC) has been widely used for the study of a variety of phase transformations. There has been much work done on the calculation and modeling of the kinetics of phase transformations for different systems based on the results from DSC study. In the present work, the kinetics of the β ⇒ α transformation in a Ti-6Al-4V titanium alloy were studied using DSC, at continuous cooling conditions with constant cooling rates of 5 °C, 10 °C, 20 °C, 30 °C, 40 °C, and 50 °C/min. The results from calorimetry were then used to trace and model the transformation kinetics in continuous cooling conditions. Based on suitably interpreted DSC results, continuous cooling-transformation (CCT) diagrams were calculated with lines of isotransformed fraction. The kinetics of transformation were modeled using the Johnson-Mehl-Avrami (JMA) theory and by applying the “concept of additivity.” The JMA kinetic parameters were derived. Good agreement between the calculated and experimental transformed fractions is demonstrated. Using the derived kinetic parameters, the β ⇒ α transformation in a Ti-6Al-4V alloy can be described for any cooling path and condition. An interpretation of the results from the point of view of activation energy for nucleation is also presented.

The role of surface oxides on hydrogen sorption kinetics in titanium thin films

NASA Astrophysics Data System (ADS)

Hadjixenophontos, Efi; Michalek, Lukas; Roussel, Manuel; Hirscher, Michael; Schmitz, Guido

2018-05-01

Titanium is presently discussed as a catalyst to accelerate the hydrogenation kinetics of hydrogen storage materials. It is however known that H absorption in Ti decisively depends on the surface conditions (presence or absence of the natural surface oxide). In this work, we use Ti thin films of controlled thickness (50-800 nm) as a convenient tool for quantifying the atomic transport. XRD and TEM investigations allow us to follow the hydrogenation progress inside the film. Hydrogenation of TiO2/Ti bi-layers is studied at 300 °C, for different durations (10 s to 600 min) and at varying pressures of pure H2 atmosphere. Under these conditions, the hydrogenation is found to be linear in time. By comparing films with and without TiO2, as well as by studying the pressure dependence of hydrogenation, it is demonstrated that hydrogen transport across the oxide represents the decisive kinetic barrier rather than the splitting of H2 molecules at the surface. Hydrogenation appears by a layer-like reaction initiated by heterogeneous nucleation at the backside interface to the substrate. The linear growth constant and the H diffusion coefficient inside the oxide are quantified, as well as a reliable lower bound to the hydrogen diffusion coefficient in Ti is derived. The pressure dependence of hydrogen absorption is quantitatively modelled.

Quantitative in vivo cell-surface receptor imaging in oncology: kinetic modeling & paired-agent principles from nuclear medicine and optical imaging

PubMed Central

Tichauer, Kenneth M.; Wang, Yu; Pogue, Brian W.; Liu, Jonathan T. C.

2015-01-01

The development of methods to accurately quantify cell-surface receptors in living tissues would have a seminal impact in oncology. For example, accurate measures of receptor density in vivo could enhance early detection or surgical resection of tumors via protein-based contrast, allowing removal of cancer with high phenotype specificity. Alternatively, accurate receptor expression estimation could be used as a biomarker to guide patient-specific clinical oncology targeting of the same molecular pathway. Unfortunately, conventional molecular contrast-based imaging approaches are not well adapted to accurately estimating the nanomolar-level cell-surface receptor concentrations in tumors, as most images are dominated by nonspecific sources of contrast such as high vascular permeability and lymphatic inhibition. This article reviews approaches for overcoming these limitations based upon tracer kinetic modeling and the use of emerging protocols to estimate binding potential and the related receptor concentration. Methods such as using single time point imaging or a reference-tissue approach tend to have low accuracy in tumors, whereas paired-agent methods or advanced kinetic analyses are more promising to eliminate the dominance of interstitial space in the signals. Nuclear medicine and optical molecular imaging are the primary modalities used, as they have the nanomolar level sensitivity needed to quantify cell-surface receptor concentrations present in tissue, although each likely has a different clinical niche. PMID:26134619

Real-time Full-spectral Imaging and Affinity Measurements from 50 Microfluidic Channels using Nanohole Surface Plasmon Resonance†

PubMed Central

Lee, Si Hoon; Lindquist, Nathan C.; Wittenberg, Nathan J.; Jordan, Luke R.; Oh, Sang-Hyun

2012-01-01

With recent advances in high-throughput proteomics and systems biology, there is a growing demand for new instruments that can precisely quantify a wide range of receptor-ligand binding kinetics in a high-throughput fashion. Here we demonstrate a surface plasmon resonance (SPR) imaging spectroscopy instrument capable of extracting binding kinetics and affinities from 50 parallel microfluidic channels simultaneously. The instrument utilizes large-area (~cm2) metallic nanohole arrays as SPR sensing substrates and combines a broadband light source, a high-resolution imaging spectrometer and a low-noise CCD camera to extract spectral information from every channel in real time with a refractive index resolution of 7.7 × 10−6. To demonstrate the utility of our instrument for quantifying a wide range of biomolecular interactions, each parallel microfluidic channel is coated with a biomimetic supported lipid membrane containing ganglioside (GM1) receptors. The binding kinetics of cholera toxin b (CTX-b) to GM1 are then measured in a single experiment from 50 channels. By combining the highly parallel microfluidic device with large-area periodic nanohole array chips, our SPR imaging spectrometer system enables high-throughput, label-free, real-time SPR biosensing, and its full-spectral imaging capability combined with nanohole arrays could enable integration of SPR imaging with concurrent surface-enhanced Raman spectroscopy. PMID:22895607

Quantifying risks with exact analytical solutions of derivative pricing distribution

NASA Astrophysics Data System (ADS)

Zhang, Kun; Liu, Jing; Wang, Erkang; Wang, Jin

2017-04-01

Derivative (i.e. option) pricing is essential for modern financial instrumentations. Despite of the previous efforts, the exact analytical forms of the derivative pricing distributions are still challenging to obtain. In this study, we established a quantitative framework using path integrals to obtain the exact analytical solutions of the statistical distribution for bond and bond option pricing for the Vasicek model. We discuss the importance of statistical fluctuations away from the expected option pricing characterized by the distribution tail and their associations to value at risk (VaR). The framework established here is general and can be applied to other financial derivatives for quantifying the underlying statistical distributions.

Velocity Inversion In Cylindrical Couette Gas Flows

NASA Astrophysics Data System (ADS)

Dongari, Nishanth; Barber, Robert W.; Emerson, David R.; Zhang, Yonghao; Reese, Jason M.

2012-05-01

We investigate a power-law probability distribution function to describe the mean free path of rarefied gas molecules in non-planar geometries. A new curvature-dependent model is derived by taking into account the boundary-limiting effects on the molecular mean free path for surfaces with both convex and concave curvatures. In comparison to a planar wall, we find that the mean free path for a convex surface is higher at the wall and exhibits a sharper gradient within the Knudsen layer. In contrast, a concave wall exhibits a lower mean free path near the surface and the gradients in the Knudsen layer are shallower. The Navier-Stokes constitutive relations and velocity-slip boundary conditions are modified based on a power-law scaling to describe the mean free path, in accordance with the kinetic theory of gases, i.e. transport properties can be described in terms of the mean free path. Velocity profiles for isothermal cylindrical Couette flow are obtained using the power-law model. We demonstrate that our model is more accurate than the classical slip solution, especially in the transition regime, and we are able to capture important non-linear trends associated with the non-equilibrium physics of the Knudsen layer. In addition, we establish a new criterion for the critical accommodation coefficient that leads to the non-intuitive phenomena of velocity-inversion. Our results are compared with conventional hydrodynamic models and direct simulation Monte Carlo data. The power-law model predicts that the critical accommodation coefficient is significantly lower than that calculated using the classical slip solution and is in good agreement with available DSMC data. Our proposed constitutive scaling for non-planar surfaces is based on simple physical arguments and can be readily implemented in conventional fluid dynamics codes for arbitrary geometric configurations.

On Kinetic Slow Modes, Fluid Slow Modes, and Pressure-balanced Structures in the Solar Wind

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

Verscharen, Daniel; Chen, Christopher H. K.; Wicks, Robert T., E-mail: daniel.verscharen@unh.edu, E-mail: christopher.chen@imperial.ac.uk, E-mail: r.wicks@ucl.ac.uk

Observations in the solar wind suggest that the compressive component of inertial-range solar-wind turbulence is dominated by slow modes. The low collisionality of the solar wind allows for nonthermal features to survive, which suggests the requirement of a kinetic plasma description. The least-damped kinetic slow mode is associated with the ion-acoustic (IA) wave and a nonpropagating (NP) mode. We derive analytical expressions for the IA-wave dispersion relation in an anisotropic plasma in the framework of gyrokinetics and then compare them to fully kinetic numerical calculations, results from two-fluid theory, and magnetohydrodynamics (MHD). This comparison shows major discrepancies in the predictedmore » wave phase speeds from MHD and kinetic theory at moderate to high β . MHD and kinetic theory also dictate that all plasma normal modes exhibit a unique signature in terms of their polarization. We quantify the relative amplitude of fluctuations in the three lowest particle velocity moments associated with IA and NP modes in the gyrokinetic limit and compare these predictions with MHD results and in situ observations of the solar-wind turbulence. The agreement between the observations of the wave polarization and our MHD predictions is better than the kinetic predictions, which suggests that the plasma behaves more like a fluid in the solar wind than expected.« less

Inorganic nanostructured materials for high performance electrochemical supercapacitors

NASA Astrophysics Data System (ADS)

Liu, Sheng; Sun, Shouheng; You, Xiao-Zeng

2014-01-01

Electrochemical supercapacitors (ES) are a well-known energy storage system that has high power density, long life-cycle and fast charge-discharge kinetics. Nanostructured materials are a new generation of electrode materials with large surface area and short transport/diffusion path for ions and electrons to achieve high specific capacitance in ES. This mini review highlights recent developments of inorganic nanostructure materials, including carbon nanomaterials, metal oxide nanoparticles, and metal oxide nanowires/nanotubes, for high performance ES applications.

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

Agafonov, A. I., E-mail: aai@isssph.kiae.ru

The inelastic scattering of cold neutrons by a ring leads to quantum jumps of a superconducting current which correspond to a decrease in the fluxoid quantum number by one or several units while the change in the ring energy is transferred to the kinetic energy of the scattered neutron. The scattering cross sections of transversely polarized neutrons have been calculated for a thin type-II superconductor ring, the thickness of which is smaller than the field penetration depth but larger than the electron mean free path.

Inorganic nanostructured materials for high performance electrochemical supercapacitors.

PubMed

Liu, Sheng; Sun, Shouheng; You, Xiao-Zeng

2014-02-21

Electrochemical supercapacitors (ES) are a well-known energy storage system that has high power density, long life-cycle and fast charge-discharge kinetics. Nanostructured materials are a new generation of electrode materials with large surface area and short transport/diffusion path for ions and electrons to achieve high specific capacitance in ES. This mini review highlights recent developments of inorganic nanostructure materials, including carbon nanomaterials, metal oxide nanoparticles, and metal oxide nanowires/nanotubes, for high performance ES applications.

Development of Bicarbonate-Activated Peroxide as a Chemical and Biological Warfare Agent Decontaminant

DTIC Science & Technology

2006-06-30

may operate for certain substrates. The reaction of equation 1 proceeds with the intermediacy of CO2 as shown in Figure 1. Although it is well...competition between paths 5 and 6 will depend on the conditions and the nature of the substrate S. Note that figures, equations , etc. in the...1 shows the complete reaction scheme used to model the equilibration reaction at low temperature. Table 1 Kinetic equations and their

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

Nitric Oxide Reduction to Ammonia by TiO 2 Electrons in Colloid Solution via Consecutive One-Electron Transfer Steps

DOE PAGES

Goldstein, Sara; Behar, David; Rajh, Tijana; ...

2015-03-02

The reaction mechanism of nitric oxide (NO) reduction by excess electrons on TiO 2 nanoparticles (e TiO2–) has been studied under anaerobic conditions. TiO 2 was loaded with 10–130 electrons per particle using γ-irradiation of acidic TiO 2 colloid solutions containing 2-propanol. The study is based on time-resolved kinetics and reactants and products analysis. The reduction of NO by e TiO2– is interpreted in terms of competition between a reaction path leading to formation of NH 3 and a path leading to N 2O and N 2. The proposed mechanism involves consecutive one-electron transfers of NO, and its reduction intermediatesmore » HNO, NH 2O•, and NH 2OH. The results show that e TiO2– does not reduce N 2O and N 2. Second-order rate constants of e TiO2– reactions with NO (740 ± 30 M –1 s –1) and NH 2OH (270 ± 30 M –1 s –1) have been determined employing the rapid-mixing stopped-flow technique and that with HNO (>1.3 × 10 6 M –1 s –1) was derived from fitting the kinetic traces to the suggested reaction mechanism, which is discussed in detail.« less

Understanding the in vivo uptake kinetics of a phosphatidylethanolamine-binding agent 99mTc-Duramycin

PubMed Central

Audi, Said; Li, Zhixin; Capacete, Joseph; Liu, Yu; Fang, Wei; Shu, Laura G.; Zhao, Ming

2013-01-01

Introduction 99mTc-Duramycin is a peptide-based molecular probe that binds specifically to phosphatidylethanolamine (PE). The goal was to characterize the kinetics of molecular interactions between 99mTc-Duramycin and the target tissue. Methods High level of accessible PE is induced in cardiac tissues by myocardial ischemia (30 min) and reperfusion (120 min) in Sprague Dawley rats. Target binding and biodistribution of 99mTc-duramycin was captured using SPECT/CT. To quantify the binding kinetics, the presence of radioactivity in ischemic versus normal cardiac tissues was measured by gamma counting at 3, 10, 20, 60 and 180 min after injection. A partially inactivated form of 99mTc-Duramycin was analyzed in the same fashion. A compartment model was developed to quantify the uptake kinetics of 99mTc-Duramycin in normal and ischemic myocardial tissue. Results 99mTc-duramycin binds avidly to the damaged tissue with a high target-to-background radio. Compartment modeling shows that accessibility of binding sites in myocardial tissue to 99mTc-Duramycin is not a limiting factor and the rate constant of target binding in the target tissue is at 2.2 ml/nmol/min/g. The number of available binding sites for 99mTc-Duramycin in ischemic myocardium was estimated at 0.14 nmol/g. Covalent modification of D15 resulted in a 9 fold reduction in binding affinity. Conclusion 99mTc-Duramycin accumulates avidly in target tissues in a PE-dependent fashion. Model results reflect an efficient uptake mechanism, consistent with the low molecular weight of the radiopharmaceutical and the relatively high density of available binding sites. These data help better define the imaging utilities of 99mTc-Duramycin as a novel PE-binding agent. PMID:22534031

Hip kinetics during gait are clinically meaningful outcomes in young boys with Duchenne muscular dystrophy.

PubMed

Heberer, Kent; Fowler, Eileen; Staudt, Loretta; Sienko, Susan; Buckon, Cathleen E; Bagley, Anita; Sison-Williamson, Mitell; McDonald, Craig M; Sussman, Michael D

2016-07-01

Duchenne muscular dystrophy (DMD) is an X-linked genetic neuromuscular disorder characterized by progressive proximal to distal muscle weakness. The success of randomized clinical trials for novel therapeutics depends on outcome measurements that are sensitive to change. As the development of motor skills may lead to functional improvements in young boys with DMD, their inclusion may potentially confound clinical trials. Three-dimensional gait analysis is an under-utilized approach that can quantify joint moments and powers, which reflect functional muscle strength. In this study, gait kinetics, kinematics, spatial-temporal parameters, and timed functional tests were quantified over a one-year period for 21 boys between 4 and 8 years old who were enrolled in a multisite natural history study. At baseline, hip moments and powers were inadequate. Between the two visits, 12 boys began a corticosteroid regimen (mean duration 10.8±2.4 months) while 9 boys remained steroid-naïve. Significant between-group differences favoring steroid use were found for primary kinetic outcomes (peak hip extensor moments (p=.007), duration of hip extensor moments (p=.007), peak hip power generation (p=.028)), and spatial-temporal parameters (walking speed (p=.016) and cadence (p=.021)). Significant between-group differences were not found for kinematics or timed functional tests with the exception of the 10m walk test (p=.03), which improves in typically developing children within this age range. These results indicate that hip joint kinetics can be used to identify weakness in young boys with DMD and are sensitive to corticosteroid intervention. Inclusion of gait analysis may enhance detection of a treatment effect in clinical trials particularly for young boys with more preserved muscle function. Copyright © 2016 Elsevier B.V. All rights reserved.

Kinematic and kinetic comparisons between American and Korean professional baseball pitchers.

PubMed

Escamilla, Rafael; Fleisig, Glen; Barrentine, Steven; Andrews, James; Moorman, Claude

2002-07-01

The purpose of this study was to quantify and compare kinematic, temporal, and kinetic characteristics of American and Korean professional pitchers in order to investigate differences in pitching mechanics, performance, and injury risks among two different cultures and populations of baseball pitchers. Eleven American and eight Korean healthy professional baseball pitchers threw multiple fastball pitches off an indoor throwing mound positioned at regulation distance from home plate. A Motion Analysis three-dimensional automatic digitizing system was used to collect 200 Hz video data from four electronically synchronized cameras. Twenty kinematic, six temporal, and 11 kinetic variables were analyzed at lead foot contact, during the arm cocking and arm acceleration phases, at ball release, and during the arm deceleration phase. A radar gun was used to quantify ball velocity. At lead foot contact, the American pitchers had significantly greater horizontal abduction of the throwing shoulder, while Korean pitchers exhibited significantly greater abduction and external rotation of the throwing shoulder. During arm cocking, the American pitchers displayed significantly greater maximum shoulder external rotation and maximum pelvis angular velocity. At the instant of ball release, the American pitchers had significantly greater forward trunk tilt and ball velocity and significantly less knee flexion, which help explain why the American pitchers had 10% greater ball velocity compared to the Korean pitchers. The American pitchers had significantly greater maximum shoulder internal rotation torque and maximum elbow varus torque during arm cocking, significantly greater elbow flexion torque during arm acceleration, and significantly greater shoulder and elbow proximal forces during arm deceleration. While greater shoulder and elbow forces and torques generated in the American pitchers helped generate greater ball velocity for the American group, these greater kinetics may predispose this group to a higher risk of shoulder and elbow injuries.

Total solids content and degree of hydrolysis influence proteolytic inactivation kinetics following whey protein hydrolysate manufacture.

PubMed

Conesa, Celia; FitzGerald, Richard J

2013-10-23

The kinetics and thermodynamics of the thermal inactivation of Corolase PP in two different whey protein concentrate (WPC) hydrolysates with degree of hydrolysis (DH) values of ~10 and 21%, and at different total solids (TS) levels (from 5 to 30% w/v), were studied. Inactivation studies were performed in the temperature range from 60 to 75 °C, and residual enzyme activity was quantified using the azocasein assay. The inactivation kinetics followed a first-order model. Analysis of the activation energy, thermodynamic parameters, and D and z values, demonstrated that the inactivation of Corolase PP was dependent on solution TS. The intestinal enzyme preparation was more heat sensitive at low TS. Moreover, it was also found that the enzyme was more heat sensitive in solutions at higher DH.

Limitations of bootstrap current models

DOE PAGES

Belli, Emily A.; Candy, Jefferey M.; Meneghini, Orso; ...

2014-03-27

We assess the accuracy and limitations of two analytic models of the tokamak bootstrap current: (1) the well-known Sauter model and (2) a recent modification of the Sauter model by Koh et al. For this study, we use simulations from the first-principles kinetic code NEO as the baseline to which the models are compared. Tests are performed using both theoretical parameter scans as well as core- to-edge scans of real DIII-D and NSTX plasma profiles. The effects of extreme aspect ratio, large impurity fraction, energetic particles, and high collisionality are studied. In particular, the error in neglecting cross-species collisional couplingmore » – an approximation inherent to both analytic models – is quantified. Moreover, the implications of the corrections from kinetic NEO simulations on MHD equilibrium reconstructions is studied via integrated modeling with kinetic EFIT.« less

The Magnetorotational Instability in a Collisionless Plasma

NASA Astrophysics Data System (ADS)

Quataert, Eliot; Dorland, William; Hammett, Gregory W.

2002-09-01

We consider the linear axisymmetric stability of a differentially rotating collisionless plasma in the presence of a weak magnetic field; we restrict our analysis to wavelengths much larger than the proton Larmor radius. This is the kinetic version of the magnetorotational instability explored extensively as a mechanism for magnetic field amplification and angular momentum transport in accretion disks. The kinetic calculation is appropriate for hot accretion flows onto compact objects and for the growth of very weak magnetic fields, where the collisional mean free path is larger than the wavelength of the unstable modes. We show that the kinetic instability criterion is the same as in MHD, namely that the angular velocity decrease outward. However, nearly every mode has a linear kinetic growth rate that differs from its MHD counterpart. The kinetic growth rates also depend explicitly on β, i.e., on the ratio of the gas pressure to the pressure of the seed magnetic field. For β~1 the kinetic growth rates are similar to the MHD growth rates, while for β>>1 they differ significantly. For β>>1, the fastest growing mode has a growth rate ~sqrt(3)Ω for a Keplerian disk, larger than its MHD counterpart; there are also many modes whose growth rates are negligible, <~β-1/2Ω<<Ω. We provide a detailed physical interpretation of these results and show that gas pressure forces, rather than just magnetic forces, are central to the behavior of the magnetorotational instability in a collisionless plasma. We also discuss the astrophysical implications of our analysis.

Mode Reduction and Upscaling of Reactive Transport Under Incomplete Mixing

NASA Astrophysics Data System (ADS)

Lester, D. R.; Bandopadhyay, A.; Dentz, M.; Le Borgne, T.

2016-12-01

Upscaling of chemical reactions in partially-mixed fluid environments is a challenging problem due to the detailed interactions between inherently nonlinear reaction kinetics and complex spatio-temporal concentration distributions under incomplete mixing. We address this challenge via the development of an order reduction method for the advection-diffusion-reaction equation (ADRE) via projection of the reaction kinetics onto a small number N of leading eigenmodes of the advection-diffusion operator (the so-called "strange eigenmodes" of the flow) as an N-by-N nonlinear system, whilst mixing dynamics only are projected onto the remaining modes. For simple kinetics and moderate Péclet and Damkhöler numbers, this approach yields analytic solutions for the concentration mean, evolving spatio-temporal distribution and PDF in terms of the well-mixed reaction kinetics and mixing dynamics. For more complex kinetics or large Péclet or Damkhöler numbers only a small number of modes are required to accurately quantify the mixing and reaction dynamics in terms of the concentration field and PDF, facilitating greatly simplified approximation and analysis of reactive transport. Approximate solutions of this low-order nonlinear system provide quantiative predictions of the evolving concentration PDF. We demonstrate application of this method to a simple random flow and various mass-action reaction kinetics.

Preferential flow in municipal solid waste and implications for long-term leachate quality: valuation of laboratory-scale experiments.

PubMed

Rosqvist, N H; Dollar, L H; Fourie, A B

2005-08-01

In this paper, we study and quantify pollutant concentrations after long-term leaching at relatively low flow rates and residual concentrations after heavy flushing of a 0.14 m3 municipal solid waste sample. Moreover, water flow and solute transport through preferential flow paths are studied by model interpretation of experimental break-through curves (BTCs), generated by tracer tests. In the study it was found that high concentrations of chloride remain after several pore volumes of water have percolated through the waste sample. The residual concentration was found to be considerably higher than can be predicted by degradation models. For model interpretations of the experimental BTCs, two probabilistic model approaches were applied, the transfer function model and the Lagrangian transport formulation. The experimental BTCs indicated the presence of preferential flow through the waste mass and the model interpretation of the BTCs suggested that between 19 and 41% of the total water content participated in the transport of solute through preferential flow paths. In the study, the occurrence of preferential flow was found to be dependent on the flow rate in the sense that a high flow rate enhances the preferential flow. However, to fully quantify the possible dependence between flow rate and preferential flow, experiments on a broader range of experimental conditions are suggested. The chloride washout curve obtained over the 4-year study period shows that as a consequence of the water flow in favoured flow paths, bypassing other parts of the solid waste body, the leachate quality may reflect only the flow paths and their surroundings. The results in this study thus show that in order to improve long-term prediction of the leachate quality and quantity the magnitude of the preferential water flow through a landfill must be taken into account.

iSCHRUNK--In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks.

