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

The 3-D numerical study of airflow in the compressor/combustor prediffuser and dump diffuser of an industrial gas turbine

NASA Technical Reports Server (NTRS)

Agrawal, Ajay K.; Yang, Tah-Teh

1993-01-01

This paper describes the 3D computations of a flow field in the compressor/combustor diffusers of an industrial gas turbine. The geometry considered includes components such as the combustor support strut, the transition piece and the impingement sleeve with discrete cooling air holes on its surface. Because the geometry was complex and 3D, the airflow path was divided into two computational domains sharing an interface region. The body-fitted grid was generated independently in each of the two domains. The governing equations for incompressible Navier-Stokes equations were solved using the finite volume approach. The results show that the flow in the prediffuser is strongly coupled with the flow in the dump diffuser and vice versa. The computations also revealed that the flow in the dump diffuser is highly nonuniform.

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.

On the transition between two-phase and single-phase interface dynamics in multicomponent fluids at supercritical pressures

NASA Astrophysics Data System (ADS)

Dahms, Rainer N.; Oefelein, Joseph C.

2013-09-01

A theory that explains the operating pressures where liquid injection processes transition from exhibiting classical two-phase spray atomization phenomena to single-phase diffusion-dominated mixing is presented. Imaging from a variety of experiments have long shown that under certain conditions, typically when the pressure of the working fluid exceeds the thermodynamic critical pressure of the liquid phase, the presence of discrete two-phase flow processes become diminished. Instead, the classical gas-liquid interface is replaced by diffusion-dominated mixing. When and how this transition occurs, however, is not well understood. Modern theory still lacks a physically based model to quantify this transition and the precise mechanisms that lead to it. In this paper, we derive a new model that explains how the transition occurs in multicomponent fluids and present a detailed analysis to quantify it. The model applies a detailed property evaluation scheme based on a modified 32-term Benedict-Webb-Rubin equation of state that accounts for the relevant real-fluid thermodynamic and transport properties of the multicomponent system. This framework is combined with Linear Gradient Theory, which describes the detailed molecular structure of the vapor-liquid interface region. Our analysis reveals that the two-phase interface breaks down not necessarily due to vanishing surface tension forces, but due to thickened interfaces at high subcritical temperatures coupled with an inherent reduction of the mean free molecular path. At a certain point, the combination of reduced surface tension, the thicker interface, and reduced mean free molecular path enter the continuum length scale regime. When this occurs, inter-molecular forces approach that of the multicomponent continuum where transport processes dominate across the interfacial region. This leads to a continuous phase transition from compressed liquid to supercritical mixture states. Based on this theory, a regime diagram for liquid injection is developed that quantifies the conditions under which classical sprays transition to dense-fluid jets. It is shown that the chamber pressure required to support diffusion-dominated mixing dynamics depends on the composition and temperature of the injected liquid and ambient gas. To illustrate the method and analysis, we use conditions typical of diesel engine injection. We also present a companion set of high-speed images to provide experimental validation of the presented theory. The basic theory is quite general and applies to a wide range of modern propulsion and power systems such as liquid rockets, gas turbines, and reciprocating engines. Interestingly, the regime diagram associated with diesel engine injection suggests that classical spray phenomena at typical injection conditions do not occur.

Short-Path Statistics and the Diffusion Approximation

NASA Astrophysics Data System (ADS)

Blanco, Stéphane; Fournier, Richard

2006-12-01

In the field of first return time statistics in bounded domains, short paths may be defined as those paths for which the diffusion approximation is inappropriate. This is at the origin of numerous open questions concerning the characterization of residence time distributions. We show here how general integral constraints can be derived that make it possible to address short-path statistics indirectly by application of the diffusion approximation to long paths. Application to the moments of the distribution at the low-Knudsen limit leads to simple practical results and novel physical pictures.

Diffusion paths formation for Cu{sup +} ions in superionic Cu{sub 6}PS{sub 5}I single crystals studied in terms of structural phase transition

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

Gagor, A.; Pietraszko, A.; Kaynts, D.

2005-11-15

In order to understand the structural transformations leading to high ionic conductivity of Cu{sup +} ions in Cu{sub 6}PS{sub 5}I argyrodite compound, the detailed structure analysis based on single-crystal X-ray diffraction has been performed. Below the phase transition at T{sub c}=(144-169)K Cu{sub 6}PS{sub 5}I belongs to monoclinic, ferroelastic phase (space group Cc) with ordered copper sublattice. Above T{sub c} delocalization of copper ions begins and crystal changes the symmetry to cubic superstructure with space group F-43c (a{sup '}=19.528A, z=32). Finally, above T{sub 1}=274K increasing disordering of the Cu{sup +} ions heightens the symmetry to F-43m (a=9.794A, z=4). In this work,more » the final structural model of two cubic phases is presented including the detailed temperature evolution of positions and site occupation factors of copper ions (R{sub 1}=0.0397 for F-43c phase, and 0.0245 for F-43m phase). Possible diffusion paths for the copper ions are represented by means of the atomic displacement factors and split model. The structural results coincide well with the previously reported non-Arrhenius behavior of conductivity and indicate significant change in conduction mechanism.« less

Transition path time distributions

NASA Astrophysics Data System (ADS)

Laleman, M.; Carlon, E.; Orland, H.