PubMed

Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

2016-01-01

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-based metabolic flux analysis contribute to improved understanding of steady-state properties of metabolism. However, knowledge about kinetics and enzyme activities though essential for quantitative understanding of metabolic dynamics remains scarce and involves uncertainty. Here, we present a computational methodology that allow us to determine and quantify the kinetic parameters that correspond to a certain physiology as it is described by a given metabolic flux profile and a given metabolite concentration vector. Though we initially determine kinetic parameters that involve a high degree of uncertainty, through the use of kinetic modeling and machine learning principles we are able to obtain more accurate ranges of kinetic parameters, and hence we are able to reduce the uncertainty in the model analysis. We computed the distribution of kinetic parameters for glucose-fed E. coli producing 1,4-butanediol and we discovered that the observed physiological state corresponds to a narrow range of kinetic parameters of only a few enzymes, whereas the kinetic parameters of other enzymes can vary widely. Furthermore, this analysis suggests which are the enzymes that should be manipulated in order to engineer the reference state of the cell in a desired way. The proposed approach also sets up the foundations of a novel type of approaches for efficient, non-asymptotic, uniform sampling of solution spaces. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Physical and mechanical metallurgy of zirconium alloys for nuclear applications: a multi-scale computational study

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

Glazoff, Michael Vasily

2014-10-01

In the post-Fukushima world, the stability of materials under extreme conditions is an important issue for the safety of nuclear reactors. Because the nuclear industry is going to continue using advanced zirconium cladding materials in the foreseeable future, it become critical to gain fundamental understanding of the several interconnected problems. First, what are the thermodynamic and kinetic factors affecting the oxidation and hydrogen pick-up by these materials at normal, off-normal conditions, and in long-term storage? Secondly, what protective coatings (if any) could be used in order to gain extremely valuable time at off-normal conditions, e.g., when temperature exceeds the criticalmore » value of 2200°F? Thirdly, the kinetics of oxidation of such protective coating or braiding needs to be quantified. Lastly, even if some degree of success is achieved along this path, it is absolutely critical to have automated inspection algorithms allowing identifying defects of cladding as soon as possible. This work strives to explore these interconnected factors from the most advanced computational perspective, utilizing such modern techniques as first-principles atomistic simulations, computational thermodynamics of materials, diffusion modeling, and the morphological algorithms of image processing for defect identification. Consequently, it consists of the four parts dealing with these four problem areas preceded by the introduction and formulation of the studied problems. In the 1st part an effort was made to employ computational thermodynamics and ab initio calculations to shed light upon the different stages of oxidation of ziraloys (2 and 4), the role of microstructure optimization in increasing their thermal stability, and the process of hydrogen pick-up, both in normal working conditions and in long-term storage. The 2nd part deals with the need to understand the influence and respective roles of the two different plasticity mechanisms in Zr nuclear alloys: twinning (at low T) and crystallographic slip (higher T’s). For that goal, a description of the advanced plasticity model is outlined featuring the non-associated flow rule in hcp materials including Zr. The 3rd part describes the kinetic theory of oxidation of the several materials considered to be perspective coating materials for Zr alloys: SiC and ZrSiO 4. In the 4th part novel and advanced projectional algorithms for defect identification in zircaloy coatings are described. In so doing, the author capitalized on some 12 years of his applied industrial research in this area. Our conclusions and recommendations are presented in the 5th part of this work, along with the list of used literature and the scripts for atomistic, thermodynamic, kinetic, and morphological computations.« less

Modeling of the Effect of Path Planning on Thermokinetic Evolutions in Laser Powder Deposition Process

NASA Astrophysics Data System (ADS)

Foroozmehr, Ehsan; Kovacevic, Radovan

2011-07-01

A thermokinetic model coupling finite-element heat transfer with transformation kinetics is developed to determine the effect of deposition patterns on the phase-transformation kinetics of laser powder deposition (LPD) process of a hot-work tool steel. The finite-element model is used to define the temperature history of the process used in an empirical-based kinetic model to analyze the tempering effect of the heating and cooling cycles of the deposition process. An area is defined to be covered by AISI H13 on a substrate of AISI 1018 with three different deposition patterns: one section, two section, and three section. The two-section pattern divides the area of the one-section pattern into two sections, and the three-section pattern divides that area into three sections. The results show that dividing the area under deposition into smaller areas can influence the phase transformation kinetics of the process and, consequently, change the final hardness of the deposited material. The two-section pattern shows a higher average hardness than the one-section pattern, and the three-section pattern shows a fully hardened surface without significant tempered zones of low hardness. To verify the results, a microhardness test and scanning electron microscope were used.

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

Chiral anomaly, Berry phase, and chiral kinetic theory from worldlines in quantum field theory

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

Mueller, Niklas; Venugopalan, Raju

Here, we outline a novel chiral kinetic theory framework for systematic computations of the Chiral Magnetic Effect (CME) in ultrarelativistic heavy-ion collisions. The real part of the fermion determinant in the QCD effective action is expressed as a supersymmetric world-line action of spinning, colored, Grassmanian point particles in background gauge fields, with equations of motion that are covariant generalizations of the Bargmann-Michel-Telegdi and Wong equations. Berry’s phase is obtained in a consistent non-relativistic adiabatic limit. The chiral anomaly, in contrast, arises from the phase of the fermion determinant; its topological properties are therefore distinct from those of the Berry phase.more » We show that the imaginary contribution to the fermion determinant too can be expressed as a point particle world-line path integral and derive the corresponding anomalous axial vector current. Our results can be used to derive a covariant relativistic chiral kinetic theory including the effects of topological fluctuations that has overlap with classical-statistical simulations of the CME at early times and anomalous hydrodynamics at late times.« less

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

DOE PAGES

Gao, Connie W.; Allen, Joshua W.; Green, William H.; ...

2016-02-24

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involvingmore » carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.« less

Chiral anomaly, Berry phase, and chiral kinetic theory from worldlines in quantum field theory

DOE PAGES

Mueller, Niklas; Venugopalan, Raju

2018-03-21

Here, we outline a novel chiral kinetic theory framework for systematic computations of the Chiral Magnetic Effect (CME) in ultrarelativistic heavy-ion collisions. The real part of the fermion determinant in the QCD effective action is expressed as a supersymmetric world-line action of spinning, colored, Grassmanian point particles in background gauge fields, with equations of motion that are covariant generalizations of the Bargmann-Michel-Telegdi and Wong equations. Berry’s phase is obtained in a consistent non-relativistic adiabatic limit. The chiral anomaly, in contrast, arises from the phase of the fermion determinant; its topological properties are therefore distinct from those of the Berry phase.more » We show that the imaginary contribution to the fermion determinant too can be expressed as a point particle world-line path integral and derive the corresponding anomalous axial vector current. Our results can be used to derive a covariant relativistic chiral kinetic theory including the effects of topological fluctuations that has overlap with classical-statistical simulations of the CME at early times and anomalous hydrodynamics at late times.« less

Power beaming research at NASA

NASA Technical Reports Server (NTRS)

Rather, John D. G.

1992-01-01

NASA's current research activities to evaluate laser power beaming systems are summarized with regard to their applications of greatest interest. Key technical certainties and uncertainties pertaining to laser power beaming systems appropriate for space applications are quantified. A path of development is presented that includes maturation of key technology components for reliable laser and millimeter wave power beaming systems during the 1990s.

Thin Layer Sensory Cues Affect Antarctic Krill Swimming Kinematics

NASA Astrophysics Data System (ADS)

True, A. C.; Webster, D. R.; Weissburg, M. J.; Yen, J.

2013-11-01

A Bickley jet (laminar, planar free jet) is employed in a recirculating flume system to replicate thin shear and phytoplankton layers for krill behavioral assays. Planar laser-induced fluorescence (LIF) and particle image velocimetry (PIV) measurements quantify the spatiotemporal structure of the chemical and free shear layers, respectively, ensuring a close match to in situ hydrodynamic and biochemical conditions. Path kinematics from digitized trajectories of free-swimming Euphausia superba examine the effects of hydrodynamic sensory cues (deformation rate) and bloom level phytoplankton patches (~1000 cells/mL, Tetraselamis spp.) on krill behavior (body orientation, swimming modes and kinematics, path fracticality). Krill morphology is finely tuned for receiving and deciphering both hydrodynamic and chemical information that is vital for basic life processes such as schooling behaviors, predator/prey, and mate interactions. Changes in individual krill behavior in response to ecologically-relevant sensory cues have the potential to produce population-scale phenomena with significant ecological implications. Krill are a vital trophic link between primary producers (phytoplankton) and larger animals (seabirds, whales, fish, penguins, seals) as well as the subjects of a valuable commercial fishery in the Southern Ocean; thus quantifying krill behavioral responses to relevant sensory cues is an important step towards accurately modeling Antarctic ecosystems.

Multi-criteria robustness analysis of metro networks

NASA Astrophysics Data System (ADS)

Wang, Xiangrong; Koç, Yakup; Derrible, Sybil; Ahmad, Sk Nasir; Pino, Willem J. A.; Kooij, Robert E.

2017-05-01

Metros (heavy rail transit systems) are integral parts of urban transportation systems. Failures in their operations can have serious impacts on urban mobility, and measuring their robustness is therefore critical. Moreover, as physical networks, metros can be viewed as topological entities, and as such they possess measurable network properties. In this article, by using network science and graph theory, we investigate ten theoretical and four numerical robustness metrics and their performance in quantifying the robustness of 33 metro networks under random failures or targeted attacks. We find that the ten theoretical metrics capture two distinct aspects of robustness of metro networks. First, several metrics place an emphasis on alternative paths. Second, other metrics place an emphasis on the length of the paths. To account for all aspects, we standardize all ten indicators and plot them on radar diagrams to assess the overall robustness for metro networks. Overall, we find that Tokyo and Rome are the most robust networks. Rome benefits from short transferring and Tokyo has a significant number of transfer stations, both in the city center and in the peripheral area of the city, promoting both a higher number of alternative paths and overall relatively short path-lengths.

A physical mechanism of cancer heterogeneity

NASA Astrophysics Data System (ADS)

Chen, Cong; Wang, Jin

2016-02-01

We studied a core cancer gene regulatory network motif to uncover possible source of cancer heterogeneity from epigenetic sources. When the time scale of the protein regulation to the gene is faster compared to the protein synthesis and degradation (adiabatic regime), normal state, cancer state and an intermediate premalignant state emerge. Due to the epigenetics such as DNA methylation and histone remodification, the time scale of the protein regulation to the gene can be slower or comparable to the protein synthesis and degradation (non-adiabatic regime). In this case, many more states emerge as possible phenotype alternations. This gives the origin of the heterogeneity. The cancer heterogeneity is reflected from the emergence of more phenotypic states, larger protein concentration fluctuations, wider kinetic distributions and multiplicity of kinetic paths from normal to cancer state, higher energy cost per gene switching, and weaker stability.

Direct solar-pumped iodine laser amplifier

NASA Technical Reports Server (NTRS)

Han, Kwang S.; Kim, K. H.; Stock, L. V.

1986-01-01

In order to evaluate the feasibility of the solar pumped dye laser, the parametric study of a dye laser amplifier pumped by a solar simulator and flashlamp was carried out, and the amplifier gains were measured at various pump beam irradiances on the dye cell. Rhodamine 6G was considered as a candidate for the solar pumped laser because of its good utilization of the solar spectrum and high quantum efficiency. The measurement shows that a solar concentration of 20,000 is required to reach the threshold of the dye. The work to construct a kinetic model algorithm which predicts the output parameter of laser was progressed. The kinetic model was improved such that there is good agreement between the theoretical model and experimental data for the systems defined previously as flashlamp pumped laser oscillator, and the long path length solar pumped laser.

Roads at risk - traffic detours from debris flows in southern Norway

NASA Astrophysics Data System (ADS)

Meyer, N. K.; Schwanghart, W.; Korup, O.; Nadim, F.

2014-10-01

Globalization and interregional exchange of people, goods, and services has boosted the importance of and reliance on all kinds of transport networks. The linear structure of road networks is especially sensitive to natural hazards. In southern Norway, steep topography and extreme weather events promote frequent traffic disruption caused by debris flows. Topographic susceptibility and trigger frequency maps serve as input into a hazard appraisal at the scale of first-order catchments to quantify the impact of debris flows on the road network in terms of a failure likelihood of each link connecting two network vertices, e.g., road junctions. We compute total additional traffic loads as a function of traffic volume and excess distance, i.e. the extra length of an alternative path connecting two previously disrupted network vertices using a shortest-path algorithm. Our risk metric of link failure is the total additional annual traffic load expressed as vehicle kilometers because of debris-flow related road closures. We present two scenarios demonstrating the impact of debris flows on the road network, and quantify the associated path failure likelihood between major cities in southern Norway. The scenarios indicate that major routes crossing the central and northwestern part of the study area are associated with high link failure risk. Yet options for detours on major routes are manifold, and incur only little additional costs provided that drivers are sufficiently well informed about road closures. Our risk estimates may be of importance to road network managers and transport companies relying of speedy delivery of services and goods.

Roads at risk: traffic detours from debris flows in southern Norway

NASA Astrophysics Data System (ADS)

Meyer, N. K.; Schwanghart, W.; Korup, O.; Nadim, F.

2015-05-01

Globalisation and interregional exchange of people, goods, and services has boosted the importance of and reliance on all kinds of transport networks. The linear structure of road networks is especially sensitive to natural hazards. In southern Norway, steep topography and extreme weather events promote frequent traffic disruption caused by debris flows. Topographic susceptibility and trigger frequency maps serve as input into a hazard appraisal at the scale of first-order catchments to quantify the impact of debris flows on the road network in terms of a failure likelihood of each link connecting two network vertices, e.g. road junctions. We compute total additional traffic loads as a function of traffic volume and excess distance, i.e. the extra length of an alternative path connecting two previously disrupted network vertices using a shortest-path algorithm. Our risk metric of link failure is the total additional annual traffic load, expressed as vehicle kilometres, because of debris-flow-related road closures. We present two scenarios demonstrating the impact of debris flows on the road network and quantify the associated path-failure likelihood between major cities in southern Norway. The scenarios indicate that major routes crossing the central and north-western part of the study area are associated with high link-failure risk. Yet options for detours on major routes are manifold and incur only little additional costs provided that drivers are sufficiently well informed about road closures. Our risk estimates may be of importance to road network managers and transport companies relying on speedy delivery of services and goods.

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

PubMed

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

Moisture Risk in Unvented Attics Due to Air Leakage Paths

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

Prahl, D.; Shaffer, M.

2014-11-01

IBACOS completed an initial analysis of moisture damage potential in an unvented attic insulated with closed-cell spray polyurethane foam. To complete this analysis, the research team collected field data, used computational fluid dynamics to quantify the airflow rates through individual airflow (crack) paths, simulated hourly flow rates through the leakage paths with CONTAM software, correlated the CONTAM flow rates with indoor humidity ratios from Building Energy Optimization software, and used Wärme und Feuchte instationär Pro two-dimensional modeling to determine the moisture content of the building materials surrounding the cracks. Given the number of simplifying assumptions and numerical models associated withmore » this analysis, the results indicate that localized damage due to high moisture content of the roof sheathing is possible under very low airflow rates. Reducing the number of assumptions and approximations through field studies and laboratory experiments would be valuable to understand the real-world moisture damage potential in unvented attics.« less

Moisture Risk in Unvented Attics Due to Air Leakage Paths

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

Prahl, D.; Shaffer, M.

2014-11-01

IBACOS completed an initial analysis of moisture damage potential in an unvented attic insulated with closed-cell spray polyurethane foam. To complete this analysis, the research team collected field data, used computational fluid dynamics to quantify the airflow rates through individual airflow (crack) paths, simulated hourly flow rates through the leakage paths with CONTAM software, correlated the CONTAM flow rates with indoor humidity ratios from Building Energy Optimization software, and used Warme und Feuchte instationar Pro two-dimensional modeling to determine the moisture content of the building materials surrounding the cracks. Given the number of simplifying assumptions and numerical models associated withmore » this analysis, the results indicate that localized damage due to high moisture content of the roof sheathing is possible under very low airflow rates. Reducing the number of assumptions and approximations through field studies and laboratory experiments would be valuable to understand the real-world moisture damage potential in unvented attics.« less

ARM Evaluation Product : Droplet Number Concentration Value-Added Product

DOE Data Explorer

Riihimaki, Laura

2014-05-15

Cloud droplet number concentration is an important factor in understanding aerosol-cloud interactions. As aerosol concentration increases, it is expected that droplet number concentration, Nd, will increase and droplet size decrease, for a given liquid water path (Twomey 1977), which will greatly affect cloud albedo as smaller droplets reflect more shortwave radiation. However, the magnitude and variability of these processes under different environmental conditions is still uncertain. McComiskey et al. (2009) have implemented a method, based on Boers and Mitchell (1994), for calculating Nd from ground-based remote sensing measurements of optical depth and liquid water path. They show that the magnitude of the aerosol-cloud interactions (ACI) varies with a range of factors, including the relative value of the cloud liquid water path (LWP), the aerosol size distribution, and the cloud updraft velocity. Estimates of Nd under a range of cloud types and conditions and at a variety of sites are needed to further quantify the impacts of aerosol cloud interactions.

An adaptive multi-level simulation algorithm for stochastic biological systems

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

Lester, C., E-mail: lesterc@maths.ox.ac.uk; Giles, M. B.; Baker, R. E.

2015-01-14

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Montemore » Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10(1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.« less

Simple Potentiometric Determination of Reducing Sugars

ERIC Educational Resources Information Center

Moresco, Henry; Sanson, Pedro; Seoane, Gustavo

2008-01-01

In this article a potentiometric method for reducing sugar quantification is described. Copper(II) ion reacts with the reducing sugar (glucose, fructose, and others), and the excess is quantified using a copper wire indicator electrode. In order to accelerate the kinetics of the reaction, working conditions such as pH and temperature must be…

Host - HIF- 1alpha Pathway And Hypoxia: In Vitro Studies And Mathematical Model

DTIC Science & Technology

2016-08-30

TERMS mathematical model, signaling pathways, hypoxia, immunohistochemistry, ELISA , inhalation chamber 16. SECURITY CLASSIFICATION OF: U 17...B. HIF-1α ELISA Procedure ........................................................................................27 Appendix C. HIF-1α Model...Quantifying Induction of HIF-1α Expression using ELISA .........................................15 Figure 10. Simulation Outputs from HIF-1α Kinetic

Cone photopigment in older subjects: decreased optical density in early age-related macular degeneration

NASA Astrophysics Data System (ADS)

Elsner, Ann E.; Burns, Stephen A.; Weiter, John J.

2002-01-01

We measured changes to cone photoreceptors in patients with early age-related macular degeneration. The data of 53 patients were compared with normative data for color matching measurements of long- and middle-wavelength-sensitive cones in the central macula. A four-parameter model quantified cone photopigment optical density and kinetics. Cone photopigment optical density was on average less for the patients than for normal subjects and was uncorrelated with visual acuity. More light was needed to reduce the photopigment density by 50% in the steady state for patients. These results imply that cone photopigment optical density is reduced by factors other than slowed kinetics.

A new chlorophycean nickel hyperaccumulator.

PubMed

Harish; Sundaramoorthy, S; Kumar, Devendra; Vaijapurkar, S G

2008-06-01

Bioremediation of nickel by chlorophycean bioremediator, Chlorococcum hemicolum was investigated. The growth rates at various concentrations of Ni2+ were assessed in terms of protein level and 12 mg L(-1) of the Ni2+ is the tolerance limit (46.76% level of growth kinetics). Absorption/adsorption kinetics was estimated after 240 h of Ni2+ treatments. Absorptions were higher than adsorption with maximum accumulation factor (AF) of 1.37. Ni2+ concentration and absorption were linearly related (r=0.98; p>0.01). Other biochemical parameters like total sugar, chlorophyll and carotenoids were also quantified to correlate the state of metabolism and these exhibited reduction due to heavy metal stress.

Atomic-scale to Meso-scale Simulation Studies of Thermal Ageing and Irradiation Effects in Fe- Cr Alloys

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

Stanley, Eugene; Liu, Li

In this project, we target at three primary objectives: (1) Molecular Dynamics (MD) code development for Fe-Cr alloys, which can be utilized to provide thermodynamic and kinetic properties as inputs in mesoscale Phase Field (PF) simulations; (2) validation and implementation of the MD code to explain thermal ageing and radiation damage; and (3) an integrated modeling platform for MD and PF simulations. These two simulation tools, MD and PF, will ultimately be merged to understand and quantify the kinetics and mechanisms of microstructure and property evolution of Fe-Cr alloys under various thermal and irradiation environments

Experimental characterization of seasonal variations in infrasonic traveltimes on the Korean Peninsula with implications for infrasound event location

NASA Astrophysics Data System (ADS)

Che, Il-Young; Stump, Brian W.; Lee, Hee-Il

2011-04-01

The dependence of infrasound propagation on the season and path environment was quantified by the analysis of more than 1000 repetitive infrasonic ground-truth events at an active, open-pit mine over two years. Blast-associated infrasonic signals were analysed from two infrasound arrays (CHNAR and ULDAR) located at similar distances of 181 and 169 km, respectively, from the source but in different azimuthal directions and with different path environments. The CHNAR array is located to the NW of the source area with primarily a continental path, whereas the ULDAR is located East of the source with a path dominated by open ocean. As a result, CHNAR observations were dominated by stratospheric phases with characteristic celerities of 260-289 m s-1 and large seasonal variations in the traveltime, whereas data from ULDAR consisted primarily of tropospheric phases with larger celerities from 322 to 361 m s-1 and larger daily than seasonal variation in the traveltime. The interpretation of these observations is verified by ray tracing using atmospheric models incorporating daily weather balloon data that characterizes the shallow atmosphere for the two years of the study. Finally, experimental celerity models that included seasonal path effects were constructed from the long-term data set. These experimental celerity models were used to constrain traveltime variations in infrasonic location algorithms providing improved location estimates as illustrated with the empirical data set.

Global fully kinetic models of planetary magnetospheres with iPic3D

NASA Astrophysics Data System (ADS)

Gonzalez, D.; Sanna, L.; Amaya, J.; Zitz, A.; Lembege, B.; Markidis, S.; Schriver, D.; Walker, R. J.; Berchem, J.; Peng, I. B.; Travnicek, P. M.; Lapenta, G.

2016-12-01

We report on the latest developments of our approach to model planetary magnetospheres, mini magnetospheres and the Earth's magnetosphere with the fully kinetic, electromagnetic particle in cell code iPic3D. The code treats electrons and multiple species of ions as full kinetic particles. We review: 1) Why a fully kinetic model and in particular why kinetic electrons are needed for capturing some of the most important aspects of the physics processes of planetary magnetospheres. 2) Why the energy conserving implicit method (ECIM) in its newest implementation [1] is the right approach to reach this goal. We consider the different electron scales and study how the new IECIM can be tuned to resolve only the electron scales of interest while averaging over the unresolved scales preserving their contribution to the evolution. 3) How with modern computing planetary magnetospheres, mini magnetosphere and eventually Earth's magnetosphere can be modeled with fully kinetic electrons. The path from petascale to exascale for iPiC3D is outlined based on the DEEP-ER project [2], using dynamic allocation of different processor architectures (Xeon and Xeon Phi) and innovative I/O technologies.Specifically results from models of Mercury are presented and compared with MESSENGER observations and with previous hybrid (fluid electrons and kinetic ions) simulations. The plasma convection around the planets includes the development of hydrodynamic instabilities at the flanks, the presence of the collisionless shocks, the magnetosheath, the magnetopause, reconnection zones, the formation of the plasma sheet and the magnetotail, and the variation of ion/electron plasma flows when crossing these frontiers. Given the full kinetic nature of our approach we focus on detailed particle dynamics and distribution at locations that can be used for comparison with satellite data. [1] Lapenta, G. (2016). Exactly Energy Conserving Implicit Moment Particle in Cell Formulation. arXiv preprint arXiv:1602.06326.[2] www.deep-er.eu

Online Aerial Terrain Mapping for Ground Robot Navigation

PubMed Central

Peterson, John; Chaudhry, Haseeb; Abdelatty, Karim; Bird, John; Kochersberger, Kevin

2018-01-01

This work presents a collaborative unmanned aerial and ground vehicle system which utilizes the aerial vehicle’s overhead view to inform the ground vehicle’s path planning in real time. The aerial vehicle acquires imagery which is assembled into a orthomosaic and then classified. These terrain classes are used to estimate relative navigation costs for the ground vehicle so energy-efficient paths may be generated and then executed. The two vehicles are registered in a common coordinate frame using a real-time kinematic global positioning system (RTK GPS) and all image processing is performed onboard the unmanned aerial vehicle, which minimizes the data exchanged between the vehicles. This paper describes the architecture of the system and quantifies the registration errors between the vehicles. PMID:29461496

Online Aerial Terrain Mapping for Ground Robot Navigation.