2017-12-01

Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the barrier. Average transition path times and, recently, their full probability distribution have been measured for several biomolecular systems, e.g., in the folding of nucleic acids or proteins. Motivated by these experiments, we have calculated the full transition path time distribution for a single stochastic particle crossing a parabolic barrier, including inertial terms which were neglected in previous studies. These terms influence the short time scale dynamics of a stochastic system and can be of experimental relevance in view of the short duration of transition paths. We derive the full transition path time distribution as well as the average transition path times and discuss the similarities and differences with the high friction limit.

Structures and phase transitions of the A7PSe6 (A = Ag, Cu) argyrodite-type ionic conductors. II. Beta- and gamma-Cu7PSe6

PubMed

Gaudin; Boucher; Petricek; Taulelle; Evain

2000-06-01

The crystal structures of two of the three polymorphic forms of the Cu7PSe6 argyrodite compound are determined by means of single-crystal X-ray diffraction. In the high-temperature form, at 353 K, i.e. 33 K above the first phase transition, gamma-Cu7PSe6 crystallizes in cubic symmetry, space group F43m. The full-matrix least-squares refinement of the structure leads to the residual factors R = 0.0201 and wR = 0.0245 for 31 parameters and 300 observed independent reflections. In the intermediate form, at room temperature, beta-Cu7PSe6 crystallizes again in cubic symmetry, but with space group P2(1)3. Taking into account a merohedric twinning, the refinement of the beta-Cu7PSe6 structure leads to the residual factors R = 0.0297 and wR = 0.0317 for 70 parameters and 874 observed, independent reflections. The combination of a Gram-Charlier development of the Debye-Waller factor and a split model for copper cations reveals the possible diffusion paths of the d10 species in the gamma-Cu7PSe6 ionic conducting phase. The partial ordering of the Cu+ d10 element at the phase transition is found in concordance with the highest probability density sites of the high-temperature phase diffusion paths. A comparison between the two Cu7PSe6 and Ag7PSe6 analogues is carried out, stressing the different mobility of Cu+ and Ag+ and their relative stability in low-coordination chalcogenide environments.

Virtual Electrochemical Strain Microscopy of Polycrystalline LiCoO2 Films

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

Chung, Ding-wen; Balke, Nina; Kalinin, Sergei V

2011-01-01

A recently developed technique, electrochemical strain microscopy (ESM), utilizes the strong coupling between ionic current and anisotropic volumetric chemical expansion of lithium-ion electrode materials to dynamically probe the sub-one-hundred? nm inter-facial kinetic intercalation properties. A numerical technique based on the finite element method was developed to analyze the underlying physics that govern the ESM signal generation and establish relations to battery performance. The performed analysis demonstrates that the diffusion path within a thin film is tortuous and the extent of lithium diffusion into the electrode is dependent on the SPM-tip-imposed overpotential frequency. The detected surface actuation gives rise to themore » development of an electromechanical hysteresis loop whose shape is dependent on grain size and overpotential frequency. Shape and tilting angle of the loop are classified into low and high frequency regimes, separated by a transition frequency which is also a function of lithium diffusivity and grain size, f{sub T} = D//{sup 2}. Research shows that the crystallographic orientation of the surface actuated grain has a significant impact on the shape of the loop. The polycrystalline crystallographic orientation of the grains induces a diffusion path network in the electrode which impacts on the mechanical reliability of the battery. Simulations demonstrate that continuous battery cycling results in a cumulative capacity loss as a result of the hysteric non-reversible lithium intercalation. Furthermore, results suggest that ESM has the capability to infer the local out-of-plane lithium diffusivity and the out-of-plane contribution to Vegard tensor.« less

Virtual Electrochemical Strain Microscopy of Polycrystalline LiCoO2 Films

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

Chung, Ding-Wen; Balke, Nina; Kalinin, Sergei V.