PubMed

Peterson, John; Chaudhry, Haseeb; Abdelatty, Karim; Bird, John; Kochersberger, Kevin

2018-02-20

This work presents a collaborative unmanned aerial and ground vehicle system which utilizes the aerial vehicle's overhead view to inform the ground vehicle's path planning in real time. The aerial vehicle acquires imagery which is assembled into a orthomosaic and then classified. These terrain classes are used to estimate relative navigation costs for the ground vehicle so energy-efficient paths may be generated and then executed. The two vehicles are registered in a common coordinate frame using a real-time kinematic global positioning system (RTK GPS) and all image processing is performed onboard the unmanned aerial vehicle, which minimizes the data exchanged between the vehicles. This paper describes the architecture of the system and quantifies the registration errors between the vehicles.

Thermodynamics and computation during collective motion near criticality

NASA Astrophysics Data System (ADS)

Crosato, Emanuele; Spinney, Richard E.; Nigmatullin, Ramil; Lizier, Joseph T.; Prokopenko, Mikhail

2018-01-01

We study self-organization of collective motion as a thermodynamic phenomenon in the context of the first law of thermodynamics. It is expected that the coherent ordered motion typically self-organises in the presence of changes in the (generalized) internal energy and of (generalized) work done on, or extracted from, the system. We aim to explicitly quantify changes in these two quantities in a system of simulated self-propelled particles and contrast them with changes in the system's configuration entropy. In doing so, we adapt a thermodynamic formulation of the curvatures of the internal energy and the work, with respect to two parameters that control the particles' alignment. This allows us to systematically investigate the behavior of the system by varying the two control parameters to drive the system across a kinetic phase transition. Our results identify critical regimes and show that during the phase transition, where the configuration entropy of the system decreases, the rates of change of the work and of the internal energy also decrease, while their curvatures diverge. Importantly, the reduction of entropy achieved through expenditure of work is shown to peak at criticality. We relate this both to a thermodynamic efficiency and the significance of the increased order with respect to a computational path. Additionally, this study provides an information-geometric interpretation of the curvature of the internal energy as the difference between two curvatures: the curvature of the free entropy, captured by the Fisher information, and the curvature of the configuration entropy.

A study of dynamical behavior of space environment

NASA Technical Reports Server (NTRS)

Wu, S. T.

1974-01-01

Studies have covered a wide range of problems in the space environment, such as the problems of the dynamical behavior of the thermosphere, hydromagnetic wave propagation in the ionosphere, and interplanetary space environment. The theories used to analyze these problems range from a continuum theory of magnetohydrodynamics to the kinetic theory of free molecular flow. This is because the problems encountered covered the entire range of the Knudsen number (i.e., the ratio of mean free path to the characteristic length). Significant results are summarized.

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

Laser Atmospheric Propagation Kinetics

DTIC Science & Technology

1975-07-01

the available data. Section III also describes the mathematical model used to calculate the relaxation of the vibrational degrees of freedom in...has been used. This relation is derived in Appendix C, 11 -30- ---— ^^^^UM^ MUfi L^^MAamMMWaaMbAaMMMMMAMÜMMMM MMUMfa*,«« M^Mi mmm \\i •s T...is when the change in the optical path length is of the order of \\/2-n. Mathematically , this is expressed by the formula t vf (n - l)4jrdx = O

Quantum annealing of the traveling-salesman problem.

PubMed

Martonák, Roman; Santoro, Giuseppe E; Tosatti, Erio

2004-11-01

We propose a path-integral Monte Carlo quantum annealing scheme for the symmetric traveling-salesman problem, based on a highly constrained Ising-like representation, and we compare its performance against standard thermal simulated annealing. The Monte Carlo moves implemented are standard, and consist in restructuring a tour by exchanging two links (two-opt moves). The quantum annealing scheme, even with a drastically simple form of kinetic energy, appears definitely superior to the classical one, when tested on a 1002-city instance of the standard TSPLIB.

Single Cell Force Spectroscopy for Quantification of Cellular Adhesion on Surfaces

NASA Astrophysics Data System (ADS)

Christenson, Wayne B.

Cell adhesion is an important aspect of many biological processes. The atomic force microscope (AFM) has made it possible to quantify the forces involved in cellular adhesion using a technique called single cell force spectroscopy (SCFS). AFM based SCFS offers versatile control over experimental conditions for probing directly the interaction between specific cell types and specific proteins, surfaces, or other cells. Transmembrane integrins are the primary proteins involved in cellular adhesion to the extra cellular matix (ECM). One of the chief integrins involved in the adhesion of leukocyte cells is alpha Mbeta2 (Mac-1). The experiments in this dissertation quantify the adhesion of Mac-1 expressing human embryonic kidney (HEK Mac-1), platelets, and neutrophils cells on substrates with different concentrations of fibrinogen and on fibrin gels and multi-layered fibrinogen coated fibrin gels. It was shown that multi-layered fibrinogen reduces the adhesion force of these cells considerably. A novel method was developed as part of this research combining total internal reflection microscopy (TIRFM) with SCFS allowing for optical microscopy of HEK Mac-1 cells interacting with bovine serum albumin (BSA) coated glass after interacting with multi-layered fibrinogen. HEK Mac-1 cells are able to remove fibrinogen molecules from the multi-layered fibrinogen matrix. An analysis methodology for quantifying the kinetic parameters of integrin-ligand interactions from SCFS experiments is proposed, and the kinetic parameters of the Mac-1 fibrinogen bond are quantified. Additional SCFS experiments quantify the adhesion of macrophages and HEK Mac-1 cells on functionalized glass surfaces and normal glass surfaces. Both cell types show highest adhesion on a novel functionalized glass surface that was prepared to induce macrophage fusion. These experiments demonstrate the versatility of AFM based SCFS, and how it can be applied to address many questions in cellular biology offering quantitative insights.

Thermal Boundary Layer Effects on Line-of-Sight Tunable Diode Laser Absorption Spectroscopy (TDLAS) Gas Concentration Measurements.

PubMed

Qu, Zhechao; Werhahn, Olav; Ebert, Volker

2018-06-01

The effects of thermal boundary layers on tunable diode laser absorption spectroscopy (TDLAS) measurement results must be quantified when using the line-of-sight (LOS) TDLAS under conditions with spatial temperature gradient. In this paper, a new methodology based on spectral simulation is presented quantifying the LOS TDLAS measurement deviation under conditions with thermal boundary layers. The effects of different temperature gradients and thermal boundary layer thickness on spectral collisional widths and gas concentration measurements are quantified. A CO 2 TDLAS spectrometer, which has two gas cells to generate the spatial temperature gradients, was employed to validate the simulation results. The measured deviations and LOS averaged collisional widths are in very good agreement with the simulated results for conditions with different temperature gradients. We demonstrate quantification of thermal boundary layers' thickness with proposed method by exploitation of the LOS averaged the collisional width of the path-integrated spectrum.

CO oxidation reaction on Pt(111) studied by the dynamic Monte Carlo method including lateral interactions of adsorbates.

PubMed

Nagasaka, Masanari; Kondoh, Hiroshi; Nakai, Ikuyo; Ohta, Toshiaki

2007-01-28

The dynamics of adsorbate structures during CO oxidation on Pt(111) surfaces and its effects on the reaction were studied by the dynamic Monte Carlo method including lateral interactions of adsorbates. The lateral interaction energies between adsorbed species were calculated by the density functional theory method. Dynamic Monte Carlo simulations were performed for the oxidation reaction over a mesoscopic scale, where the experimentally determined activation energies of elementary paths were altered by the calculated lateral interaction energies. The simulated results reproduced the characteristics of the microscopic and mesoscopic scale adsorbate structures formed during the reaction, and revealed that the complicated reaction kinetics is comprehensively explained by a single reaction path affected by the surrounding adsorbates. We also propose from the simulations that weakly adsorbed CO molecules at domain boundaries promote the island-periphery specific reaction.

Theoretical Study of Decomposition Pathways for HArF and HKrF

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Lundell, Jan; Gerber, R. Benny; Kwak, Donchan (Technical Monitor)

2002-01-01

To provide theoretical insights into the stability and dynamics of the new rare gas compounds HArF and HKrF, reaction paths for decomposition processes HRgF to Rg + HF and HRgF to H + Rg + F (Rg = Ar, Kr) are calculated using ab initio electronic structure methods. The bending channels, HRgF to Rg + HF, are described by single-configurational MP2 and CCSD(T) electronic structure methods, while the linear decomposition paths, HRgF to H + Rg + F, require the use of multi-configurational wave functions that include dynamic correlation and are size extensive. HArF and HKrF molecules are found to be energetically stable with respect to atomic dissociation products (H + Rg + F) and separated by substantial energy barriers from Rg + HF products, which ensure their kinetic stability. The results are compatible with experimental data on these systems.

Kinetics of conjugative gene transfer on surfaces in granular porous media

NASA Astrophysics Data System (ADS)

Massoudieh, A.; Crain, C.; Lambertini, E.; Nelson, K. E.; Barkouki, T.; L'Amoreaux, P.; Loge, F. J.; Ginn, T. R.

2010-03-01

The transfer of genetic material among bacteria in the environment can occur both in the planktonic and attached state. Given the propensity of organisms to exist in sessile microbial communities in oligotrophic subsurface conditions, and that such conditions typify the subsurface, this study focuses on exploratory modeling of horizontal gene transfer among surface-associated Escherichiacoli in the subsurface. The mathematics so far used to describe the kinetics of conjugation in biofilms are developed largely from experimental observations of planktonic gene transfer, and are absent of lags or plasmid stability that appear experimentally. We develop a model and experimental system to quantify bacterial filtration and gene transfer in the attached state, on granular porous media. We include attachment kinetics described in Nelson et al. (2007) using the filtration theory approach of Nelson and Ginn (2001, 2005) with motility of E. coli described according to Biondi et al. (1998).

Ion distribution in the hot spot of an inertial confinement fusion plasma

NASA Astrophysics Data System (ADS)

Tang, Xianzhu; Guo, Zehua; Berk, Herb

2012-10-01

Maximizing the fusion gain of inertial confinement fusion (ICF) for inertial fusion energy (IFE) applications leads to the standard scenario of central hot spot ignition followed by propagating burn wave through the cold/dense assembled fuel. The fact that the hot spot is surrounded by cold but dense fuel layer introduces subtle plasma physics which requires a kinetic description. Here we perform Fokker-Planck calculations and kinetic PIC simulations for an ICF plasma initially in pressure balance but having large temperature gradient over a narrow transition layer. The loss of the fast ion tail from the hot spot, which is important for fusion reactivity, is quantified by Fokker-Planck models. The role of electron energy transport and the ambipolar electric field is investigated via kinetic simulations and the fluid moment models. The net effect on both hot spot ion temperature and the ion tail distribution, and hence the fusion reactivity, is elucidated.

Adaptive characterization of recrystallization kinetics in IF steel by electron backscatter diffraction.

PubMed

Kim, Dong-Kyu; Park, Won-Woong; Lee, Ho Won; Kang, Seong-Hoon; Im, Yong-Taek

2013-12-01

In this study, a rigorous methodology for quantifying recrystallization kinetics by electron backscatter diffraction is proposed in order to reduce errors associated with the operator's skill. An adaptive criterion to determine adjustable grain orientation spread depending on the recrystallization stage is proposed to better identify the recrystallized grains in the partially recrystallized microstructure. The proposed method was applied in characterizing the microstructure evolution during annealing of interstitial-free steel cold rolled to low and high true strain levels of 0.7 and 1.6, respectively. The recrystallization kinetics determined by the proposed method was found to be consistent with the standard method of Vickers microhardness. The application of the proposed method to the overall recrystallization stages showed that it can be used for the rigorous characterization of progressive microstructure evolution, especially for the severely deformed material. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

Quantum correlations and Bell’s inequality violation in a Heisenberg spin dimer via neutron scattering

NASA Astrophysics Data System (ADS)

Cruz, C.

The characterization of quantum information quantifiers has attracted a considerable attention of the scientific community, since they are a useful tool to verify the presence of quantum correlations in a quantum system. In this context, in the present work we show a theoretical study of some quantifiers, such as entanglement witness, entanglement of formation, Bell’s inequality violation and geometric quantum discord as a function of the diffractive properties of neutron scattering. We provide one path toward identifying the presence of quantum correlations and quantum nonlocality in a molecular magnet as a Heisenberg spin-1/2 dimer, by diffractive properties typically obtained via neutron scattering experiments.

Robot-Assisted Arm Assessments in Spinal Cord Injured Patients: A Consideration of Concept Study

PubMed Central

Albisser, Urs; Rudhe, Claudia; Curt, Armin; Riener, Robert; Klamroth-Marganska, Verena

2015-01-01

Robotic assistance is increasingly used in neurological rehabilitation for enhanced training. Furthermore, therapy robots have the potential for accurate assessment of motor function in order to diagnose the patient status, to measure therapy progress or to feedback the movement performance to the patient and therapist in real time. We investigated whether a set of robot-based assessments that encompasses kinematic, kinetic and timing metrics is applicable, safe, reliable and comparable to clinical metrics for measurement of arm motor function. Twenty-four healthy subjects and five patients after spinal cord injury underwent robot-based assessments using the exoskeleton robot ARMin. Five different tasks were performed with aid of a visual display. Ten kinematic, kinetic and timing assessment parameters were extracted on joint- and end-effector level (active and passive range of motion, cubic reaching volume, movement time, distance-path ratio, precision, smoothness, reaction time, joint torques and joint stiffness). For cubic volume, joint torques and the range of motion for most joints, good inter- and intra-rater reliability were found whereas precision, movement time, distance-path ratio and smoothness showed weak to moderate reliability. A comparison with clinical scores revealed good correlations between robot-based joint torques and the Manual Muscle Test. Reaction time and distance-path ratio showed good correlation with the “Graded and Redefined Assessment of Strength, Sensibility and Prehension” (GRASSP) and the Van Lieshout Test (VLT) for movements towards a predefined position in the center of the frontal plane. In conclusion, the therapy robot ARMin provides a comprehensive set of assessments that are applicable and safe. The first results with spinal cord injured patients and healthy subjects suggest that the measurements are widely reliable and comparable to clinical scales for arm motor function. The methods applied and results can serve as a basis for the future development of end-effector and exoskeleton-based robotic assessments. PMID:25996374

Kinetic Effects in Inertial Confinement Fusion

NASA Astrophysics Data System (ADS)

Kagan, Grigory

2014-10-01

Sharp background gradients, inevitably introduced during ICF implosion, are likely responsible for the discrepancy between the predictions of the standard single-fluid rad-hydro codes and the experimental observations. On the one hand, these gradients drive the inter-ion-species transport, so the fuel composition no longer remains constant, unlike what the single-fluid codes assume. On the other hand, once the background scale is comparable to the mean free path, a fluid description becomes invalid. This point takes on special significance in plasmas, where the particle's mean free path scales with the square of this particle's energy. The distribution function of energetic ions may therefore be far from Maxwellian, even if thermal ions are nearly equilibrated. Ironically, it is these energetic, or tail, ions that are supposed to fuse at the onset of ignition. A combination of studies has been conducted to clarify the role of such kinetic effects on ICF performance. First, transport formalism applicable to multi-component plasmas has been developed. In particular, a novel ``electro-diffusion'' mechanism of the ion species separation has been shown to exist. Equally important, in drastic contrast to the classical case of the neutral gas mixture, thermo-diffusion is predicted to be comparable to, or even much larger than, baro-diffusion. By employing the effective potential theory this formalism has then been generalized to the case of a moderately coupled plasma with multiple ion species, making it applicable to the problem of mix at the shell/fuel interface in ICF implosion. Second, distribution function for the energetic ions has been found from first principles and the fusion reactivity reduction has been calculated for hot-spot relevant conditions. A technique for approximate evaluation of the distribution function has been identified. This finding suggests a path to effectively introducing the tail modification effects into mainline rad-hydro codes, while being in good agreement with the first principle based solution. This work was partially supported by the Laboratory Directed Research and Development (LDRD) program of LANL.

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

PubMed Central

Erickson, David W; Schink, Severin J.; Patsalo, Vadim; Williamson, James R.; Gerland, Ulrich; Hwa, Terence

2018-01-01

A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms1–3 and they remain a topic of active investigation4–11. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations12–17, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models15,18–20 from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions. PMID:29072300

Water-use efficiency of a poplar plantation in Northern China

Treesearch

Jie Zhou; Zhiqiang Zhang; Ge sun; Xianrui Fang; Tonggang Zha; Jiquan Chen; Asko Noormets; Junting Guo; Steve McNulty

2014-01-01

The water-use efficiency (WUE) of an ecosystem—defined as the gross ecosystem production (GEP) divided by the evapotranspiration (ET)—is an important index for understanding the coupling of water and carbon and quantifying water–carbon trade-offs in forests. An open-path eddy covariance technique and a microclimate measurement system were deployed to investigate the...

Photogrammetric Verification of Fiber Optic Shape Sensors on Flexible Aerospace Structures

NASA Technical Reports Server (NTRS)

Moore, Jason P.; Rogge, Matthew D.; Jones, Thomas W.

2012-01-01

Multi-core fiber (MCF) optic shape sensing offers the possibility of providing in-flight shape measurements of highly flexible aerospace structures and control surfaces for such purposes as gust load alleviation, flutter suppression, general flight control and structural health monitoring. Photogrammetric measurements of surface mounted MCF shape sensing cable can be used to quantify the MCF installation path and verify measurement methods.

Redistribution of soil metals and organic carbon via lateral flowpaths at the catchment scale in a glaciated upland setting

Treesearch

Rebecca R. Bourgault; Donald S. Ross; Scott W. Bailey; Thomas D. Bullen; Kevin J. McGuire; John P. Gannon

2017-01-01

Emerging evidence shows that interactions between soils and subsurface flow paths contribute to spatial variations in stream water chemistry in headwater catchments. However, few have yet attempted to quantify chemical variations in soils at catchment and hillslope scales. Watershed 3 (WS3) at Hubbard Brook Experimental Forest, New Hampshire, USA, was studied in order...

Using corporate finance to engineer an organizational turnaround.

PubMed

Sussman, Jason H; Dziesinski, Ray R

2002-11-01

Georgia's Southern Regional Medical Center used a proven corporate finance approach to dramatically improve its financial position and integrate its strategic and financial planning. Managers throughout the organization were educated about principles of corporate finance. Reliable cash-flow projections were used to create a multiyear glide path to financial stability. Initiatives were tied to specific time frames and quantifiable financial goals and underwent a standardized review process.

Characterization and Comparison of Vibration Transfer Paths in a Helicopter Gearbox and a Fixture Mounted Gearbox

NASA Technical Reports Server (NTRS)

Islam, Akm Anwarul; Dempsey, Paula J.; Feldman, Jason; Larsen, Chris

2014-01-01

Health monitoring of rotorcraft components, currently being performed by Health and Usage Monitoring Systems through analyses of vibration signatures of dynamic mechanical components, is very important for their safe and economic operation. HUMS analyze vibration signatures associated with faults and quantify them as condition indicators to predict component behavior. Vibration transfer paths are characterized by frequency response functions derived from the input/output relationship between applied force and dynamic response through a structure as a function of frequency. With an objective to investigate the differences in transfer paths, transfer path measurements were recorded under similar conditions in the left and right nose gearboxes of an AH-64 helicopter and in an isolated left nose gearbox in a test fixture at NASA Glenn Research Center. The test fixture enabled the application of measured torques-common during an actual operation. An impact hammer as well as commercial and lab piezo shakers, were used in conjunction with two types of commercially available accelerometers to collect the vibration response under various test conditions. The frequency response functions measured under comparable conditions of both systems were found to be consistent. Measurements made on the fixture indicated certain real-world installation and maintenance issues, such as sensor alignments, accelerometer locations and installation torques, had minimal effect. However, gear vibration transfer path dynamics appeared to be somewhat dependent on the presence of oil, and the transfer path dynamics were notably different if the force input was on the internal ring gear rather than on the external gearbox case.

Laboratory studies of stratospheric bromine chemistry: Kinetics of the reactions of bromine monoxide with nitrogen dioxide and atomic oxygen

NASA Astrophysics Data System (ADS)

Thorn, Robert Peyton

A laser flash photolysis - long path absorption - technique has been employed to study the kinetics of the reaction BrO+NO2+M(k(sub 16)) yields products as a function of temperature (248-346 K), pressure (16-800 Torr), and buffer gas identity (N2, CF4). 351 nm photolysis of NO2/Br2/N2 mixtures generated BrO. The BrO decay in the presence of excess NO2 was followed by UV absorption at 338.3 nm. The reaction is in the falloff regime between third and second order over the entire range of conditions investigated. This is the first study where temperature dependent measurements of k(sub 16)(P,T) have been reported at pressures greater than 12 Torr; hence, these results help constrain choices of k(sub 16)(P,T) for use in modeling stratospheric BrO(x) chemistry. The kinetics of the important stratospheric reaction BrO+O(P-3)(k(sub 14)) yields Br+O2 in N2 buffer gas have been studied as a function of temperature (233-328 K) and pressure (25-150 Torr) using a novel dual laser flash photolysis/long path absorption/resonance fluorescence technique. 248 nm pulsed laser photolysis of Br2/O3/N2 mixtures produces O atoms in excess over Br2. After a delay sufficient for BrO to be generated, a 532 nm laser pulse photolysis a small fraction of the O3 to generate O(P-3). The decay of O(P-3) in the presence of an excess, known concentration of BrO, as determined by UV absorption at 338.3 nm and by numerical simulation, is then followed by time-resoved atomic resonance fluorescence spectroscopy. The experimental results have shown the reaction kinetics to be independent of pressure, to increase with decreasing temperature, and to be faster than suggested by the only previous (indirect) measurement. The resulting Anhenius expression for k(sub 14)(T) is k(sub 14)(T) = 1.64 x 10(exp -11) exp(263/T) cm(exp 3) molecule(exp-1)s(exp -1). The absolute accuracy of k(sub 14)(T) at any temperature within the range studied is estimated to be +/- 25%. Possible kinetic interferences from production of vibrationally or electronically excited O2 are discussed. The effect of the faster reaction rate coefficients that are reported for the BrO + NO2 + M and BrO + O(P-3) reactions upon bromine partitioning and ozone depletion in the stratosphere is discussed.

Laboratory Studies of Stratospheric Bromine Chemistry: Kinetics of the Reactions of Bromine Monoxide with Nitrogen Dioxide and Atomic Oxygen.

NASA Astrophysics Data System (ADS)

Thorn, Robert Peyton, Jr.

A laser flash photolysis - long path absorption technique has been employed to study the kinetics of the reaction rm BrO + NO_2 + M{k _{16}atopto} products as a function of temperature (248-346 K), pressure (16 -800 Torr), and buffer gas identity (rm N _2,CF_4). 351 nm photolysis of rm NO_2/Br_2/N_2 mixtures generated BrO. The BrO decay in the presence of excess NO_2 was followed by UV absorption at 338.3 nm. The reaction is in the falloff regime between third and second order over the entire range of conditions investigated. This is the first study where temperature dependent measurements of k_{16} (P,T) have been reported at pressures greater than 12 Torr; hence, these results help constrain choices of k_{16}(P,T) for use in modeling stratospheric BrO_{rm x} chemistry. The kinetics of the important stratospheric reaction rm BrO+O(^3P)_sp{to }{k_{14}}Br+O_2 in N_2 buffer gas have been studied as a function of temperature (233-328 K) and pressure (25 -150 Torr) using a novel dual laser flash photolysis/long path absorption/resonance fluorescence technique. 248 nm pulsed laser photolysis of rm Br_2/O _3/N_2 mixtures produces O atoms in excess over Br_2. After a delay sufficient for BrO to be generated, a 532 nm laser pulse photolyses a small fraction of the O_3 to generate O(^3P). The decay of O(^3P) in the presence of an excess, known concentration of BrO, as determined by UV absorption at 338.3 nm and by numerical simulation, is then followed by time-resolved atomic resonance fluorescence spectroscopy. The experimental results have shown the reaction kinetics to be independent of pressure, to increase with decreasing temperature, and to be faster than suggested by the only previous (indirect) measurement. The resulting Anhenius expression for k_{14}(T) is given below.rm k_{14 }(T) = 1.64times 10^{-11} exp (263/T) cm^3 molecule ^{-1} s^{-1} The absolute accuracy of k_{14 }(T) at any temperature within the range studied is estimated to be +/-25%. Possible kinetic interferences from production of vibrationally or electronically excited O_2 are discussed. The effect of the faster reaction rate coefficients that are reported for the rm BrO + NO_2 + M and BrO + O(^3P) reactions upon bromine partitioning and ozone depletion in the stratosphere is discussed.

Estimation of Sintering Kinetics of Oxidized Magnetite Pellet Using Optical Dilatometer

NASA Astrophysics Data System (ADS)

Sandeep Kumar, T. K.; Viswanathan, Neelakantan Nurni; Ahmed, Hesham M.; Andersson, Charlotte; Björkman, Bo

2015-04-01

The quality of magnetite pellet is primarily determined by the physico-chemical changes the pellet undergoes as it makes excursion through the gaseous and thermal environment in the induration furnace. Among these physico-chemical processes, the oxidation of magnetite phase and the sintering of oxidized magnetite (hematite) and magnetite (non-oxidized) phases are vital. Rates of these processes not only depend on the thermal and gaseous environment the pellet gets exposed in the induration reactor but also interdependent on each other. Therefore, a systematic study should involve understanding these processes in isolation to the extent possible and quantify them seeking the physics. With this motivation, the present paper focusses on investigating the sintering kinetics of oxidized magnetite pellet. For the current investigation, sintering experiments were carried out on pellets containing more than 95 pct magnetite concentrate from LKAB's mine, dried and oxidized to completion at sufficiently low temperature to avoid sintering. The sintering behavior of this oxidized pellet is quantified through shrinkage captured by Optical Dilatometer. The extent of sintering characterized by sintering ratio found to follow a power law with time i.e., Kt n . The rate constant K for sintering was determined for different temperatures from isothermal experiments. The rate constant, K, varies with temperature as and the activation energy ( Q) and reaction rate constant ( K') are estimated. Further, the sintering kinetic equation was also extended to a non-isothermal environment and validated using laboratory experiments.

(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

Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin.

PubMed

Orlowski, Slawomir; Nowak, Wieslaw

2007-07-01

Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.

Measuring kinetic energy changes in the mesoscale with low acquisition rates

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

Roldán, É.; GISC–Grupo Interdisciplinar de Sistemas Complejos, Madrid; Martínez, I. A.

2014-06-09

We report on the measurement of the average kinetic energy changes in isothermal and non-isothermal quasistatic processes in the mesoscale, realized with a Brownian particle trapped with optical tweezers. Our estimation of the kinetic energy change allows to access to the full energetic description of the Brownian particle. Kinetic energy estimates are obtained from measurements of the mean square velocity of the trapped bead sampled at frequencies several orders of magnitude smaller than the momentum relaxation frequency. The velocity is tuned applying a noisy electric field that modulates the amplitude of the fluctuations of the position and velocity of themore » Brownian particle, whose motion is equivalent to that of a particle in a higher temperature reservoir. Additionally, we show that the dependence of the variance of the time-averaged velocity on the sampling frequency can be used to quantify properties of the electrophoretic mobility of a charged colloid. Our method could be applied to detect temperature gradients in inhomogeneous media and to characterize the complete thermodynamics of biological motors and of artificial micro and nanoscopic heat engines.« less

Kinematic and kinetic synergies of the lower extremities during the pull in olympic weightlifting.

PubMed

Kipp, Kristof; Redden, Josh; Sabick, Michelle; Harris, Chad

2012-07-01

The purpose of this study was to identify multijoint lower extremity kinematic and kinetic synergies in weightlifting and compare these synergies between joints and across different external loads. Subjects completed sets of the clean exercise at loads equal to 65, 75, and 85% of their estimated 1-RM. Functional data analysis was used to extract principal component functions (PCF's) for hip, knee, and ankle joint angles and moments of force during the pull phase of the clean at all loads. The PCF scores were then compared between joints and across loads to determine how much of each PCF was present at each joint and how it differed across loads. The analyses extracted two kinematic and four kinetic PCF's. The statistical comparisons indicated that all kinematic and two of the four kinetic PCF's did not differ across load, but scaled according to joint function. The PCF's captured a set of joint- and load-specific synergies that quantified biomechanical function of the lower extremity during Olympic weightlifting and revealed important technical characteristics that should be considered in sports training and future research.

VO2 kinetics in supra-anaerobic threshold constant tests allow the visualization and quantification of the O2 saving after cytochrome c oxidase inhibition by aerobic training or nitrate administration.

PubMed

Maione, D; Cicero, A Fg; Bacchelli, S; Cosentino, E; Degli Esposti, D; Senaldi, R; Strocchi, E; D'Addato, S; Borghi, C

2013-01-01

We tested whether the known cytochrome c oxidase (COX) inhibition by nitric oxide (NO) could be quantified by VO(2) kinetics during constant load supra-Anaerobic Threshold (AT) exercises in healthy trained or untrained subjects following aerobic training or nitrate administration. In cycle ergometer constant load exercises supra-AT, identified in previous incremental tests, VO(2) kinetics describe a double exponential curve, one rapid and one appreciably slower, allowing the area between them to be calculate in O(2) l. After training, with increased NO availability, this area decreases in inverse ratio to treatment efficacy. In fact, in 11 healthy subjects after aerobic training for 6-7 weeks, area was decreased on average by 51 %. In 11 untrained subjects, following the assumption of an NO donor, 20 mg isosorbide 5 mononitrate, area was decreased on average by 53 %. In conclusion, supra-AT VO(2) kinetics in constant load exercises permit the quantification of the inhibitory effect NO-dependent on COX after either physical training or nitrate assumption.

Higher-order kinetic expansion of quantum dissipative dynamics: mapping quantum networks to kinetic networks.

PubMed

Wu, Jianlan; Cao, Jianshu

2013-07-28

We apply a new formalism to derive the higher-order quantum kinetic expansion (QKE) for studying dissipative dynamics in a general quantum network coupled with an arbitrary thermal bath. The dynamics of system population is described by a time-convoluted kinetic equation, where the time-nonlocal rate kernel is systematically expanded of the order of off-diagonal elements of the system Hamiltonian. In the second order, the rate kernel recovers the expression of the noninteracting-blip approximation method. The higher-order corrections in the rate kernel account for the effects of the multi-site quantum coherence and the bath relaxation. In a quantum harmonic bath, the rate kernels of different orders are analytically derived. As demonstrated by four examples, the higher-order QKE can reliably predict quantum dissipative dynamics, comparing well with the hierarchic equation approach. More importantly, the higher-order rate kernels can distinguish and quantify distinct nontrivial quantum coherent effects, such as long-range energy transfer from quantum tunneling and quantum interference arising from the phase accumulation of interactions.

Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation.

PubMed

Hu, Shenshen; Sharma, Sudhir C; Scouras, Alexander D; Soudackov, Alexander V; Carr, Cody A Marcus; Hammes-Schiffer, Sharon; Alber, Tom; Klinman, Judith P

2014-06-11

The enzyme soybean lipoxygenase (SLO) has served as a prototype for hydrogen-tunneling reactions, as a result of its unusual kinetic isotope effects (KIEs) and their temperature dependencies. Using a synergy of kinetic, structural, and theoretical studies, we show how the interplay between donor-acceptor distance and active-site flexibility leads to catalytic behavior previously predicted by quantum tunneling theory. Modification of the size of two hydrophobic residues by site-specific mutagenesis in SLO reduces the reaction rate 10(4)-fold and is accompanied by an enormous and unprecedented room-temperature KIE. Fitting of the kinetic data to a non-adiabatic model implicates an expansion of the active site that cannot be compensated by donor-acceptor distance sampling. A 1.7 Å resolution X-ray structure of the double mutant further indicates an unaltered backbone conformation, almost identical side-chain conformations, and a significantly enlarged active-site cavity. These findings show the compelling property of room-temperature hydrogen tunneling within a biological context and demonstrate the very high sensitivity of such tunneling to barrier width.

Demonstration of Ion Kinetic Effects in Inertial Confinement Fusion Implosions and Investigation of Magnetic Reconnection Using Laser-Produced Plasmas

NASA Astrophysics Data System (ADS)

Rosenberg, M. J.

2016-10-01

Shock-driven laser inertial confinement fusion (ICF) implosions have demonstrated the presence of ion kinetic effects in ICF implosions and also have been used as a proton source to probe the strongly driven reconnection of MG magnetic fields in laser-generated plasmas. Ion kinetic effects arise during the shock-convergence phase of ICF implosions when the mean free path for ion-ion collisions (λii) approaches the size of the hot-fuel region (Rfuel) and may impact hot-spot formation and the possibility of ignition. To isolate and study ion kinetic effects, the ratio of N - K =λii /Rfuel was varied in D3He-filled, shock-driven implosions at the Omega Laser Facility and the National Ignition Facility, from hydrodynamic-like conditions (NK 0.01) to strongly kinetic conditions (NK 10). A strong trend of decreasing fusion yields relative to the predictions of hydrodynamic models is observed as NK increases from 0.1 to 10. Hydrodynamics simulations that include basic models of the kinetic effects that are likely to be present in these experiments-namely, ion diffusion and Knudsen-layer reduction of the fusion reactivity-are better able to capture the experimental results. This type of implosion has also been used as a source of monoenergetic 15-MeV protons to image magnetic fields driven to reconnect in laser-produced plasmas at conditions similar to those encountered at the Earth's magnetopause. These experiments demonstrate that for both symmetric and asymmetric magnetic-reconnection configurations, when plasma flows are much stronger than the nominal Alfvén speed, the rate of magnetic-flux annihilation is determined by the flow velocity and is largely insensitive to initial plasma conditions. This work was supported by the Department of Energy Grant Number DENA0001857.

Cyber Contingency Analysis version 1.x

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

Contingency analysis based approach for quantifying and examining the resiliency of a cyber system in respect to confidentiality, integrity and availability. A graph representing an organization's cyber system and related resources is used for the availability contingency analysis. The mission critical paths associated with an organization are used to determine the consequences of a potential contingency. A node (or combination of nodes) are removed from the graph to analyze a particular contingency. The value of all mission critical paths that are disrupted by that contingency are used to quantify its severity. A total severity score can be calculated based onmore » the complete list of all these contingencies. A simple n1 analysis can be done in which only one node is removed at a time for the analysis. We can also compute nk analysis, where k is the number of nodes to simultaneously remove for analysis. A contingency risk score can also be computed, which takes the probability of the contingencies into account. In addition to availability, we can also quantify confidentiality and integrity scores for the system. These treat user accounts as potential contingencies. The amount (and type) of files that an account can read to is used to compute the confidentiality score. The amount (and type) of files that an account can write to is used to compute the integrity score. As with availability analysis, we can use this information to compute total severity scores in regards to confidentiality and integrity. We can also take probability into account to compute associated risk scores.« less

Barrierless growth of precursor-free, ultrafast laser-fragmented noble metal nanoparticles by colloidal atom clusters - A kinetic in situ study.

PubMed

Jendrzej, Sandra; Gökce, Bilal; Amendola, Vincenzo; Barcikowski, Stephan

2016-02-01

Unintended post-synthesis growth of noble metal colloids caused by excess amounts of reactants or highly reactive atom clusters represents a fundamental problem in colloidal chemistry, affecting product stability or purity. Hence, quantified kinetics could allow defining nanoparticle size determination in dependence of the time. Here, we investigate in situ the growth kinetics of ps pulsed laser-fragmented platinum nanoparticles in presence of naked atom clusters in water without any influence of reducing agents or surfactants. The nanoparticle growth is investigated for platinum covering a time scale of minutes to 50days after nanoparticle generation, it is also supplemented by results obtained from gold and palladium. Since a minimum atom cluster concentration is exceeded, a significant growth is determined by time resolved UV/Vis spectroscopy, analytical disc centrifugation, zeta potential measurement and transmission electron microscopy. We suggest a decrease of atom cluster concentration over time, since nanoparticles grow at the expense of atom clusters. The growth mechanism during early phase (<1day) of laser-synthesized colloid is kinetically modeled by rapid barrierless coalescence. The prolonged slow nanoparticle growth is kinetically modeled by a combination of coalescence and Lifshitz-Slyozov-Wagner kinetic for Ostwald ripening, validated experimentally by the temperature dependence of Pt nanoparticle size and growth quenching by Iodide anions. Copyright © 2015. Published by Elsevier Inc.

In Situ Study of Microstructure Evolution in Solidification of Hypereutectic Al-Si Alloys with Application of Thermal Analysis and Neutron Diffraction

NASA Astrophysics Data System (ADS)

Sediako, Dimitry G.; Kasprzak, Wojciech

2015-09-01

Understanding of the kinetics of solid-phase evolution in solidification of hypereutectic aluminum alloys is a key to control their as-cast microstructure and resultant mechanical properties, and in turn, to enhance the service characteristics of actual components. This study was performed to evaluate the solidification kinetics for three P-modified hypereutectic Al-19 pct Si alloys: namely, Al-Si binary alloy and with the subsequent addition of 2.8 pct Cu and 2.8 pct Cu + 0.7 pct Mg. Metallurgical evaluation included thermodynamic calculations of the solidification process using the FactSage™ 6.2 software package, as well as experimental thermal analysis, and in situ neutron diffraction. The study revealed kinetics of solid α-Al, solid Si, Al2Cu, and Mg2Si evolution, as well as the individual effects of Cu and Mg alloying additions on the solidification path of the Al-Si system. Various techniques applied in this study resulted in some discrepancies in the results. For example, the FactSage computations, in general, resulted in 281 K to 286 K (8 °C to 13 °C) higher Al-Si eutectic temperatures than the ones recorded in the thermal analysis, which are also ~278 K (~5 °C) higher than those observed in the in situ neutron diffraction. None of the techniques can provide a definite value for the solidus temperature, as this is affected by the chosen calculation path [283 K to 303 K (10 °C to 30 °C) higher for equilibrium solidification vs non-equilibrium] for the FactSage analysis; and further complicated by evolution of secondary Al-Cu and Mg-Si phases that commenced at the end of solidification. An explanation of the discrepancies observed and complications associated with every technique applied is offered in the paper.

EFFECT OF AQUEOUS PHASE PROPERTIES ON CLAY PARTICLE ZETA POTENTIAL AND ELECTRO-OSMOTIC PERMEABILITY: IMPLICATIONS FOR ELECTRO-KINETIC SOIL REMEDIATION PROCESSES

EPA Science Inventory

The influence of aqueous phase properties (pH, ionic strength and divalent metal ion concentration) on clay particle zeta potential and packed-bed electro-osmotic permeability was quantified. Although pH strongly altered the zeta potential of a Georgia kaolinite, it did not signi...

Kinetic Analysis of Amylase Using Quantitative Benedict's and Iodine Starch Reagents

ERIC Educational Resources Information Center

Cochran, Beverly; Lunday, Deborah; Miskevich, Frank

2008-01-01

Quantitative analysis of carbohydrates is a fundamental analytical tool used in many aspects of biology and chemistry. We have adapted a technique developed by Mathews et al. using an inexpensive scanner and open-source image analysis software to quantify amylase activity using both the breakdown of starch and the appearance of glucose. Breakdown…

Role of rumen butyrate in regulation of nitrogen utilization and urea nitrogen kinetics in growing sheep

USDA-ARS?s Scientific Manuscript database

Butyrate, a major rumen VFA, has been indirectly linked to enhancement of urea recycling based on increased expression of urea transporter (UT-B) in the rumen epithelia of steers fed a rumen butyrate-enhancing diet. Two studies were conducted to quantify the effect of elevated rumen butyrate concent...

General mechanism of two-state protein folding kinetics.

PubMed

Rollins, Geoffrey C; Dill, Ken A

2014-08-13

We describe here a general model of the kinetic mechanism of protein folding. In the Foldon Funnel Model, proteins fold in units of secondary structures, which form sequentially along the folding pathway, stabilized by tertiary interactions. The model predicts that the free energy landscape has a volcano shape, rather than a simple funnel, that folding is two-state (single-exponential) when secondary structures are intrinsically unstable, and that each structure along the folding path is a transition state for the previous structure. It shows how sequential pathways are consistent with multiple stochastic routes on funnel landscapes, and it gives good agreement with the 9 order of magnitude dependence of folding rates on protein size for a set of 93 proteins, at the same time it is consistent with the near independence of folding equilibrium constant on size. This model gives estimates of folding rates of proteomes, leading to a median folding time in Escherichia coli of about 5 s.

Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy

PubMed Central

Ladoux, Benoit; Quivy, Jean-Pierre; Doyle, Patrick; Roure, Olivia du; Almouzni, Geneviève; Viovy, Jean-Louis

2000-01-01

Fluorescence videomicroscopy and scanning force microscopy were used to follow, in real time, chromatin assembly on individual DNA molecules immersed in cell-free systems competent for physiological chromatin assembly. Within a few seconds, molecules are already compacted into a form exhibiting strong similarities to native chromatin fibers. In these extracts, the compaction rate is more than 100 times faster than expected from standard biochemical assays. Our data provide definite information on the forces involved (a few piconewtons) and on the reaction path. DNA compaction as a function of time revealed unique features of the assembly reaction in these extracts. They imply a sequential process with at least three steps, involving DNA wrapping as the final event. An absolute and quantitative measure of the kinetic parameters of the early steps in chromatin assembly under physiological conditions could thus be obtained. PMID:11114182

The Path of Carbon in Photosynthesis XVI. Kinetic Relationships of the Intermediates in Steady State Photosynthesis

DOE R&D Accomplishments Database

Benson, A. A.; Kawaguchi, S.; Hayes, P.; Calvin, M.

1952-06-05

A kinetic study of the accumulation of C{sup 14} in the intermediates of steady state photosynthesis in C{sup 14}O{sub 2} provides information regarding the sequence of reactions involved. The work described applied the radio-chromatographic technique for analysis of the labeled early products. The simultaneous carboxylation reaction resulting in malic acid as well as phosphoglycerate is demonstrated in experiments at high light intensity. A comparison of radioactivities in a number of phosphorylated sugars as a function of time reveals concurrent synthesis of fructose and sedoheptulose phosphates followed by that of ribulose phosphates and later by that of glucose phosphates. The possibility that the cleavage of C{sub 4} compounds to C{sub 2} carbon dioxide acceptors may involve C{sub 7} and C{sub 5} sugars and evidence for this mechanism is presented.

Uncertainty propagation in q and current profiles derived from motional Stark effect polarimetry on TFTR (abstract)a)

NASA Astrophysics Data System (ADS)

Batha, S. H.; Levinton, F. M.; Bell, M. G.; Wieland, R. M.; Hirschman, S. P.

1995-01-01

The magnetic-field pitch-angle profile, γp(R)≡arctan(Bpol/Btor), is measured on the TFTR tokamak using a motional Stark effect (MSE) polarimeter. Measured profiles are converted to q profiles with the equilibrium code vmec. Uncertainties in the q profile due to uncertainties in the γp(R), magnetics, and kinetic measurements are quantified. Subsequent uncertainties in the vmec-calculated profiles of current density and shear, both of which are important for stability and transport analyses, are also quantified. Examples of circular plasmas under various confinement modes, including the supershot and L mode, will be given.

Catalytic hydrodeoxygenation of methyl-substituted phenols: correlations of kinetic parameters with molecular properties.

PubMed

Massoth, F E; Politzer, P; Concha, M C; Murray, J S; Jakowski, J; Simons, Jack

2006-07-27

The hydrodeoxygenation of methyl-substituted phenols was carried out in a flow microreactor at 300 degrees C and 2.85 MPa hydrogen pressure over a sulfided CoMo/Al(2)O(3) catalyst. The primary reaction products were methyl-substituted benzene, cyclohexene, cyclohexane, and H(2)O. Analysis of the results suggests that two independent reaction paths are operative, one leading to aromatics and the other to partially or completely hydrogenated cyclohexanes. The reaction data were analyzed using Langmuir-Hinshelwood kinetics to extract the values of the reactant-to-catalyst adsorption constant and of the rate constants characterizing the two reaction paths. The adsorption constant was found to be the same for both reactions, suggesting that a single catalytic site center is operative in both reactions. Ab initio electronic structure calculations were used to evaluate the electrostatic potentials and valence orbital ionization potentials for all of the substituted phenol reactants. Correlations were observed between (a) the adsorption constant and the two reaction rate constants measured for various methyl-substitutions and (b) certain moments of the electrostatic potentials and certain orbitals' ionization potentials of the isolated phenol molecules. On the basis of these correlations to intrinsic reactant-molecule properties, a reaction mechanism is proposed for each pathway, and it is suggested that the dependencies of adsorption and reaction rates upon methyl-group substitution are a result of the substituents' effects on the electrostatic potential and orbitals rather than geometric (steric) effects.

Exploring the Underlying Mechanisms of the Xenopus laevis Embryonic Cell Cycle.

PubMed

Zhang, Kun; Wang, Jin

2018-05-31

The cell cycle is an indispensable process in proliferation and development. Despite significant efforts, global quantification and physical understanding are still challenging. In this study, we explored the mechanisms of the Xenopus laevis embryonic cell cycle by quantifying the underlying landscape and flux. We uncovered the Mexican hat landscape of the Xenopus laevis embryonic cell cycle with several local basins and barriers on the oscillation path. The local basins characterize the different phases of the Xenopus laevis embryonic cell cycle, and the local barriers represent the checkpoints. The checkpoint mechanism of the cell cycle is revealed by the landscape basins and barriers. While landscape shape determines the stabilities of the states on the oscillation path, the curl flux force determines the stability of the cell cycle flow. Replication is fundamental for biology of living cells. We quantify the input energy (through the entropy production) as the thermodynamic requirement for initiation and sustainability of single cell life (cell cycle). Furthermore, we also quantify curl flux originated from the input energy as the dynamical requirement for the emergence of a new stable phase (cell cycle). This can provide a new quantitative insight for the origin of single cell life. In fact, the curl flux originated from the energy input or nutrition supply determines the speed and guarantees the progression of the cell cycle. The speed of the cell cycle is a hallmark of cancer. We characterized the quality of the cell cycle by the coherence time and found it is supported by the flux and energy cost. We are also able to quantify the degree of time irreversibility by the cross correlation function forward and backward in time from the stochastic traces in the simulation or experiments, providing a way for the quantification of the time irreversibility and the flux. Through global sensitivity analysis upon landscape and flux, we can identify the key elements for controlling the cell cycle speed. This can help to design an effective strategy for drug discovery against cancer.

Kinetic Control in the Cleavage of Unsymmetrical Disilanes.

PubMed

Hevesi, Làszlò; Dehon, Michael; Crutzen, Raphael; Lazarescu-Grigore, Adriana

1997-04-04

A series of 12 phenyl-substituted arylpentamethyldisilanes 1a-l have been synthesized in order to examine the regioselectivity of their nucleophilic Si,Si bond cleavage reactions under Still's conditions (MeLi/HMPA/0 degrees C). It has been found that the sensitivity of these reactions to the electronic effects of the substituents in the phenyl ring could be described by the Hammett-type equation log(k(A)/k(B)) = 0.4334 + 2.421(Sigmasigma); (correlation coefficient R = 0.983). The k(A)/k(B) ratio represents the relative rate of attack at silicon atom A (linked to the aryl ring) or at silicon atom B (away from the aryl ring) of the unsymmetrical disilanes. Thus, the present investigation shows that the earlier belief according to which the nucleophilic cleavage of unsymmetrical disilanes always produces the more stable silyl anionic species (thermodynamic control) should be abandoned, or at least seriously amended: kinetic factors appear to exert a primary influence on the regioselectivity of such reactions. Since the two major kinetic factors (i.e., electrophilic character of and steric hindrance at a given silicon atom) have opposite effects on the orientation of the reaction, it may happen that kinetic and thermodynamic control lead to the same result. For some of the unsymmetrical disilanes studied, the major reaction path was not the Si,Si bond cleavage; instead, Si-aryl bond breaking occurred, producing the corresponding aryl anions.

Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography

PubMed Central

Chu, Xiakun; Wang, Jin

2014-01-01

Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less) flexibility leads to weaker (stronger) coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition. PMID:25144525

Specificity and affinity quantification of flexible recognition from underlying energy landscape topography.

PubMed

Chu, Xiakun; Wang, Jin

2014-08-01

Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less) flexibility leads to weaker (stronger) coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition.

Hyporheic zone denitrification: controls on effective reaction depth and contribution to whole-stream mass balance

USGS Publications Warehouse

Harvey, Judson W.; Böhlke, John Karl; Voytek, Mary A.; Scott, Durelle; Tobias, Craig R.

2013-01-01

Stream denitrification is thought to be enhanced by hyporheic transport but there is little direct evidence from the field. To demonstrate at a field site, we injected 15NO3−, Br (conservative tracer), and SF6 (gas exchange tracer) and compared measured whole-stream denitrification with in situ hyporheic denitrification in shallow and deeper flow paths of contrasting geomorphic units. Hyporheic denitrification accounted for between 1 and 200% of whole-stream denitrification. The reaction rate constant was positively related to hyporheic exchange rate (greater substrate delivery), concentrations of substrates DOC and nitrate, microbial denitrifier abundance (nirS), and measures of granular surface area and presence of anoxic microzones. The dimensionless product of the reaction rate constant and hyporheic residence time, λhzτhz define a Damköhler number, Daden-hz that was optimal in the subset of hyporheic flow paths where Daden-hz ≈ 1. Optimal conditions exclude inefficient deep pathways transport where substrates are used up and also exclude inefficient shallow pathways that require repeated hyporheic entries and exits to complete the reaction. The whole-stream reaction significance, Rs (dimensionless), was quantified by multiplying Daden-hz by the proportion of stream discharge passing through the hyporheic zone. Together these two dimensionless metrics, one flow-path scale and the other reach-scale, quantify the whole-stream significance of hyporheic denitrification. One consequence is that the effective zone of significant denitrification often differs from the full depth of the hyporheic zone, which is one reason why whole-stream denitrification rates have not previously been explained based on total hyporheic-zone metrics such as hyporheic-zone size or residence time.

Information content of thermal infrared a microwave bands for simultaneous retrieval of cirrus ice water path and particle effective diameter

NASA Astrophysics Data System (ADS)

Bell, A.; Tang, G.; Yang, P.; Wu, D.

2017-12-01

Due to their high spatial and temporal coverage, cirrus clouds have a profound role in regulating the Earth's energy budget. Variability of their radiative, geometric, and microphysical properties can pose significant uncertainties in global climate model simulations if not adequately constrained. Thus, the development of retrieval methodologies able to accurately retrieve ice cloud properties and present associated uncertainties is essential. The effectiveness of cirrus cloud retrievals relies on accurate a priori understanding of ice radiative properties, as well as the current state of the atmosphere. Current studies have implemented information content theory analyses prior to retrievals to quantify the amount of information that should be expected on parameters to be retrieved, as well as the relative contribution of information provided by certain measurement channels. Through this analysis, retrieval algorithms can be designed in a way to maximize the information in measurements, and therefore ensure enough information is present to retrieve ice cloud properties. In this study, we present such an information content analysis to quantify the amount of information to be expected in retrievals of cirrus ice water path and particle effective diameter using sub-millimeter and thermal infrared radiometry. Preliminary results show these bands to be sensitive to changes in ice water path and effective diameter, and thus lend confidence their ability to simultaneously retrieve these parameters. Further quantification of sensitivity and the information provided from these bands can then be used to design and optimal retrieval scheme. While this information content analysis is employed on a theoretical retrieval combining simulated radiance measurements, the methodology could in general be applicable to any instrument or retrieval approach.

Wide field of view common-path lateral-shearing digital holographic interference microscope

NASA Astrophysics Data System (ADS)

Vora, Priyanka; Trivedi, Vismay; Mahajan, Swapnil; Patel, Nimit; Joglekar, Mugdha; Chhaniwal, Vani; Moradi, Ali-Reza; Javidi, Bahram; Anand, Arun

2017-12-01

Quantitative three-dimensional (3-D) imaging of living cells provides important information about the cell morphology and its time variation. Off-axis, digital holographic interference microscopy is an ideal tool for 3-D imaging, parameter extraction, and classification of living cells. Two-beam digital holographic microscopes, which are usually employed, provide high-quality 3-D images of micro-objects, albeit with lower temporal stability. Common-path digital holographic geometries, in which the reference beam is derived from the object beam, provide higher temporal stability along with high-quality 3-D images. Self-referencing geometry is the simplest of the common-path techniques, in which a portion of the object beam itself acts as the reference, leading to compact setups using fewer optical elements. However, it has reduced field of view, and the reference may contain object information. Here, we describe the development of a common-path digital holographic microscope, employing a shearing plate and converting one of the beams into a separate reference by employing a pin-hole. The setup is as compact as self-referencing geometry, while providing field of view as wide as that of a two-beam microscope. The microscope is tested by imaging and quantifying the morphology and dynamics of human erythrocytes.

Wide field of view common-path lateral-shearing digital holographic interference microscope.

PubMed

Vora, Priyanka; Trivedi, Vismay; Mahajan, Swapnil; Patel, Nimit; Joglekar, Mugdha; Chhaniwal, Vani; Moradi, Ali-Reza; Javidi, Bahram; Anand, Arun

2017-12-01

Quantitative three-dimensional (3-D) imaging of living cells provides important information about the cell morphology and its time variation. Off-axis, digital holographic interference microscopy is an ideal tool for 3-D imaging, parameter extraction, and classification of living cells. Two-beam digital holographic microscopes, which are usually employed, provide high-quality 3-D images of micro-objects, albeit with lower temporal stability. Common-path digital holographic geometries, in which the reference beam is derived from the object beam, provide higher temporal stability along with high-quality 3-D images. Self-referencing geometry is the simplest of the common-path techniques, in which a portion of the object beam itself acts as the reference, leading to compact setups using fewer optical elements. However, it has reduced field of view, and the reference may contain object information. Here, we describe the development of a common-path digital holographic microscope, employing a shearing plate and converting one of the beams into a separate reference by employing a pin-hole. The setup is as compact as self-referencing geometry, while providing field of view as wide as that of a two-beam microscope. The microscope is tested by imaging and quantifying the morphology and dynamics of human erythrocytes. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Quantitative impact of small angle forward scatter on whole blood oximetry using a Beer-Lambert absorbance model.

PubMed

LeBlanc, Serge Emile; Atanya, Monica; Burns, Kevin; Munger, Rejean

2011-04-21

It is well known that red blood cell scattering has an impact on whole blood oximetry as well as in vivo retinal oxygen saturation measurements. The goal of this study was to quantify the impact of small angle forward scatter on whole blood oximetry for scattering angles found in retinal oximetry light paths. Transmittance spectra of whole blood were measured in two different experimental setups: one that included small angle scatter in the transmitted signal and one that measured the transmitted signal only, at absorbance path lengths of 25, 50, 100, 250 and 500 µm. Oxygen saturation was determined by multiple linear regression in the 520-600 nm wavelength range and compared between path lengths and experimental setups. Mean calculated oxygen saturation differences between setups were greater than 10% at every absorbance path length. The deviations to the Beer-Lambert absorbance model had different spectral dependences between experimental setups, with the highest deviations found in the 520-540 nm range when scatter was added to the transmitted signal. These results are consistent with other models of forward scatter that predict different spectral dependences of the red blood cell scattering cross-section and haemoglobin extinction coefficients in this wavelength range.

Video-Based Method of Quantifying Performance and Instrument Motion During Simulated Phonosurgery

PubMed Central

Conroy, Ellen; Surender, Ketan; Geng, Zhixian; Chen, Ting; Dailey, Seth; Jiang, Jack

2015-01-01

Objectives/Hypothesis To investigate the use of the Video-Based Phonomicrosurgery Instrument Tracking System to collect instrument position data during simulated phonomicrosurgery and calculate motion metrics using these data. We used this system to determine if novice subject motion metrics improved over 1 week of training. Study Design Prospective cohort study. Methods Ten subjects performed simulated surgical tasks once per day for 5 days. Instrument position data were collected and used to compute motion metrics (path length, depth perception, and motion smoothness). Data were analyzed to determine if motion metrics improved with practice time. Task outcome was also determined each day, and relationships between task outcome and motion metrics were used to evaluate the validity of motion metrics as indicators of surgical performance. Results Significant decreases over time were observed for path length (P <.001), depth perception (P <.001), and task outcome (P <.001). No significant change was observed for motion smoothness. Significant relationships were observed between task outcome and path length (P <.001), depth perception (P <.001), and motion smoothness (P <.001). Conclusions Our system can estimate instrument trajectory and provide quantitative descriptions of surgical performance. It may be useful for evaluating phonomicrosurgery performance. Path length and depth perception may be particularly useful indicators. PMID:24737286

Phase-Shifted Laser Feedback Interferometry

NASA Technical Reports Server (NTRS)

Ovryn, Benjie

1999-01-01

Phase-shifted, laser feedback interferometry is a new diagnostic tool developed at the NASA Lewis Research Center under the Advanced Technology Development (ATD) Program directed by NASA Headquarters Microgravity Research Division. It combines the principles of phase-shifting interferometry (PSI) and laser-feedback interferometry (LFI) to produce an instrument that can quantify both optical path length changes and sample reflectivity variations. In a homogenous medium, the optical path length between two points is the product of the index of refraction and the geometric distance between the two points. LFI differs from other forms of interferometry by using the laser as both the source and the phase detector. In LFI, coherent feedback of the incident light either reflected directly from a surface or reflected after transmission through a region of interest will modulate the output intensity of the laser. The combination of PSI and LFI has produced a robust instrument, based on a low-power helium-neon (HeNe) gas laser, with a high dynamic range that can be used to measure either static or oscillatory changes of the optical path length. Small changes in optical path length are limited by the fraction of a fringe that can be measured; we can measure nonoscillatory changes with a root mean square (rms) error of the wavelength/1000 without averaging.

Continuous monitoring of enzymatic activity within native electrophoresis gels: Application to mitochondrial oxidative phosphorylation complexes

PubMed Central

Covian, Raul; Chess, David; Balaban, Robert S.

2012-01-01

Native gel electrophoresis allows the separation of very small amounts of protein complexes while retaining aspects of their activity. In-gel enzymatic assays are usually performed by using reaction-dependent deposition of chromophores or light scattering precipitates quantified at fixed time points after gel removal and fixation, limiting the ability to analyze enzyme reaction kinetics. Herein, we describe a custom reaction chamber with reaction media recirculation and filtering and an imaging system that permits the continuous monitoring of in-gel enzymatic activity even in the presence of turbidity. Images were continuously collected using time-lapse high resolution digital imaging, and processing routines were developed to obtain kinetic traces of the in-gel activities and analyze reaction time courses. This system also permitted the evaluation of enzymatic activity topology within the protein bands of the gel. This approach was used to analyze the reaction kinetics of two mitochondrial complexes in native gels. Complex IV kinetics showed a short initial linear phase where catalytic rates could be calculated, whereas Complex V activity revealed a significant lag phase followed by two linear phases. The utility of monitoring the entire kinetic behavior of these reactions in native gels, as well as the general application of this approach, is discussed. PMID:22975200

Concentration-dependent photodegradation kinetics and hydroxyl-radical oxidation of phenicol antibiotics.

PubMed

Li, Kai; Zhang, Peng; Ge, Linke; Ren, Honglei; Yu, Chunyan; Chen, Xiaoyang; Zhao, Yuanfeng

2014-09-01

Thiamphenicol and florfenicol are two phenicol antibiotics widely used in aquaculture and are ubiquitous as micropollutants in surface waters. The present study investigated their photodegradation kinetics, hydroxyl-radical (OH) oxidation reactivities and products. Firstly, the photolytic kinetics of the phenicols in pure water was studied as a function of initial concentrations (C0) under UV-vis irradiation (λ>200nm). It was found that the kinetics was influenced by C0. A linear plot of the pseudo-first-order rate constant vs C0 was observed with a negative slope. Secondly, the reaction between the phenicol antibiotics and OH was examined with a competition kinetic method under simulated solar irradiation (λ>290nm), which quantified their bimolecular reaction rate constants of (2.13±0.02)×10(9)M(-1)s(-1) and (1.82±0.10)×10(9)M(-1)s(-1) for thiamphenicol and florfenicol, respectively. Then the corresponding OH oxidated half-lives in sunlit surface waters were calculated to be 90.5-106.1h. Some main intermediates were formed from the reaction, which suggested that the two phenicols underwent hydroxylation, oxygenation and dehydrogenation when OH existed. These results are of importance to assess the phenicol persistence in wastewater treatment and sunlit surface waters. Copyright © 2014 Elsevier Ltd. All rights reserved.

The removal of COD and NH3-N from atrazine production wastewater treatment using UV/O3: experimental investigation and kinetic modeling.

PubMed

Jing, Liang; Chen, Bing; Wen, Diya; Zheng, Jisi; Zhang, Baiyu

2018-01-01

In this study, a UV/O 3 hybrid advanced oxidation system was used to remove chemical oxygen demand (COD), ammonia nitrogen (NH 3 -N), and atrazine (ATZ) from ATZ production wastewater. The removal of COD and NH 3 -N, under different UV and O 3 conditions, was found to follow pseudo-first-order kinetics with rate constants ranging from 0.0001-0.0048 and 0.0015-0.0056 min -1 , respectively. The removal efficiency of ATZ was over 95% after 180 min treatment, regardless the level of UV power. A kinetic model was further proposed to simulate the removal processes and to quantify the individual roles and contributions of photolysis, direct O 3 oxidation, and hydroxyl radical (OH·) induced oxidation. The experimental and kinetic modeling results agreed reasonably well with deviations of 12.2 and 13.1% for the removal of COD and NH 3 -N, respectively. Photolysis contributed appreciably to the degradation of ATZ, while OH· played a dominant role for the removal of both COD and NH 3 -N, especially in alkaline environments. This study provides insights into the treatment of ATZ containing wastewater using UV/O 3 and broadens the knowledge of kinetics of ozone-based advanced oxidation processes.

Blood modulates the kinetics of reactive oxygen release in pancreatic ischemia-reperfusion injury.

PubMed

Neeff, Hannes P; Sommer, Olaf; Meyer, Sebastian; Tinelli, Anja; Scholtes, Moritz; Hopt, Ulrich T; Drognitz, Oliver; von Dobschuetz, Ernst

2012-10-01

Reason for the unsuccessful use of antioxidants in transplantation might be the unknown kinetics of reactive oxygen species (ROS) release. In this study, we compared the kinetics of ROS release from rat pancreata in the presence and absence of blood. In vivo, ischemia-reperfusion injury (IRI) was induced in pancreata of male Wistar rats by occlusion of the arterial blood supply for 1 or 2 hours. In vitro, isolated pancreata were single-pass perfused with Krebs-Henseleit bicarbonate solution. Reactive oxygen species were quantified by electron spin resonance spectroscopy using CMH (1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine) as spin label. Thiols (glutathione), nicotinamide adenine dinucleotide phosphate-oxidase activity, myeloperoxidase activity, and adenosine triphosphate content were measured. During reperfusion, an increase in IRI-induced ROS in arterial blood was noted after 2 hours of warm ischemia. In sharp contrast, ROS release was immediate and short lived in blood-free perfused organs. The degree of tissue damage correlated with nicotinamide adenine dinucleotide phosphate-oxidase activity and adenosine triphosphate content. Antioxidative capacity of tissues was reduced. Electron spin resonance spectroscopy in conjunction with spin labels allows for the detection of ROS kinetics in pancreatic IRI. Reactive oxygen species kinetics are dependent on the length of the ischemic period and the presence or absence of blood.

Continuous monitoring of enzymatic activity within native electrophoresis gels: application to mitochondrial oxidative phosphorylation complexes.

PubMed

Covian, Raul; Chess, David; Balaban, Robert S

2012-12-01

Native gel electrophoresis allows the separation of very small amounts of protein complexes while retaining aspects of their activity. In-gel enzymatic assays are usually performed by using reaction-dependent deposition of chromophores or light-scattering precipitates quantified at fixed time points after gel removal and fixation, limiting the ability to analyze the enzyme reaction kinetics. Herein, we describe a custom reaction chamber with reaction medium recirculation and filtering and an imaging system that permits the continuous monitoring of in-gel enzymatic activity even in the presence of turbidity. Images were continuously collected using time-lapse high-resolution digital imaging, and processing routines were developed to obtain kinetic traces of the in-gel activities and analyze reaction time courses. This system also permitted the evaluation of enzymatic activity topology within the protein bands of the gel. This approach was used to analyze the reaction kinetics of two mitochondrial complexes in native gels. Complex IV kinetics showed a short initial linear phase in which catalytic rates could be calculated, whereas Complex V activity revealed a significant lag phase followed by two linear phases. The utility of monitoring the entire kinetic behavior of these reactions in native gels, as well as the general application of this approach, is discussed. Published by Elsevier Inc.

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.

Correlation between hierarchical structure of crystal networks and macroscopic performance of mesoscopic soft materials and engineering principles.

PubMed

Lin, Naibo; Liu, Xiang Yang

2015-11-07

This review examines how the concepts and ideas of crystallization can be extended further and applied to the field of mesoscopic soft materials. It concerns the structural characteristics vs. the macroscopic performance, and the formation mechanism of crystal networks. Although this subject can be discussed in a broad sense across the area of mesoscopic soft materials, our main focus is on supramolecular materials, spider and silkworm silks, and biominerals. First, the occurrence of a hierarchical structure, i.e. crystal network and domain network structures, will facilitate the formation kinetics of mesoscopic phases and boost up the macroscopic performance of materials in some cases (i.e. spider silk fibres). Second, the structure and performance of materials can be correlated in some way by the four factors: topology, correlation length, symmetry/ordering, and strength of association of crystal networks. Moreover, four different kinetic paths of crystal network formation are identified, namely, one-step process of assembly, two-step process of assembly, mixed mode of assembly and foreign molecule mediated assembly. Based on the basic mechanisms of crystal nucleation and growth, the formation of crystal networks, such as crystallographic mismatch (or noncrystallographic) branching (tip branching and fibre side branching) and fibre/polymeric side merging, are reviewed. This facilitates the rational design and construction of crystal networks in supramolecular materials. In this context, the (re-)construction of a hierarchical crystal network structure can be implemented by thermal, precipitate, chemical, and sonication stimuli. As another important class of soft materials, the unusual mechanical performance of spider and silkworm silk fibres are reviewed in comparison with the regenerated silk protein derivatives. It follows that the considerably larger breaking stress and unusual breaking strain of spider silk fibres vs. silkworm silk fibres can be interpreted according to the synergistically correlated hierarchical structures of the domain and crystal networks, which can be quantified by the hierarchical structural correlation and the four structural parameters. Based on the concept of crystal networks, the new understanding acquired will transfer the research and engineering of mesoscopic materials, particularly, soft functional materials, to a new phase.

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.

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

PubMed Central

Schadt, Eric E.; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H.; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A.; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types. PMID:23093720

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

PubMed

Schadt, Eric E; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.

Machine learning framework for analysis of transport through complex networks in porous, granular media: A focus on permeability

NASA Astrophysics Data System (ADS)

van der Linden, Joost H.; Narsilio, Guillermo A.; Tordesillas, Antoinette

2016-08-01

We present a data-driven framework to study the relationship between fluid flow at the macroscale and the internal pore structure, across the micro- and mesoscales, in porous, granular media. Sphere packings with varying particle size distribution and confining pressure are generated using the discrete element method. For each sample, a finite element analysis of the fluid flow is performed to compute the permeability. We construct a pore network and a particle contact network to quantify the connectivity of the pores and particles across the mesoscopic spatial scales. Machine learning techniques for feature selection are employed to identify sets of microstructural properties and multiscale complex network features that optimally characterize permeability. We find a linear correlation (in log-log scale) between permeability and the average closeness centrality of the weighted pore network. With the pore network links weighted by the local conductance, the average closeness centrality represents a multiscale measure of efficiency of flow through the pore network in terms of the mean geodesic distance (or shortest path) between all pore bodies in the pore network. Specifically, this study objectively quantifies a hypothesized link between high permeability and efficient shortest paths that thread through relatively large pore bodies connected to each other by high conductance pore throats, embodying connectivity and pore structure.

Near-Field Characterization of Methane Emission Variability from a Compressor Station Using a Model Aircraft.

PubMed

Nathan, Brian J; Golston, Levi M; O'Brien, Anthony S; Ross, Kevin; Harrison, William A; Tao, Lei; Lary, David J; Johnson, Derek R; Covington, April N; Clark, Nigel N; Zondlo, Mark A

2015-07-07

A model aircraft equipped with a custom laser-based, open-path methane sensor was deployed around a natural gas compressor station to quantify the methane leak rate and its variability at a compressor station in the Barnett Shale. The open-path, laser-based sensor provides fast (10 Hz) and precise (0.1 ppmv) measurements of methane in a compact package while the remote control aircraft provides nimble and safe operation around a local source. Emission rates were measured from 22 flights over a one-week period. Mean emission rates of 14 ± 8 g CH4 s(-1) (7.4 ± 4.2 g CH4 s(-1) median) from the station were observed or approximately 0.02% of the station throughput. Significant variability in emission rates (0.3-73 g CH4 s(-1) range) was observed on time scales of hours to days, and plumes showed high spatial variability in the horizontal and vertical dimensions. Given the high spatiotemporal variability of emissions, individual measurements taken over short durations and from ground-based platforms should be used with caution when examining compressor station emissions. More generally, our results demonstrate the unique advantages and challenges of platforms like small unmanned aerial vehicles for quantifying local emission sources to the atmosphere.

Use of open-path FTIR and inverse dispersion technique to quantify gaseous nitrogen loss from an intensive vegetable production site

NASA Astrophysics Data System (ADS)

Bai, Mei; Suter, Helen; Lam, Shu Kee; Sun, Jianlei; Chen, Deli

2014-09-01

An open-path Fourier transform infrared (OP-FTIR) spectroscopic technique in combination with a backward Lagrangian stochastic (bLS) dispersion model (WindTrax) can be used to simultaneously measure gaseous emissions of N2O, NH3, CH4 and CO2. We assessed the capability of this technique for measuring NH3 and N2O emissions following the application of calcium nitrate (Ca(NO3)2), Nitrophoska (NPK) and chicken manure on a celery farm at Boneo, Victoria, during April and May 2013. We found that the OP-FTIR/WindTrax method was able to measure the diurnal variation in NH3 flux from the field site following application of chicken manure with measured emissions ranging from approximately 0.1-9.8 kg NH3-N ha-1 day-1. The OP-FTIR/WindTrax method also detected a diurnal variation in N2O flux of 1.5-6.2 kg N2O-N ha-1 day-1 and N2O flux increased in response to application of the Ca(NO3)2. We concluded that the OP-FTIR/WindTrax technique can quantify gaseous N loss from vegetable production systems.

Kinetic Monte Carlo Simulation of Cation Diffusion in Low-K Ceramics

NASA Technical Reports Server (NTRS)

Good, Brian

2013-01-01

Low thermal conductivity (low-K) ceramic materials are of interest to the aerospace community for use as the thermal barrier component of coating systems for turbine engine components. In particular, zirconia-based materials exhibit both low thermal conductivity and structural stability at high temperature, making them suitable for such applications. Because creep is one of the potential failure modes, and because diffusion is a mechanism by which creep takes place, we have performed computer simulations of cation diffusion in a variety of zirconia-based low-K materials. The kinetic Monte Carlo simulation method is an alternative to the more widely known molecular dynamics (MD) method. It is designed to study "infrequent-event" processes, such as diffusion, for which MD simulation can be highly inefficient. We describe the results of kinetic Monte Carlo computer simulations of cation diffusion in several zirconia-based materials, specifically, zirconia doped with Y, Gd, Nb and Yb. Diffusion paths are identified, and migration energy barriers are obtained from density functional calculations and from the literature. We present results on the temperature dependence of the diffusivity, and on the effects of the presence of oxygen vacancies in cation diffusion barrier complexes as well.

First-principles study on influence of molybdenum on acicular ferrite formation on TiC particles in microallyed steels

NASA Astrophysics Data System (ADS)

Hua, Guomin; Li, Changsheng; Cheng, Xiaonong; Zhao, Xinluo; Feng, Quan; Li, Zhijie; Li, Dongyang; Szpunar, Jerzy A.

2018-01-01

In this study, influences of molybdenum on acicular ferrite formation on precipitated TiC particles are investigated from thermodynamic and kinetic respects. In thermodynamics, Segregation of Mo towards austenite/TiC interface releases the interfacial energy and induces phase transformation from austenite to acicular ferrite on the precipitated TiC particles. The Phase transformation can be achieved by displacive deformation along uniaxial Bain path. In addition, the segregation of Mo atom will also lead to the enhanced stability of ferrite in comparison with austenite no matter at low temperature or at high temperature. In kinetics, the Mo solute in acicular ferrite can effectively suppress the diffusion of carbon atoms, which ensures that orientation relationship between acicular ferrite and austenitized matrix can be satisfied during the diffusionless phase transformation. In contrast to ineffectiveness of TiC particles, the alloying Mo element can facilitate the formation of acicular ferrite on precipitated TiC particles, which is attributed to the above thermodynamic and kinetic reasons. Furthermore, Interfacial toughness and ductility of as-formed acicular ferrite/TiC interface can be improved simultaneously by segregation of Mo atom.

Kinetic and mechanistic aspects of sensitized photodegradation of β-lactam antibiotics: microbiological implications.

PubMed

Reynoso, E; Nesci, A; Allegretti, P; Criado, S; Biasutti, M A

2012-01-01

Amoxicillin (Amx) and cephalexin (Cfx) are β-lactam antibiotics widely used in human and veterinary medicine. Two points of interest surrounding these molecules are the photodegradation of the molecules and their microbiological implications, as well as the persistence and bioaccumulation in the environment which may cause resistance to bacterial strains. The kinetic and mechanistic aspects of the photosensitized degradation of Amx and Cfx have been studied in water at pH 7.4 and 10 by stationary and time-resolved methods. Kinetic evidence indicates that the Rose Bengal-sensitized photooxidation of Amx at pH 7.4 proceeds via O(2)((1)Δ(g)) and O(2•-) mechanisms while at pH 10 the degradation path occurs, principally, via O(2)((1)Δ(g)). For Cfx, this process is attributed to O(2)((1)Δ(g)) and O(2•-). Photoproducts, which arise from the addition of oxygen atoms and subsequent oxidation of the groups -CH(3) to -COOH, were detected. For both antibiotics the bacteriostatic activity decreases in parallel to their photodegradation. The results of this study could potentially help scientists to better understand and predict the photodegradability of these antibiotics on living organisms and in different environmental compartments.

A Newtonian approach to extraordinarily strong negative refraction.

PubMed

Yoon, Hosang; Yeung, Kitty Y M; Umansky, Vladimir; Ham, Donhee

2012-08-02

Metamaterials with negative refractive indices can manipulate electromagnetic waves in unusual ways, and can be used to achieve, for example, sub-diffraction-limit focusing, the bending of light in the 'wrong' direction, and reversed Doppler and Cerenkov effects. These counterintuitive and technologically useful behaviours have spurred considerable efforts to synthesize a broad array of negative-index metamaterials with engineered electric, magnetic or optical properties. Here we demonstrate another route to negative refraction by exploiting the inertia of electrons in semiconductor two-dimensional electron gases, collectively accelerated by electromagnetic waves according to Newton's second law of motion, where this acceleration effect manifests as kinetic inductance. Using kinetic inductance to attain negative refraction was theoretically proposed for three-dimensional metallic nanoparticles and seen experimentally with surface plasmons on the surface of a three-dimensional metal. The two-dimensional electron gas that we use at cryogenic temperatures has a larger kinetic inductance than three-dimensional metals, leading to extraordinarily strong negative refraction at gigahertz frequencies, with an index as large as -700. This pronounced negative refractive index and the corresponding reduction in the effective wavelength opens a path to miniaturization in the science and technology of negative refraction.

Production of oxygen from lunar ilmenite

NASA Technical Reports Server (NTRS)

Zhao, Y.; Shadman, F.

1990-01-01

The following subjects are addressed: (1) the mechanism and kinetics of carbothermal reduction of simulated lunar ilmenite using carbon and, particularly, CO as reducing agents; (2) the determination of the rate-limiting steps; (3) the investigation of the effect of impurities, particularly magnesium; (4) the search for catalysts suitable for enhancement of the rate-limiting step; (5) the comparison of the kinetics of carbothermal reduction with those of hydrogen reduction; (6) the study of the combined use of CO and hydrogen as products of gasification of carbonaceous solids; (7) the development of reduction methods based on the use of waste carbonaceous compounds for the process; (8) the development of a carbothermal reaction path that utilizes gasification of carbonaceous solids to reducing gaseous species (hydrocarbons and carbon monoxide) to facilitate the reduction reaction kinetics and make the process more flexible in using various forms of carbonaceous feeds; (9) the development of advanced gas separation techniques, including the use of high-temperature ceramic membranes; (10) the development of an optimum process flow sheet for carbothermal reduction, and comparison of this process with the hydrogen reduction scheme, as well as a general comparison with other leading oxygen production schemes; and (11) the use of new and advanced material processing and separation techniques.

Paths from meso to submesoscale processes in the western Mediterranean Sea

NASA Astrophysics Data System (ADS)

Capó, Esther; Mason, Evan; Hernández-Carrasco, Ismael; Orfila, Alejandro

2017-04-01

In this work we characterize the mesoscale dynamics in the western Mediterranean (WMed) by analyzing the different contributions to the kinetic energy budgets using a 20 year high-resolution numerical model. The length of the numerical solution allows us to consider statistically stationary state of the ocean, a necessary condition for using the quantification of energy budgets as a tool for analyzing dynamical processes. To identify and characterize the different submesoscale processes, we isolate the terms in the energy balance equations (the Lorenz Energy Cycle, LEC, equations) responsible for the production (conversion and generation) of the eddy kinetic energy (EKE). Firstly, by comparing the predominance of each conversion term among the others, three different submesoscale instabilities can be identified in a certain region: baroclinic, barotropic and Kelvin-Helmholtz type. Conversely, given the crucial role of the wind forcing in the dynamics of this area, the generation of kinetic energy by surface winds has been also considered. Finally, a regional analysis of the EKE production terms permits the identification of the areas dominated by submesoscale activity. As will be shown in this work those areas are located near the main currents, and submesoscale processes are strongly influenced by sharp bathymetry-flow interaction.

Full kinetics investigation of the formation reaction of phosphonate esters in the gas-phase: a theoretical study.

PubMed

Kazemian, Mohammad Amin; Habibi-Khorassani, Sayyed Mostafa; Maghsoodlu, Malek Taher; Ebrahimi, Ali

2014-04-01

In the present work, the proposed multiple-mechanisms have been investigated theoretically for the reaction between triphenyl phosphite and dimethyl acetylenedicarboxylate in the presence of N-H acid such as aniline for generation of phosphonate esters using ab initio molecular orbital theory in gas phase. The profile of the potential energy surface was constructed at the HF/6-311G(d,p) level of theory. The kinetics of the gas phase reaction was studied by evaluating the reaction path of various mechanisms. Between 12 speculative proposed mechanisms {step₁, step₂ (with four possibilities), step₃ (with three possibilities), and step₄} only the third speculative mechanism was recognized as a desirable mechanism. Theoretical kinetics data involving k and E(a), activation (ΔG(‡), ΔS(‡) and ΔH(‡)), and thermodynamic parameters (ΔG°, ΔS° and ΔH°) were calculated for each step of the various mechanisms. Step₁ of the desirable mechanism was identified as the rate determining step. Comparison of the theoretical desirable mechanism with the rate law that has been previously obtained by UV spectrophotometry experiments indicated that the results are in good agreement.

Optimum Pathways of Fish Spawning Migrations in Rivers

NASA Astrophysics Data System (ADS)

McElroy, B. J.; Jacobson, R. B.; Delonay, A.

2010-12-01

Many fish species migrate large distances upstream in rivers to spawn. These migrations require energetic expenditures that are inversely related to fecundity of spawners. Here we present the theory necessary to quantify relative energetic requirements of upstream migration pathways and then test the hypothesis that least-cost paths are taken by the federally endangered pallid sturgeon (Scaphyrhyncus Albus), a benthic rheophile, in the lower Missouri River, USA. Total work done by a fish through a migratory path is proportional to the size of the fish, the total drag on the fish, and the distance traversed. Normalizing by the work required to remain stationary at the beginning of a path, relative work expenditure at each point of the path is found to be the cube of the ratio of the velocity along the path to the velocity at the start of the path. This is the velocity of the fish relative to the river flow. A least-cost migratory pathway can be determined from the velocity field in a reach as the path that minimizes a fish's relative work expenditure. We combine location data from pallid sturgeon implanted with telemetric tags and pressure-sensitive data storage tags with depth and velocity data collected with an acoustic Doppler profiler. During spring 2010 individual sturgeon were closely followed as they migrated up the Missouri River to spawn. These show that, within a small margin, pallid sturgeon in the lower Missouri River select least-cost paths as they swim upstream (typical velocities near 1.0 - 1.2 m/s). Within the range of collected data, it is also seen that many alternative paths not selected for migration are two orders of magnitude more energetically expensive (typical velocities near 2.0 - 2.5 m/s). In general these sturgeon migrated along the inner banks of bends avoiding high velocities in the thalweg, crossing the channel where the thalweg crosses in the opposite direction in order to proceed up the inner bank of subsequent bends. Overall, these results suggest a management strategy for increasing fecundity and reproductive success could be to manage flows to lower levels during prespawn migrations thereby decreasing expenditure necessary to reach spawning sites.

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.

Correction factors to convert microdosimetry measurements in silicon to tissue in 12C ion therapy

NASA Astrophysics Data System (ADS)

Bolst, David; Guatelli, Susanna; Tran, Linh T.; Chartier, Lachlan; Lerch, Michael L. F.; Matsufuji, Naruhiro; Rosenfeld, Anatoly B.

2017-03-01

Silicon microdosimetry is a promising technology for heavy ion therapy (HIT) quality assurance, because of its sub-mm spatial resolution and capability to determine radiation effects at a cellular level in a mixed radiation field. A drawback of silicon is not being tissue-equivalent, thus the need to convert the detector response obtained in silicon to tissue. This paper presents a method for converting silicon microdosimetric spectra to tissue for a therapeutic 12C beam, based on Monte Carlo simulations. The energy deposition spectra in a 10 μm sized silicon cylindrical sensitive volume (SV) were found to be equivalent to those measured in a tissue SV, with the same shape, but with dimensions scaled by a factor κ equal to 0.57 and 0.54 for muscle and water, respectively. A low energy correction factor was determined to account for the enhanced response in silicon at low energy depositions, produced by electrons. The concept of the mean path length < {{l}\\text{Path}}> to calculate the lineal energy was introduced as an alternative to the mean chord length < l> because it was found that adopting Cauchy’s formula for the < l> was not appropriate for the radiation field typical of HIT as it is very directional. < {{l}\\text{Path}}> can be determined based on the peak of the lineal energy distribution produced by the incident carbon beam. Furthermore it was demonstrated that the thickness of the SV along the direction of the incident 12C ion beam can be adopted as < {{l}\\text{Path}}> . The tissue equivalence conversion method and < {{l}\\text{Path}}> were adopted to determine the RBE10, calculated using a modified microdosimetric kinetic model, applied to the microdosimetric spectra resulting from the simulation study. Comparison of the RBE10 along the Bragg peak to experimental TEPC measurements at HIMAC, NIRS, showed good agreement. Such agreement demonstrates the validity of the developed tissue equivalence correction factors and of the determination of < {{l}\\text{Path}}> .

Path integration mediated systematic search: a Bayesian model.

PubMed

Vickerstaff, Robert J; Merkle, Tobias

2012-08-21

The systematic search behaviour is a backup system that increases the chances of desert ants finding their nest entrance after foraging when the path integrator has failed to guide them home accurately enough. Here we present a mathematical model of the systematic search that is based on extensive behavioural studies in North African desert ants Cataglyphis fortis. First, a simple search heuristic utilising Bayesian inference and a probability density function is developed. This model, which optimises the short-term nest detection probability, is then compared to three simpler search heuristics and to recorded search patterns of Cataglyphis ants. To compare the different searches a method to quantify search efficiency is established as well as an estimate of the error rate in the ants' path integrator. We demonstrate that the Bayesian search heuristic is able to automatically adapt to increasing levels of positional uncertainty to produce broader search patterns, just as desert ants do, and that it outperforms the three other search heuristics tested. The searches produced by it are also arguably the most similar in appearance to the ant's searches. Copyright © 2012 Elsevier Ltd. All rights reserved.

Automatic 3D Segmentation and Quantification of Lenticulostriate Arteries from High-Resolution 7 Tesla MRA Images.

PubMed

Wei Liao; Rohr, Karl; Chang-Ki Kang; Zang-Hee Cho; Worz, Stefan

2016-01-01

We propose a novel hybrid approach for automatic 3D segmentation and quantification of high-resolution 7 Tesla magnetic resonance angiography (MRA) images of the human cerebral vasculature. Our approach consists of two main steps. First, a 3D model-based approach is used to segment and quantify thick vessels and most parts of thin vessels. Second, remaining vessel gaps of the first step in low-contrast and noisy regions are completed using a 3D minimal path approach, which exploits directional information. We present two novel minimal path approaches. The first is an explicit approach based on energy minimization using probabilistic sampling, and the second is an implicit approach based on fast marching with anisotropic directional prior. We conducted an extensive evaluation with over 2300 3D synthetic images and 40 real 3D 7 Tesla MRA images. Quantitative and qualitative evaluation shows that our approach achieves superior results compared with a previous minimal path approach. Furthermore, our approach was successfully used in two clinical studies on stroke and vascular dementia.

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

Chitra Sivaraman, PNNL

Cloud droplet number concentration is an important factor in understanding aerosol-cloud interactions. As aerosol concentration increases, it is expected that droplet number concentration (Nd) will increase and droplet size will decrease, for a given liquid water path. This will greatly affect cloud albedo as smaller droplets reflect more shortwave radiation; however, the magnitude and variability of these processes under different environmental conditions is still uncertain.McComiskey et al. (2009) have implemented a method, based onBoers and Mitchell (1994), for calculating Nd from ground-based remote sensing measurements of optical depth and liquid water path. They show that the magnitude of the aerosol-cloudmore » interactions (ACI) varies with a range of factors, including the relative value of the cloud liquid water path (LWP), the aerosol size distribution, and the cloud updraft velocity. Estimates of Nd under a range of cloud types and conditions and at a variety of sites are needed to further quantify the impacts of aerosol cloud interactions. In order to provide data sets for studying aerosol-cloud interactions, the McComiskey et al. (2009) method was implemented as the Droplet Number Concentration (NDROP) value-added product (VAP).« less

Multi-technique approach for deriving a VLBI signal extra-path variation model induced by gravity: the example of Medicina

NASA Astrophysics Data System (ADS)

Sarti, P.; Abbondanza, C.; Negusini, M.; Vittuari, L.

2009-09-01

During the measurement sessions gravity might induce significant deformations in large VLBI telescopes. If neglected or mismodelled, these deformations might bias the phase of the incoming signal thus corrupting the estimate of some crucial geodetic parameters (e.g. the height component of VLBI Reference Point). This paper describes a multi-technique approach implemented for measuring and quantifying the gravity-dependent deformations experienced by the 32-m diameter VLBI antenna of Medicina (Northern Italy). Such an approach integrates three different methods: Terrestrial Triangulations and Trilaterations (TTT), Laser Scanning (LS) and a Finite Element Model (FEM) of the antenna. The combination of the observations performed with these methods allows to accurately define an elevation-dependent model of the signal path variation which appears to be, for the Medicina telescope, non negligible. In the range [0,90] deg the signal path increases monotonically by almost 2 cm. The effect of such a variation has not been introduced in actual VLBI analysis yet; nevertheless this is the task we are going to pursue in the very next future.

Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation.

PubMed

Clark, Andrew G; Naufer, M Nabuan; Westerlund, Fredrik; Lincoln, Per; Rouzina, Ioulia; Paramanathan, Thayaparan; Williams, Mark C

2018-02-06

Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single-molecule techniques, we quantify the binding of a small metal-organic ruthenium threading intercalator (Δ,Δ-B) and compare its binding characteristics to a similar molecule with significantly larger threading moieties (Δ,Δ-P). The binding affinities of the two molecules are the same, while comparison of the binding kinetics reveals significantly faster kinetics for Δ,Δ-B. However, the kinetics is still much slower than that observed for conventional intercalators. Comparison of the two threading intercalators shows that the binding affinity is modulated independently by the intercalating section and the binding kinetics is modulated by the threading moiety. In order to thread DNA, Δ,Δ-P requires a "lock mechanism", in which a large length increase of the DNA duplex is required for both association and dissociation. In contrast, measurements of the force-dependent binding kinetics show that Δ,Δ-B requires a large DNA length increase for association but no length increase for dissociation from DNA. This contrasts strongly with conventional intercalators, for which almost no DNA length change is required for association but a large DNA length change must occur for dissociation. This result illustrates the fundamentally different mechanism of threading intercalation compared with conventional intercalation and will pave the way for the rational design of therapeutic drugs based on DNA threading intercalation.

Quantifying the Kinetic Processes Associated with HIV Infection of Target Cells (AIDS).

DTIC Science & Technology

1992-02-11

viruses. Virology 89, 95-101. Pantaleo, G., Graziosi, C., Butiu, L., Pizzo, P. A., Schnittman, S. M., Kotler , D. P., and Fauci, 5 A. S. (1991). Lymphoid...412 -425 (1963) a a 29 Cmni, E A. Ostwacuik P & Winvner E Vrology 4&, 547 550 (1983) a 30 Taylor. H P. Armstrong , S J & Dimmock, N J Virology Mill.288

Gait Pattern in Two Rare Genetic Conditions Characterized by Muscular Hypotonia: Ehlers-Danlos and Prader-Willi Syndrome

ERIC Educational Resources Information Center

Cimolin, Veronica; Galli, Manuela; Vismara, Luca; Grugni, Graziano; Camerota, Filippo; Celletti, Claudia; Albertini, Giorgio; Rigoldi, Chiara; Capodaglio, Paolo

2011-01-01

This study aimed to quantify and compare the gait pattern in Ehlers-Danlos (EDS) and Prader-Willi syndrome (PWS) patients to provide data for developing evidence-based rehabilitation strategies. Twenty EDS and 19 PWS adult patients were evaluated with an optoelectronic system and force platforms for measuring kinematic and kinetic parameters…

Estimation of detection thresholds for redirected walking techniques.

PubMed

Steinicke, Frank; Bruder, Gerd; Jerald, Jason; Frenz, Harald; Lappe, Markus

2010-01-01

In immersive virtual environments (IVEs), users can control their virtual viewpoint by moving their tracked head and walking through the real world. Usually, movements in the real world are mapped one-to-one to virtual camera motions. With redirection techniques, the virtual camera is manipulated by applying gains to user motion so that the virtual world moves differently than the real world. Thus, users can walk through large-scale IVEs while physically remaining in a reasonably small workspace. In psychophysical experiments with a two-alternative forced-choice task, we have quantified how much humans can unknowingly be redirected on physical paths that are different from the visually perceived paths. We tested 12 subjects in three different experiments: (E1) discrimination between virtual and physical rotations, (E2) discrimination between virtual and physical straightforward movements, and (E3) discrimination of path curvature. In experiment E1, subjects performed rotations with different gains, and then had to choose whether the visually perceived rotation was smaller or greater than the physical rotation. In experiment E2, subjects chose whether the physical walk was shorter or longer than the visually perceived scaled travel distance. In experiment E3, subjects estimate the path curvature when walking a curved path in the real world while the visual display shows a straight path in the virtual world. Our results show that users can be turned physically about 49 percent more or 20 percent less than the perceived virtual rotation, distances can be downscaled by 14 percent and upscaled by 26 percent, and users can be redirected on a circular arc with a radius greater than 22 m while they believe that they are walking straight.

Coupled Long-Term Simulation of Reach-Scale Water and Heat Fluxes Across the River-Groundwater Interface for Retrieving Hyporheic Residence Times and Temperature Dynamics

NASA Astrophysics Data System (ADS)

Munz, Matthias; Oswald, Sascha E.; Schmidt, Christian

2017-11-01

Flow patterns in conjunction with seasonal and diurnal temperature variations control ecological and biogeochemical conditions in hyporheic sediments. In particular, hyporheic temperatures have a great impact on many temperature-sensitive microbial processes. In this study, we used 3-D coupled water flow and heat transport simulations applying the HydroGeoSphere code in combination with high-resolution observations of hydraulic heads and temperatures to quantify reach-scale water and heat flux across the river-groundwater interface and hyporheic temperature dynamics of a lowland gravel bed river. The model was calibrated in order to constrain estimates of the most sensitive model parameters. The magnitude and variations of the simulated temperatures matched the observed ones, with an average mean absolute error of 0.7°C and an average Nash Sutcliffe efficiency of 0.87. Our results indicate that nonsubmerged streambed structures such as gravel bars cause substantial thermal heterogeneity within the saturated sediment at the reach scale. Individual hyporheic flow path temperatures strongly depend on the flow path residence time, flow path depth, river, and groundwater temperature. Variations in individual hyporheic flow path temperatures were up to 7.9°C, significantly higher than the daily average (2.8°C), but still lower than the average seasonal hyporheic temperature difference (19.2°C). The distribution between flow path temperatures and residence times follows a power law relationship with exponent of about 0.37. Based on this empirical relation, we further estimated the influence of hyporheic flow path residence time and temperature on oxygen consumption which was found to partly increase by up to 29% in simulations.

Protein adsorption in microengraving immunoassays.

PubMed

Song, Qing

2015-10-16

Microengraving is a novel immunoassay for characterizing multiple protein secretions from single cells. During the immunoassay, characteristic diffusion and kinetic time scales  and  determine the time for molecular diffusion of proteins secreted from the activated single lymphocytes and subsequent binding onto the glass slide surface respectively. Our results demonstrate that molecular diffusion plays important roles in the early stage of protein adsorption dynamics which shifts to a kinetic controlled mechanism in the later stage. Similar dynamic pathways are observed for protein adsorption with significantly fast rates and rapid shifts in transport mechanisms when  is increased a hundred times from 0.313 to 31.3. Theoretical adsorption isotherms follow the trend of experimentally obtained data. Adsorption isotherms indicate that amount of proteins secreted from individual cells and subsequently captured on a clean glass slide surface increases monotonically with time. Our study directly validates that protein secretion rates can be quantified by the microengraving immunoassay. This will enable us to apply microengraving immunoassays to quantify secretion rates from 10⁴-10⁵ single cells in parallel, screen antigen-specific cells with the highest secretion rate for clonal expansion and quantitatively reveal cellular heterogeneity within a small cell sample.

Protein Adsorption in Microengraving Immunoassays

PubMed Central

Song, Qing

2015-01-01

Microengraving is a novel immunoassay forcharacterizing multiple protein secretions from single cells. During the immunoassay, characteristic diffusion and kinetic time scales τD and τK determine the time for molecular diffusion of proteins secreted from the activated single lymphocytes and subsequent binding onto the glass slide surface respectively. Our results demonstrate that molecular diffusion plays important roles in the early stage of protein adsorption dynamics which shifts to a kinetic controlled mechanism in the later stage. Similar dynamic pathways are observed for protein adsorption with significantly fast rates and rapid shifts in transport mechanisms when C0* is increased a hundred times from 0.313 to 31.3. Theoretical adsorption isotherms follow the trend of experimentally obtained data. Adsorption isotherms indicate that amount of proteins secreted from individual cells and subsequently captured on a clean glass slide surface increases monotonically with time. Our study directly validates that protein secretion rates can be quantified by the microengraving immunoassay. This will enable us to apply microengraving immunoassays to quantify secretion rates from 104–105 single cells in parallel, screen antigen-specific cells with the highest secretion rate for clonal expansion and quantitatively reveal cellular heterogeneity within a small cell sample. PMID:26501282

Experiment-based modelling of grain boundary β-phase (Mg2Al3) evolution during sensitisation of aluminium alloy AA5083.

PubMed

Zhang, R; Steiner, M A; Agnew, S R; Kairy, S K; Davies, C H J; Birbilis, N

2017-06-07

An empirical model for the evolution of β-phase (Mg 2 Al 3 ) along grain boundaries in aluminium alloy AA5083 (Al-Mg-Mn) during isothermal exposures is proposed herein. Developing a quantitative understanding of grain boundary precipitation is important to interpreting intergranular corrosion and stress corrosion cracking in this alloy system. To date, complete ab initio models for grain boundary precipitation based upon fundamental principles of thermodynamics and kinetics are not available, despite the critical role that such precipitates play in dictating intergranular corrosion phenomena. Empirical models can therefore serve an important role in advancing the understanding of grain boundary precipitation kinetics, which is an approach applicable beyond the present context. High resolution scanning electron microscopy was to quantify the size and distribution of β-phase precipitates on Ga-embrittled intergranular fracture surfaces of AA5083. The results are compared with the degree of sensitisation (DoS) as judged by nitric acid mass loss testing (ASTM-G67-04), and discussed with models for sensitisation in 5xxx series Al-alloys. The work herein allows sensitisation to be quantified from an unambiguous microstructural perspective.

Region and Domain Dependent Action of Nomifensine

PubMed Central

Shu, Zhan; Taylor, I. Mitch; Walters, Seth H.; Michael, Adrian C.

2014-01-01

The dopamine (DA) terminal fields in the rat dorsal striatum (DS) and nucleus accumbens core (NAcc) are organized as patchworks of domains that exhibit distinct kinetics of DA release and clearance. The present study used fast-scan cyclic voltammetry recordings of electrically evoked DA overflow to test the hypothesis that nomifensine might exhibit domain-dependent actions within the NAcc, as we previously found to be the case within the DS. Within the NAcc, nomifensine preferentially enhanced evoked dopamine overflow in the slow compared to the fast domains. To seek a kinetic explanation for nomifensine’s selective actions, we quantified the apparent KM of DA clearance by numerically evaluating the derivative of the descending phase of the DA signal after the end of the stimulus. For comparison, we likewise quantified apparent KM in the domains of the DS. As expected because it is a competitive inhibitor, nomifensine significantly increased the apparent KM in both the fast and slow domains of both the NAcc and DS. However, our analysis also leads to the novel finding that nomifensine preferentially increases the apparent KM in the NAcc compared to the DS: apparent KM increased by ~500% in the NAcc and ~200% in the DS. PMID:24766210

Understanding the in vivo uptake kinetics of a phosphatidylethanolamine-binding agent (99m)Tc-Duramycin.

PubMed

Audi, Said; Li, Zhixin; Capacete, Joseph; Liu, Yu; Fang, Wei; Shu, Laura G; Zhao, Ming

2012-08-01

(99m)Tc-Duramycin is a peptide-based molecular probe that binds specifically to phosphatidylethanolamine (PE). The goal was to characterize the kinetics of molecular interactions between (99m)Tc-Duramycin and the target tissue. High level of accessible PE is induced in cardiac tissues by myocardial ischemia (30 min) and reperfusion (120 min) in Sprague-Dawley rats. Target binding and biodistribution of (99m)Tc-duramycin were captured using SPECT/CT. To quantify the binding kinetics, the presence of radioactivity in ischemic versus normal cardiac tissues was measured by gamma counting at 3, 10, 20, 60 and 180 min after injection. A partially inactivated form of (99m)Tc-Duramycin was analyzed in the same fashion. A compartment model was developed to quantify the uptake kinetics of (99m)Tc-Duramycin in normal and ischemic myocardial tissue. (99m)Tc-duramycin binds avidly to the damaged tissue with a high target-to-background radio. Compartment modeling shows that accessibility of binding sites in myocardial tissue to (99m)Tc-Duramycin is not a limiting factor and the rate constant of target binding in the target tissue is at 2.2 ml/nmol/min/g. The number of available binding sites for (99m)Tc-Duramycin in ischemic myocardium was estimated at 0.14 nmol/g. Covalent modification of D15 resulted in a 9-fold reduction in binding affinity. (99m)Tc-Duramycin accumulates avidly in target tissues in a PE-dependent fashion. Model results reflect an efficient uptake mechanism, consistent with the low molecular weight of the radiopharmaceutical and the relatively high density of available binding sites. These data help better define the imaging utilities of (99m)Tc-Duramycin as a novel PE-binding agent. Copyright © 2012 Elsevier Inc. All rights reserved.

Nonlinear oscillations of inviscid free drops

NASA Technical Reports Server (NTRS)

Patzek, T. W.; Benner, R. E., Jr.; Basaran, O. A.; Scriven, L. E.

1991-01-01

The present analysis of free liquid drops' inviscid oscillations proceeds through solution of Bernoulli's equation to obtain the free surface shape and of Laplace's equation for the velocity potential field. Results thus obtained encompass drop-shape sequences, pressure distributions, particle paths, and the temporal evolution of kinetic and surface energies; accuracy is verified by the near-constant drop volume and total energy, as well as the diminutiveness of mass and momentum fluxes across drop surfaces. Further insight into the nature of oscillations is provided by Fourier power spectrum analyses of mode interactions and frequency shifts.

Shrub invasion of desert grassland increases the strength of system feedbacks through enhanced flow-path connectivity

NASA Astrophysics Data System (ADS)

Turnbull, L.; Wainwright, J.

2012-04-01

The invasion of desert grasslands by shrubs is a process that is associated with strong ecohydrological feedbacks. As shrubs invade into grasslands, runoff-generating areas become more connected, due to changes in vegetation cover and distribution. Previous field-based experimentation has demonstrated that runoff-generating areas over grassland can become highly connected, but only under extremely large rainfall events that tend to occur infrequently. In contrast, on shrub-dominated hillslopes, it has been observed that bare areas become connected even under relatively small rainfall events. In this study we carry out a scenario-based modelling analysis, using Model for Assessing Hillslope to Landscape Erosion, Runofff, And Nutrients (MAHLERAN), to investigate changes in hydrological connectivity at over a trajectory of shrub invasion, from a grassland end member to a shrubland end member under different rainfall and antecedent soil-moisture conditions. We hypothesize that (i) as shrubs invade into grasslands the connectivity of flow paths will increase, transporting water, sediment and nutrients over greater distances leading to an increased loss of essential resources from hillslopes and (ii) the extent to which flow paths become connected will be sensitive to antecedent soil-moisture conditions, and therefore that the timing as well as magnitude of runoff events will be important, but less so with increasing levels of shrub encroachment. We quantify hydrological connectivity by using a metric to calculate the maximum length of runoff-generating cells contributing flow to a point, to quantify the connectivity of runoff and entrained sediment. The metric is normalized relative to the maximum potential flow-path length to enable standardized comparisons between plots of different types. Results show that there are critical thresholds for large flow- and sediment-production events, which are a function of both rainfall type and antecedent moisture. The implication is that the pattern of rainfall events throughout a monsoon season in the US Southwest can be critical in reinforcing feedbacks that lead to desertification by producing enhanced connectivity of flow and erosion processes.

Quantifying Variability in Growth and Thermal Inactivation Kinetics of Lactobacillus plantarum.

PubMed

Aryani, D C; den Besten, H M W; Zwietering, M H

2016-08-15

The presence and growth of spoilage organisms in food might affect the shelf life. In this study, the effects of experimental, reproduction, and strain variabilities were quantified with respect to growth and thermal inactivation using 20 Lactobacillus plantarum strains. Also, the effect of growth history on thermal resistance was quantified. The strain variability in μmax was similar (P > 0.05) to reproduction variability as a function of pH, aw, and temperature, while being around half of the reproduction variability (P < 0.05) as a function of undissociated lactic acid concentration [HLa]. The cardinal growth parameters were estimated for the L. plantarum strains, and the pHmin was between 3.2 and 3.5, the aw,min was between 0.936 and 0.953, the [HLamax], at pH 4.5, was between 29 and 38 mM, and the Tmin was between 3.4 and 8.3°C. The average D values ranged from 0.80 min to 19 min at 55°C, 0.22 to 3.9 min at 58°C, 3.1 to 45 s at 60°C, and 1.8 to 19 s at 63°C. In contrast to growth, the strain variability in thermal resistance was on average six times higher than the reproduction variability and more than ten times higher than the experimental variability. The strain variability was also 1.8 times higher (P < 0.05) than the effect of growth history. The combined effects of strain variability and growth history on D value explained all of the variability as found in the literature, although with bias. Based on an illustrative milk-processing chain, strain variability caused ∼2-log10 differences in growth between the most and least robust strains and >10-log10 differences after thermal treatment. Accurate control and realistic prediction of shelf life is complicated by the natural diversity among microbial strains, and limited information on microbiological variability is available for spoilage microorganisms. Therefore, the objectives of the present study were to quantify strain variability, reproduction (biological) variability, and experimental variability with respect to the growth and thermal inactivation kinetics of Lactobacillus plantarum and to quantify the variability in thermal resistance attributed to growth history. The quantitative knowledge obtained on experimental, reproduction, and strain variabilities can be used to improve experimental designs and to adequately select strains for challenge growth and inactivation tests. Moreover, the integration of strain variability in prediction of microbial growth and inactivation kinetics will result in more realistic predictions of L. plantarum dynamics along the food production chain. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Quantitation of ten 30S ribosomal assembly intermediates using fluorescence triple correlation spectroscopy

PubMed Central

Ridgeway, William K.; Millar, David P.; Williamson, James R.

2012-01-01

The self-assembly of bacterial 30S ribosomes involves a large number of RNA folding and RNA-protein binding steps. The sequence of steps determines the overall assembly mechanism and the structure of the mechanism has ramifications for the robustness of biogenesis and resilience against kinetic traps. Thermodynamic interdependencies of protein binding inferred from omission-reconstitution experiments are thought to preclude certain assembly pathways and thus enforce ordered assembly, but this concept is at odds with kinetic data suggesting a more parallel assembly landscape. A major challenge is deconvolution of the statistical distribution of intermediates that are populated during assembly at high concentrations approaching in vivo assembly conditions. To specifically resolve the intermediates formed by binding of three ribosomal proteins to the full length 16S rRNA, we introduce Fluorescence Triple-Correlation Spectroscopy (F3CS). F3CS identifies specific ternary complexes by detecting coincident fluctuations in three-color fluorescence data. Triple correlation integrals quantify concentrations and diffusion kinetics of triply labeled species, and F3CS data can be fit alongside auto-correlation and cross-correlation data to quantify the populations of 10 specific ribosome assembly intermediates. The distribution of intermediates generated by binding three ribosomal proteins to the entire native 16S rRNA included significant populations of species that were not previously thought to be thermodynamically accessible, questioning the current interpretation of the classic omission-reconstitution experiments. F3CS is a general approach for analyzing assembly and function of macromolecular complexes, especially those too large for traditional biophysical methods. PMID:22869699

Nanohole-based SPR Instruments with Improved Spectral Resolution Quantify a Broad Range of Antibody-Ligand Binding Kinetics

PubMed Central

Im, Hyungsoon; Sutherland, Jamie N.; Maynard, Jennifer A.; Oh, Sang-Hyun

2012-01-01

We demonstrate an affordable low-noise SPR instrument based on extraordinary optical transmission (EOT) in metallic nanohole arrays and quantify a broad range of antibody-ligand binding kinetics with equilibrium dissociation constants ranging from 200 pM to 40 nM. This nanohole-based SPR instrument is straightforward to construct, align, and operate, since it is built around a standard microscope and a portable fiber-optic spectrometer. The measured refractive index resolution of this platform is 3.1 × 10−6 without on-chip cooling, which is among the lowest reported for SPR sensors based on EOT. This is accomplished via rapid full-spectrum acquisition in 10 milliseconds followed by frame averaging of the EOT spectra, which is made possible by the production of template-stripped gold nanohole arrays with homogeneous optical properties over centimeter-sized areas. Sequential SPR measurements are performed using a 12-channel microfluidic flow cell after optimizing surface modification protocols and antibody injection conditions to minimize mass-transport artifacts. The immobilization of a model ligand, the protective antigen of anthrax on the gold surface, is monitored in real-time with a signal-to-noise ratio of ~860. Subsequently, real-time binding kinetic curves were measured quantitatively between the antigen and a panel of small, 25 kDa single-chain antibodies at concentrations down to 1 nM. These results indicate that nanohole-based SPR instruments have potential for quantitative antibody screening and as a general-purpose platform for integrating SPR sensors with other bioanalytical tools. PMID:22235895

Net growth rate of continuum heterogeneous biofilms with inhibition kinetics.

PubMed

Gonzo, Elio Emilio; Wuertz, Stefan; Rajal, Veronica B

2018-01-01

Biofilm systems can be modeled using a variety of analytical and numerical approaches, usually by making simplifying assumptions regarding biofilm heterogeneity and activity as well as effective diffusivity. Inhibition kinetics, albeit common in experimental systems, are rarely considered and analytical approaches are either lacking or consider effective diffusivity of the substrate and the biofilm density to remain constant. To address this obvious knowledge gap an analytical procedure to estimate the effectiveness factor (dimensionless substrate mass flux at the biofilm-fluid interface) was developed for a continuum heterogeneous biofilm with multiple limiting-substrate Monod kinetics to different types of inhibition kinetics. The simple perturbation technique, previously validated to quantify biofilm activity, was applied to systems where either the substrate or the inhibitor is the limiting component, and cases where the inhibitor is a reaction product or the substrate also acts as the inhibitor. Explicit analytical equations are presented for the effectiveness factor estimation and, therefore, the calculation of biomass growth rate or limiting substrate/inhibitor consumption rate, for a given biofilm thickness. The robustness of the new biofilm model was tested using kinetic parameters experimentally determined for the growth of Pseudomonas putida CCRC 14365 on phenol. Several additional cases have been analyzed, including examples where the effectiveness factor can reach values greater than unity, characteristic of systems with inhibition kinetics. Criteria to establish when the effectiveness factor can reach values greater than unity in each of the cases studied are also presented.

Laminated helmet materials characterization by terahertz kinetics spectroscopy

NASA Astrophysics Data System (ADS)

Rahman, Anis; Rahman, Aunik K.

2015-05-01

High speed acquisition of reflected terahertz energy constitutes a kinetics spectrum that is an effective tool for layered materials' deformation characterization under ballistic impact. Here we describe utilizing the kinetics spectrum for quantifying a deformation event due to impact in material used for Soldier's helmet. The same technique may be utilized for real-time assessment of trauma by measuring the helmet wore by athletes. The deformation of a laminated material (e.g., a helmet) is dependent on the nature of impact and projectile; thus can uniquely characterize the impact condition leading to a diagnostic procedure based on the energy received by an athlete during an impact. We outline the calibration process for a given material under ballistic impact and then utilize the calibration for extracting physical parameters from the measured kinetics spectrum. Measured kinetics spectra are used to outline the method and rationale for extending the concept to a diagnosis tool. In particular, captured kinetics spectra from multilayered plates subjected to ballistic hit under experimental conditions by high speed digital acquisition system. An algorithm was devised to extract deformation and deformation velocity from which the energy received on the skull was estimated via laws of nonrelativistic motion. This energy is assumed to be related to actual injury conditions, thus forming a basis for determining whether the hit would cause concussion, trauma, or stigma. Such quantification may be used for diagnosing a Soldier's trauma condition in the field or that of an athlete's.

Field evaluation of open and closed-path CO2 flux systems over asphalt surface

NASA Astrophysics Data System (ADS)

Bogoev, I.; Santos, E.

2016-12-01

Eddy covariance (EC) is a widely used method for quantifying surface fluxes of heat, water vapor and carbon dioxide between ecosystems and the atmosphere. A typical EC system consists of an ultrasonic anemometer measuring the 3D wind vector and a fast-response infrared gas analyzer for sensing the water vapor and CO2 density in the air. When using an open-path analyzer that detects the constituent's density in situ a correction for concurrent air temperature and humidity fluctuations must be applied, Webb et al. (1980). In environments with small magnitudes of CO2 flux (<5µmol m-2 s-1) and in the presence of high sensible heat flux, like wintertime over boreal forest, open-path flux measurements have been challenging since the magnitude of the density corrections are as large as the uncorrected CO2 flux itself. A new technology merging the sensing paths of the gas analyzer and the sonic anemometer has been recently developed. This new integrated instrument allows a direct measurement of CO2 mixing ratio in the open air and has the potential to improve the quality of the temperature related density corrections by synchronously measuring the sensible heat flux in the optical path of the gas analyzer. We evaluate the performance and the accuracy of this new sensor over a large parking lot with an asphalt surface where the CO2 fluxes are considered low and the interfering sensible heat fluxes are above 200 Wm-2. A co-located closed-path EC system is used as a reference measurement to examine any systematic biases and apparent CO2 uptake observed with open-path sensors under high sensible heat flux regimes. Half-hour mean and variance of CO2 and water vapor concentrations are evaluated. The relative spectral responses, covariances and corrected turbulent fluxes using a common sonic anemometer are analyzed. The influence of sensor separation and frequency response attenuation on the density corrections is discussed.

Kinetic Analysis of Rhodamines Efflux Mediated by the Multidrug Resistance Protein (MRP1)

PubMed Central

Saengkhae, Chantarawan; Loetchutinat, Chatchanok; Garnier-Suillerot, Arlette

2003-01-01

Characterization of rhodamine 123 as functional assay for MDR has been primarily focused on P-glycoprotein-mediated MDR. Several studies have suggested that Rh123 is also a substrate for MRP1. However, no quantitative studies of the MRP1-mediated efflux of rhodamines have, up to now, been performed. Measurement of the kinetic characteristics of substrate transport is a powerful approach to enhancing our understanding of their function and mechanism. In the present study, we have used a continuous fluorescence assay with four rhodamine dyes (rhodamine 6G, tetramethylrosamine, tetramethylrhodamine ethyl ester, and tetramethylrhodamine methyl ester) to quantify drug transport by MRP1 in living GLC4/ADR cells. The formation of a substrate concentration gradient was observed. MRP1-mediated transport of rhodamine was glutathione-dependent. The kinetics parameter, ka = VM/km, was very similar for the four rhodamine analogs but ∼10-fold less than the values of the same parameter determined previously for the MRP1-mediated efflux of anthracycline. The findings presented here are the first to show quantitative information about the kinetics parameters for MRP1-mediated efflux of rhodamine dyes. PMID:12944313

Kinetics and Mechanisms of γ′ Reprecipitation in a Ni-based Superalloy

PubMed Central

Masoumi, F.; Shahriari, D.; Jahazi, M.; Cormier, J.; Devaux, A.

2016-01-01

The reprecipitation mechanisms and kinetics of γ′ particles during cooling from supersolvus and subsolvus temperatures were studied in AD730TM Ni-based superalloy using Differential Thermal Analysis (DTA). The evolution in the morphology and distribution of reprecipitated γ′ particles was investigated using Field Emission Gun Scanning Electron Microscopy (FEG-SEM). Depending on the cooling rate, γ′ particles showed multi or monomodal distribution. The irregularity growth characteristics observed at lower cooling rates were analyzed in the context of Mullins and Sekerka theory, and allowed the determination of a critical size of γ′ particles above which morphological instability appears. Precipitation kinetics parameters were determined using a non-isothermal JMA model and DTA data. The Avrami exponent was determined to be in the 1.5–2.3 range, suggesting spherical or irregular growth. A methodology was developed to take into account the temperature dependence of the rate coefficient k(T) in the non-isothermal JMA equation. In that regard, a function for k(T) was developed. Based on the results obtained, reprecipitation kinetics models for low and high cooling rates are proposed to quantify and predict the volume fraction of reprecipitated γ′ particles during the cooling process. PMID:27338868

A Mobile Sensing Approach for Regional Surveillance of ...

EPA Pesticide Factsheets

This paper discusses plan-path and automated concepts for inspection to localize individual leaks and to quantify their source rates over regions with active oil and gas well pads and pipelines. This is a peer reviewed journal article submission that advances GMAP OTM 33 mobile measurement and fixed place fence line NGAM topics. This paper is focused on methods development and does not contain new or unpublished source emissions results regarding oil and gas.

Quantifying cancer cell receptors with paired-agent fluorescent imaging: a novel method to account for tissue optical property effects

NASA Astrophysics Data System (ADS)

Sadeghipour, Negar; Davis, Scott C.; Tichauer, Kenneth M.

2018-02-01

Dynamic fluorescence imaging approaches can be used to estimate the concentration of cell surface receptors in vivo. Kinetic models are used to generate the final estimation by taking the targeted imaging agent concentration as a function of time. However, tissue absorption and scattering properties cause the final readout signal to be on a different scale than the real fluorescent agent concentration. In paired-agent imaging approaches, simultaneous injection of a suitable control imaging agent with a targeted one can account for non-specific uptake and retention of the targeted agent. Additionally, the signal from the control agent can be a normalizing factor to correct for tissue optical property differences. In this study, the kinetic model used for paired-agent imaging analysis (i.e., simplified reference tissue model) is modified and tested in simulation and experimental data in a way that accounts for the scaling correction within the kinetic model fit to the data to ultimately extract an estimate of the targeted biomarker concentration.

Accelerated hydrolysis of substituted cellulose for potential biofuel production: kinetic study and modeling.

PubMed

Mu, Bingnan; Xu, Helan; Yang, Yiqi

2015-11-01

In this work, kinetics of substitution accelerated cellulose hydrolysis with multiple reaction stages was investigated to lay foundation for mechanism study and molecular design of substituting compounds. High-efficiency hydrolysis of cellulose is critical for cellulose-based bioethanol production. It is known that, substitution could substantially decrease activation energy and increase reaction rate of acidic hydrolysis of glycosidic bonds in cellulose. However, reaction kinetics and mechanism of the accelerated hydrolysis were not fully revealed. In this research, it was proved that substitution therefore accelerated hydrolysis only occurred in amorphous regions of cellulose fibers, and was a process with multiple reaction stages. With molar ratio of substitution less than 1%, the overall hydrolysis rate could be increased for around 10 times. We also quantified the relationship between the hydrolysis rate of individual reaction stage and its major influences, including molar ratio of substitution, activation energy of acidic hydrolysis, pH and temperature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure, growth kinetics, and ledge flow during vapor-solid-solid growth of copper-catalyzed silicon nanowires.

PubMed

Wen, C-Y; Reuter, M C; Tersoff, J; Stach, E A; Ross, F M

2010-02-10

We use real-time observations of the growth of copper-catalyzed silicon nanowires to determine the nanowire growth mechanism directly and to quantify the growth kinetics of individual wires. Nanowires were grown in a transmission electron microscope using chemical vapor deposition on a copper-coated Si substrate. We show that the initial reaction is the formation of a silicide, eta'-Cu(3)Si, and that this solid silicide remains on the wire tips during growth so that growth is by the vapor-solid-solid mechanism. Individual wire directions and growth rates are related to the details of orientation relation and catalyst shape, leading to a rich morphology compared to vapor-liquid-solid grown nanowires. Furthermore, growth occurs by ledge propagation at the silicide/silicon interface, and the ledge propagation kinetics suggest that the solubility of precursor atoms in the catalyst is small, which is relevant to the fabrication of abrupt heterojunctions in nanowires.

Rate theory of ion pairing at the water liquid-vapor interface: A case of sodium iodide.

PubMed

Dang, Liem X; Schenter, Gregory K

2018-06-14

Studies on ion pairing at interfaces have been intensified recently because of their importance in many chemical reactive phenomena, such as ion-ion interactions that are affected by interfaces and their influence on kinetic processes. In this study, we performed simulations to examine the thermodynamics and kinetics of small polarizable sodium iodide ions in the bulk and near the water liquid-vapor interface. Using classical transition state theory, we calculated the dissociation rates and corrected them with transmission coefficients obtained from the reactive flux formalism and Grote-Hynes theory. Our results show that in addition to affecting the free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results on the relaxation time obtained using the reactive flux formalism and Grote-Hynes theory present an unequivocal picture that the interface suppresses ion dissociation. The effects of the use of molecular models on the ion interactions as well as the ion-pair configurations at the interface are also quantified and discussed.

Rate theory of ion pairing at the water liquid-vapor interface: A case of sodium iodide

NASA Astrophysics Data System (ADS)

Dang, Liem X.; Schenter, Gregory K.

2018-06-01

Studies on ion pairing at interfaces have been intensified recently because of their importance in many chemical reactive phenomena, such as ion-ion interactions that are affected by interfaces and their influence on kinetic processes. In this study, we performed simulations to examine the thermodynamics and kinetics of small polarizable sodium iodide ions in the bulk and near the water liquid-vapor interface. Using classical transition state theory, we calculated the dissociation rates and corrected them with transmission coefficients obtained from the reactive flux formalism and Grote-Hynes theory. Our results show that in addition to affecting the free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results on the relaxation time obtained using the reactive flux formalism and Grote-Hynes theory present an unequivocal picture that the interface suppresses ion dissociation. The effects of the use of molecular models on the ion interactions as well as the ion-pair configurations at the interface are also quantified and discussed.

Modeling bubble dynamics and radical kinetics in ultrasound induced microalgal cell disruption.

PubMed

Wang, Meng; Yuan, Wenqiao

2016-01-01

Microalgal cell disruption induced by acoustic cavitation was simulated through solving the bubble dynamics in an acoustical field and their radial kinetics (chemical kinetics of radical species) occurring in the bubble during its oscillation, as well as calculating the bubble wall pressure at the collapse point. Modeling results indicated that increasing ultrasonic intensity led to a substantial increase in the number of bubbles formed during acoustic cavitation, however, the pressure generated when the bubbles collapsed decreased. Therefore, cumulative collapse pressure (CCP) of bubbles was used to quantify acoustic disruption of a freshwater alga, Scenedesmus dimorphus, and a marine alga, Nannochloropsis oculata and compare with experimental results. The strong correlations between CCP and the intracellular lipid fluorescence density, chlorophyll-a fluorescence density, and cell particle/debris concentration were found, which suggests that the developed models could accurately predict acoustic cell disruption, and can be utilized in the scale up and optimization of the process. Copyright © 2015 Elsevier B.V. All rights reserved.

CPMC-Lab: A MATLAB package for Constrained Path Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Nguyen, Huy; Shi, Hao; Xu, Jie; Zhang, Shiwei

2014-12-01

We describe CPMC-Lab, a MATLAB program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to ab initio calculations in molecules and solids. The present package implements the full ground-state constrained-path Monte Carlo (CPMC) method in MATLAB with a graphical interface, using the Hubbard model as an example. The package can perform calculations in finite supercells in any dimensions, under periodic or twist boundary conditions. Importance sampling and all other algorithmic details of a total energy calculation are included and illustrated. This open-source tool allows users to experiment with various model and run parameters and visualize the results. It provides a direct and interactive environment to learn the method and study the code with minimal overhead for setup. Furthermore, the package can be easily generalized for auxiliary-field quantum Monte Carlo (AFQMC) calculations in many other models for correlated electron systems, and can serve as a template for developing a production code for AFQMC total energy calculations in real materials. Several illustrative studies are carried out in one- and two-dimensional lattices on total energy, kinetic energy, potential energy, and charge- and spin-gaps.

Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model.

PubMed

Gozem, Samer; Huntress, Mark; Schapiro, Igor; Lindh, Roland; Granovsky, Alexander A; Angeli, Celestino; Olivucci, Massimo

2012-11-13

The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.

Effect of Molecule–Surface Reaction Mechanism on the Electronic Characteristics and Photovoltaic Performance of Molecularly Modified Si

PubMed Central

2013-01-01

We report on the passivation properties of molecularly modified, oxide-free Si(111) surfaces. The reaction of 1-alcohol with the H-passivated Si(111) surface can follow two possible paths, nucleophilic substitution (SN) and radical chain reaction (RCR), depending on adsorption conditions. Moderate heating leads to the SN reaction, whereas with UV irradiation RCR dominates, with SN as a secondary path. We show that the site-sensitive SN reaction leads to better electrical passivation, as indicated by smaller surface band bending and a longer lifetime of minority carriers. However, the surface-insensitive RCR reaction leads to more dense monolayers and, therefore, to much better chemical stability, with lasting protection of the Si surface against oxidation. Thus, our study reveals an inherent dissonance between electrical and chemical passivation. Alkoxy monolayers, formed under UV irradiation, benefit, though, from both chemical and electronic passivation because under these conditions both SN and RCR occur. This is reflected in longer minority carrier lifetimes, lower reverse currents in the dark, and improved photovoltaic performance, over what is obtained if only one of the mechanisms operates. These results show how chemical kinetics and reaction paths impact electronic properties at the device level. It further suggests an approach for effective passivation of other semiconductors. PMID:24205409

Drug release from slabs and the effects of surface roughness.

PubMed

Kalosakas, George; Martini, Dimitra

2015-12-30

We discuss diffusion-controlled drug release from slabs or thin films. Analytical and numerical results are presented for slabs with flat surfaces, having a uniform thickness. Then, considering slabs with rough surfaces, the influence of a non-uniform slab thickness on release kinetics is numerically investigated. The numerical release profiles are obtained using Monte Carlo simulations. Release kinetics is quantified through the stretched exponential (or Weibull) function and the resulting dependence of the two parameters of this function on the thickness of the slab, for flat surfaces, and the amplitude of surface fluctuations (or the degree of thickness variability) in case of roughness. We find that a higher surface roughness leads to a faster drug release. Copyright © 2015 Elsevier B.V. All rights reserved.

Direct Measurement of S-Nitrosothiols with an Orbitrap Fusion Mass Spectrometer: S-Nitrosoglutathione Reductase as a Model Protein.

PubMed

Guerra, Damian; Truebridge, Ian; Eyles, Stephen J; Treffon, Patrick; Vierling, Elizabeth

2018-01-01

Recent studies suggest cysteine S-nitrosation of S-nitrosoglutathione reductase (GSNOR) could regulate protein redox homeostasis. "Switch" assays enable discovery of putatively S-nitrosated proteins. However, with few exceptions, researchers have not examined the kinetics and biophysical consequences of S-nitrosation. Methods to quantify protein S-nitrosothiol (SNO) abundance and formation kinetics would bridge this mechanistic gap and allow interpretation of the consequences of specific modifications, as well as facilitate development of specific S-nitrosation inhibitors. Here, we describe a rapid assay to estimate protein SNO abundance with intact protein electrospray ionization mass spectrometry. Originally designed using recombinant GSNOR, these methods are applicable to any purified protein to test for or further study nitrosatable cysteines.

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

Majewski, Pawel W.; Yager, Kevin G.

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. Here, wemore » also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.« less

In situ monitoring of thermal crystallization of ultrathin tris(8-hydroxyquinoline) aluminum films using surface-enhanced Raman scattering.

PubMed

Muraki, Naoki

2014-01-01

Thermal crystallization of 3, 10, and 60 nm-thick tris(8-hydroxyquinoline)aluminum (Alq3) films is studied using surface-enhanced Raman scattering with a constant heating rate. An abrupt higher frequency shift of the quinoline-stretching mode is found to be an indication of a phase transition of Alq3 molecules from amorphous to crystalline. While the 60 nm-thick film shows the same crystallization temperature as a bulk sample, the thinner films were found to have a lower crystallization temperature and slower rate of crystallization. Non-isothermal kinetics analysis is performed to quantify kinetic properties such as the Avrami exponent constants and crystallization rates of ultrathin Alq3 films.

Analysis of energy dissipation and deposition in elastic bodies impacting at hypervelocities

NASA Technical Reports Server (NTRS)

Medina, David F.; Allahdadi, Firooz A.

1992-01-01

A series of impact problems were analyzed using the Eulerian hydrocode CTH. The objective was to quantify the amount of energy dissipated locally by a projectile-infinite plate impact. A series of six impact problems were formulated such that the mass and speed of each projectile were varied in order to allow for increasing speed with constant kinetic energy. The properties and dimensions of the plate were the same for each projectile impact. The resulting response of the plate was analyzed for global Kinetic Energy, global momentum, and local maximum shear stress. The percentage of energy dissipated by the various hypervelocity impact phenomena appears as a relative change of shear stress at a point away from the impact in the plate.

Line shape analysis of the K β transition in muonic hydrogen

NASA Astrophysics Data System (ADS)

Covita, Daniel S.; Anagnostopoulos, Dimitrios F.; Fuhrmann, Hermann; Gorke, Hubert; Gotta, Detlev; Gruber, Alexander; Hirtl, Albert; Ishiwatari, Tomoichi; Indelicato, Paul; Jensen, Thomas S.; Le Bigot, Eric-Olivier; Markushin, Valeri E.; Nekipelov, Michael; Pomerantsev, Vladimir N.; Popov, Vladimir P.; dos Santos, Joaquim M. F.; Schmid, Philipp; Simons, Leopold M.; Theisen, Marian; Trassinelli, Martino; Veloso, Joao F. C. A.; Zmeskal, Johann

2018-04-01

The K β transition in muonic hydrogen was measured with a high-resolution crystal spectrometer. The spectrum is shown to be sensitive to the ground-state hyperfine splitting, the corresponding triplet-to-singlet ratio, and the kinetic energy distribution in the 3 p state. The hyperfine splitting and triplet-to-singlet ratio are found to be consistent with the values expected from theoretical and experimental investigations and, therefore, were fixed accordingly in order to reduce the uncertainties in the further reconstruction of the kinetic energy distribution. The presence of high-energetic components was established and quantified in both a phenomenological, i.e. cascade-model-free fit, and in a direct deconvolution of the Doppler broadening based on the Bayesian method.

Rapid ordering of block copolymer thin films

NASA Astrophysics Data System (ADS)

Majewski, Pawel W.; Yager, Kevin G.

2016-10-01

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. We also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.

Discrete-continuous duality of protein structure space.

PubMed

Sadreyev, Ruslan I; Kim, Bong-Hyun; Grishin, Nick V

2009-06-01

Recently, the nature of protein structure space has been widely discussed in the literature. The traditional discrete view of protein universe as a set of separate folds has been criticized in the light of growing evidence that almost any arrangement of secondary structures is possible and the whole protein space can be traversed through a path of similar structures. Here we argue that the discrete and continuous descriptions are not mutually exclusive, but complementary: the space is largely discrete in evolutionary sense, but continuous geometrically when purely structural similarities are quantified. Evolutionary connections are mainly confined to separate structural prototypes corresponding to folds as islands of structural stability, with few remaining traceable links between the islands. However, for a geometric similarity measure, it is usually possible to find a reasonable cutoff that yields paths connecting any two structures through intermediates.

Chemical and quantum simulation of electron transfer through a polypeptide

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

Ungar, L.W.; Voth, G.A.; Newton, M.D.

1999-08-26

Quantum rate theory, molecular dynamics simulations, and semiempirical electronic structure calculations are used to fully investigate electron transfer mediated by a solvated polypeptide for the first time. Using a stationary-phase approximation, the nonadiabatic electron-transfer rate constant is calculated from the nuclear free energies and the electronic coupling between the initial and final states. The former are obtained from quantum path integral and classical molecular dynamics simulations; the latter are calculated using semiempirical electronic structure calculations and the generalized Mulliken-Hush method. Importantly, no parameters are fit to kinetic data. The simulated system consists of a solvated four-proline polypeptide with a tris(bipyridine)rutheniummore » donor group and an oxypentamminecobalt acceptor group. From the simulation data entropy and energy contributions to the free energies are distinguished. Quantum suppression of the barrier, including important solvent contributions, is demonstrated. Although free energy profiles along the reaction coordinate are nearly parabolic, pronounced departures from harmonic behavior are found for the separate energy and entropy functions. Harmonic models of the system are compared to simulation results in order to quantify anharmonic effects. Electronic structure calculations show that electronic coupling elements vary considerably with system conformation, even when the effective donor-acceptor separation remains roughly constant. The calculations indicate that electron transfer in a significant range of conformations linking the polypeptide to the acceptor may contribute to the overall rate constant. After correction for limitations of the solvent model, the simulations and calculations agree well with the experimental activation energy and Arrhenius prefactor.« less

Direct Observation of Parallel Folding Pathways Revealed Using a Symmetric Repeat Protein System

PubMed Central

Aksel, Tural; Barrick, Doug

2014-01-01

Although progress has been made to determine the native fold of a polypeptide from its primary structure, the diversity of pathways that connect the unfolded and folded states has not been adequately explored. Theoretical and computational studies predict that proteins fold through parallel pathways on funneled energy landscapes, although experimental detection of pathway diversity has been challenging. Here, we exploit the high translational symmetry and the direct length variation afforded by linear repeat proteins to directly detect folding through parallel pathways. By comparing folding rates of consensus ankyrin repeat proteins (CARPs), we find a clear increase in folding rates with increasing size and repeat number, although the size of the transition states (estimated from denaturant sensitivity) remains unchanged. The increase in folding rate with chain length, as opposed to a decrease expected from typical models for globular proteins, is a clear demonstration of parallel pathways. This conclusion is not dependent on extensive curve-fitting or structural perturbation of protein structure. By globally fitting a simple parallel-Ising pathway model, we have directly measured nucleation and propagation rates in protein folding, and have quantified the fluxes along each path, providing a detailed energy landscape for folding. This finding of parallel pathways differs from results from kinetic studies of repeat-proteins composed of sequence-variable repeats, where modest repeat-to-repeat energy variation coalesces folding into a single, dominant channel. Thus, for globular proteins, which have much higher variation in local structure and topology, parallel pathways are expected to be the exception rather than the rule. PMID:24988356

Association Between Contact Lens Discomfort and Pre-lens Tear Film Kinetics.

PubMed

Guillon, Michel; Dumbleton, Kathryn A; Theodoratos, Panagiotis; Wong, Stephanie; Patel, Kishan; Banks, Gaidig; Patel, Trisha

2016-08-01

The relationship between contact lens wettability and comfort has been extensively evaluated; however, a direct correlation between the characteristics of the pre-lens tear film and the symptoms associated with contact lens discomfort has yet to be established. In addition, there is relatively limited knowledge relating to the entire tear film kinetics during the inter-blink period in contact lens wearers. The purpose of this analysis was to identify the characteristics of the pre-lens tear film kinetics that may be associated with the symptoms of contact lens discomfort. The study population comprised 202 soft (hydrogel and silicone hydrogel) contact lens wearers attending pre-screening visits at the OTG-i research clinic. All participants completed the Ocular Surface Disease Index (OSDI) questionnaire and the tear film was quantified via post hoc, masked analysis of high definition digital Tearscope videos recorded at the visit. The tear film kinetics of the least symptomatic wearers (OSDI lowest quintile scores, n = 45) were compared to the tear film kinetics of the most symptomatic wearers (OSDI highest quintile scores, n = 43). The hypothesis tested was that the tear film kinetics of asymptomatic wearers were better than tear film kinetics of symptomatic wearers. The distribution of lens types worn was as follows: Daily Disposable 46.5%, 1-Month Replacement 39.6%, and 2-Week Replacement 13.6%. 48.2% of lenses were silicone hydrogel and 51.8% hydrogel. Symptomatic wearers had a shorter break-up time (4.7 s vs. 6.0 s; p = 0.003), lesser surface coverage by the tear film during the interblink period (95.1% vs. 98.5%; p < 0.001) and greater surface exposure at the time of the blink (9.4% vs. 3.9%; p = 0.001). The current study demonstrated that the tear film kinetics of asymptomatic and symptomatic contact lens wearers were different, the findings supporting the hypothesis of poorer tear film kinetics for symptomatic than asymptomatic wearers in a general contact lens wearing population.

Lipid-Derived Biofuels: Determination of Factors that Control Triglyceride Accumulation in Microalgae

DTIC Science & Technology

2012-10-30

Accumulation in Microalgae Principal Investigator Dr. K.E. Cooksey Department of Microbiology 109 Lewis Hall Montana State University...cultures to find the extent to which previously published results can be considered general for microalgae . Task 2. Quantify growth kinetics and...diatoms cultures to find the extent to which previous results can be found to be general for microalgae . Before this project, detailed

The effect of surfactants on path instability of a rising bubble

NASA Astrophysics Data System (ADS)

Tagawa, Yoshiyuki; Takagi, Shu; Matsumoto, Yoichiro

2013-11-01

We experimentally investigate the surfactant effect on path instability of an air bubble rising in quiescent water. An addition of surfactant varies the gas-water boundary condition from zero shear stress to non-zero shear stress. We report three main findings: firstly, while the drag force acting on the bubble increases with the surfactant concentration as expected, the lift force shows a non-monotonic behavior; secondly, the transient trajectory starting from helical to zigzag is observed, which has never been reported in the case of purified water; lastly, a bubble with the intermediate slip conditions between free-slip and no-slip show a helical motion for a broad range of the Reynolds number. Aforementioned results are rationalized by considering the adsorption-desorption kinetics of the surfactants on gas-water interface and the wake dynamics. Y.T. thanks for financial support from Grant-in-Aid for JSPS Fellows (20-10701). We also thank for Grant-in-Aid for Scientific Research (B) (21360079).

Essentially Entropic Lattice Boltzmann Model

NASA Astrophysics Data System (ADS)

Atif, Mohammad; Kolluru, Praveen Kumar; Thantanapally, Chakradhar; Ansumali, Santosh

2017-12-01

The entropic lattice Boltzmann model (ELBM), a discrete space-time kinetic theory for hydrodynamics, ensures nonlinear stability via the discrete time version of the second law of thermodynamics (the H theorem). Compliance with the H theorem is numerically enforced in this methodology and involves a search for the maximal discrete path length corresponding to the zero dissipation state by iteratively solving a nonlinear equation. We demonstrate that an exact solution for the path length can be obtained by assuming a natural criterion of negative entropy change, thereby reducing the problem to solving an inequality. This inequality is solved by creating a new framework for construction of Padé approximants via quadrature on appropriate convex function. This exact solution also resolves the issue of indeterminacy in case of nonexistence of the entropic involution step. Since our formulation is devoid of complex mathematical library functions, the computational cost is drastically reduced. To illustrate this, we have simulated a model setup of flow over the NACA-0012 airfoil at a Reynolds number of 2.88 ×106.

Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling.

PubMed

Dzierlenga, Michael W; Antoniou, Dimitri; Schwartz, Steven D

2015-04-02

The mechanisms involved in enzymatic hydride transfer have been studied for years, but questions remain due, in part, to the difficulty of probing the effects of protein motion and hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and human heart lactate dehydrogenase (LDH). Calculation of the work applied to the hydride allowed for observation of the change in barrier height upon inclusion of quantum dynamics. Similar calculations were performed using deuterium as the transferring particle in order to approximate kinetic isotope effects (KIEs). The change in barrier height in YADH is indicative of a zero-point energy (ZPE) contribution and is evidence that catalysis occurs via a protein compression that mediates a near-barrierless hydride transfer. Calculation of the KIE using the difference in barrier height between the hydride and deuteride agreed well with experimental results.

Shifting Surface Currents in the Northern North Atlantic Ocean

NASA Technical Reports Server (NTRS)

Hakkinen, Sirpa; Rhines, Peter B.

2007-01-01

Analysis of surface drifter tracks in the North Atlantic Ocean from the time period 1990 to 2006 provides the first evidence that the Gulf Stream waters can have direct pathways to the Nordic Seas. Prior to 2000, the drifters entering the channels leading to the Nordic Seas originated in the western and central subpolar region. Since 2001 several paths from the western subtropics have been present in the drifter tracks leading to the Rockall Trough through which the most saline North Atlantic Waters pass to the Nordic Seas. Eddy kinetic energy from altimetry shows also the increased energy along the same paths as the drifters, These near surface changes have taken effect while the altimetry shows a continual weakening of the subpolar gyre. These findings highlight the changes in the vertical structure of the northern North Atlantic Ocean, its dynamics and exchanges with the higher latitudes, and show how pathways of the thermohaline circulation can open up and maintain or increase its intensity even as the basin-wide circulation spins down.

Path-integral simulation of ice Ih: The effect of pressure

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.; Ramírez, Rafael

2011-12-01

The effect of pressure on structural and thermodynamic properties of ice Ih has been studied by means of path-integral molecular dynamics simulations at temperatures between 50 and 300 K. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Positive (compression) and negative (tension) pressures have been considered, which allowed us to approach the limits for the mechanical stability of this solid water phase. We have studied the pressure dependence of the crystal volume, bulk modulus, interatomic distances, atomic delocalization, and kinetic energy. The spinodal point at both negative and positive pressures is derived from the vanishing of the bulk modulus. For P<0, the spinodal pressure changes from -1.38 to - 0.73 GPa in the range from 50 to 300 K. At positive pressure the spinodal is associated with ice amorphization, and at low temperatures it is found to be between 1.1 and 1.3 GPa. Quantum nuclear effects cause a reduction of the metastability region of ice Ih.

Kinetic analysis of superparamagnetic iron oxide nanoparticles in the liver of body-temperature-controlled mice using dynamic susceptibility contrast magnetic resonance imaging and an empirical mathematical model.

PubMed

Murase, Kenya; Assanai, Purapan; Takata, Hiroshige; Matsumoto, Nozomi; Saito, Shigeyoshi; Nishiura, Motoko

2015-06-01

The purpose of this study was to develop a method for analyzing the kinetic behavior of superparamagnetic iron oxide nanoparticles (SPIONs) in the murine liver under control of body temperature using dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) and an empirical mathematical model (EMM). First, we investigated the influence of body temperature on the kinetic behavior of SPIONs in the liver by controlling body temperature using our temperature-control system. Second, we investigated the kinetic behavior of SPIONs in the liver when mice were injected with various doses of GdCl3, while keeping the body temperature at 36°C. Finally, we investigated it when mice were injected with various doses of zymosan, while keeping the body temperature at 36°C. We also investigated the effect of these substances on the number of Kupffer cells by immunohistochemical analysis using the specific surface antigen of Kupffer cells (CD68). To quantify the kinetic behavior of SPIONs in the liver, we calculated the upper limit of the relative enhancement (A), the rates of early contrast uptake (α) and washout or late contrast uptake (β), the parameter related to the slope of early uptake (q), the area under the curve (AUC), the maximum change of transverse relaxation rate (ΔR2) (ΔR2(max)), the time to ΔR2(max) (Tmax), and ΔR2 at the last time point (ΔR2(last)) from the time courses of ΔR2 using the EMM. The β and Tmax values significantly decreased and increased, respectively, with decreasing body temperature, suggesting that the phagocytic activity of Kupffer cells is significantly affected by body temperature. The AUC, ΔR2(max), and ΔR2(last) values decreased significantly with increasing dose of GdCl3, which was consistent with the change in the number of CD68-positive cells. They increased with increasing dose of zymosan, which was also consistent with the change in the number of CD68-positive cells. These results suggest that AUC, ΔR2(max), and ΔR2(last) reflect the number of Kupffer cells. In conclusion, we presented a method for analyzing the kinetic behavior of SPIONs in the liver using DSC-MRI and EMM, and investigated the influence of body temperature, GdCl3, and zymosan using body-temperature-controlled mice. The present study suggests that control of body temperature is essential for investigating the kinetic behavior of SPIONs in the liver and that our method will be applicable and useful for quantifying the responses of Kupffer cells to various drugs under control of body temperature. Copyright © 2015 Elsevier Inc. All rights reserved.

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

Harris, J.M.

Chemical phenomena occurring at boundaries between insulating solids and liquids (adsorption, partition, monolayer self-assembly, catalysis, and chemical reactions) are important to energy-related analytical chemistry. These phenomena are central to chromatography, solid-phase extraction, immobilized analytical reagents, and optical sensors. Chemical interactions in these processes cannot generally be identified solely by equilibrium surface concentrations, since the steady-state behavior does not reveal the mechanism or rates of surface reactions. Goal therefore is to develop surface-sensitive spectroscopies by which chemical kinetics at liquid/solid interfaces can be observed on time-scales from nanoseconds to seconds. In the first year, we have used Joule-discharge heating kinetics tomore » study pore structure of silica gels; effects of pore diameter, particle size, and chemical modification on pore connectivity were investigated. Temperature-jump relaxation measurements of sorption/desorption kinetics at liquid/solid interfaces were also carried out using Joule heating; kinetic barriers to sorption of ions from solution were found for both C18 and Cl surfaces. Through a collaboration with Fritz-Haber Institute in Berlin, we were able to acquire laser temperature-jump data on kinetics at liquid/solid interfaces using a colloidal sample. We also quantified the rate of migration of covalently attached ligands on silica surfaces; from the temperature dependence, the large energy barrier to migration was estimated. A review of applications of electronic spectroscopy (absorption and fluorescence) to reversed-phase chromatographic interfaces was published.« less