2011-08-03

A recently developed technique, electrochemical strain microscopy (ESM), utilizes the strong coupling between ionic current and anisotropic volumetric chemical expansion of lithium-ion electrode materials to dynamically probe the sub-one-hundred? nm inter-facial kinetic intercalation properties. A numerical technique based on the finite element method was developed to analyze the underlying physics that govern the ESM signal generation and establish relations to battery performance. The performed analysis demonstrates that the diffusion path within a thin film is tortuous and the extent of lithium diffusion into the electrode is dependent on the SPM-tip-imposed overpotential frequency. The detected surface actuation gives rise to themore » development of an electromechanical hysteresis loop whose shape is dependent on grain size and overpotential frequency. Shape and tilting angle of the loop are classified into low and high frequency regimes, separated by a transition frequency which is also a function of lithium diffusivity and grain size, f T = D/l₂. Research shows that the crystallographic orientation of the surface actuated grain has a significant impact on the shape of the loop. The polycrystalline crystallographic orientation of the grains induces a diffusion path network in the electrode which impacts on the mechanical reliability of the battery. Simulations demonstrate that continuous battery cycling results in a cumulative capacity loss as a result of the hysteric non-reversible lithium intercalation. Furthermore, results suggest that ESM has the capability to infer the local out-of-plane lithium diffusivity and the out-of-plane contribution to Vegard tensor.« less

Transition path time distributions for Lévy flights

NASA Astrophysics Data System (ADS)

Janakiraman, Deepika

2018-07-01

This paper presents a study of transition path time distributions for Lévy noise-induced barrier crossing. Transition paths are short segments of the reactive trajectories and span the barrier region of the potential without spilling into the reactant/product wells. The time taken to traverse this segment is referred to as the transition path time. Since the transition path is devoid of excursions in the minimum, the corresponding time will give the exclusive barrier crossing time, unlike . This work explores the distribution of transition path times for superdiffusive barrier crossing, analytically. This is made possible by approximating the barrier by an inverted parabola. Using this approximation, the distributions are evaluated in both over- and under-damped limits of friction. The short-time behaviour of the distributions, provide analytical evidence for single-step transition events—a feature in Lévy-barrier crossing as observed in prior simulation studies. The average transition path time is calculated as a function of the Lévy index (α), and the optimal value of α leading to minimum average transition path time is discussed, in both the limits of friction. Langevin dynamics simulations corroborating with the analytical results are also presented.

New mechanisms of cluster diffusion on metal fcc(100) surfaces

NASA Astrophysics Data System (ADS)

Trushin, Oleg; Salo, Petri; Alatalo, Matti; Ala-Nissila, Tapio

2001-03-01

We have studied atomic mechanisms of the diffusion of small clusters on the fcc(100) metal surfaces using semi-empirical and ab-initio molecular static calculations. Primary goal of these studies was to investigate possible many-body mechanisms of cluster motion which can contribute to low temperature crystal growth. We used embedded atom and Glue potentials in semi-empirical simulations of Cu and Al. Combination of the Nudged Elastic Band and Eigenvector Following methods allowed us to find all the possible transition paths for cluster movements on flat terrace. In case of Cu(001) we have found several new mechanisms for diffusion of clusters, including mechanisms called row-shearing and dimer-rotating in which a whole row inside an island moves according to a concerted jump and a dimer rotates at the periphery of an island, respectively. In some cases these mechanisms yield a lower energy barrier than the standard mechanisms.

Resistivity bound for hydrodynamic bad metals

PubMed Central

Lucas, Andrew; Hartnoll, Sean A.

2017-01-01

We obtain a rigorous upper bound on the resistivity ρ of an electron fluid whose electronic mean free path is short compared with the scale of spatial inhomogeneities. When such a hydrodynamic electron fluid supports a nonthermal diffusion process—such as an imbalance mode between different bands—we show that the resistivity bound becomes ρ≲AΓ. The coefficient A is independent of temperature and inhomogeneity lengthscale, and Γ is a microscopic momentum-preserving scattering rate. In this way, we obtain a unified mechanism—without umklapp—for ρ∼T2 in a Fermi liquid and the crossover to ρ∼T in quantum critical regimes. This behavior is widely observed in transition metal oxides, organic metals, pnictides, and heavy fermion compounds and has presented a long-standing challenge to transport theory. Our hydrodynamic bound allows phonon contributions to diffusion constants, including thermal diffusion, to directly affect the electrical resistivity. PMID:29073054

Transition path time distribution and the transition path free energy barrier.

PubMed

Pollak, Eli

2016-10-19

The recent experimental measurement of the transition path time distributions of proteins presents several challenges to theory. Firstly, why do the fits of the experimental data to a theoretical expression lead to barrier heights which are much lower than the free energies of activation of the observed transitions? Secondly, there is the theoretical question of determining the transition path time distribution, without invoking the Smoluchowski limit. In this paper, we derive an exact expression for a transition path time distribution which is valid for arbitrary memory friction using the normal mode transformation which underlies Kramers' rate theory. We then recall that for low barriers, there is a noticeable difference between the transition path time distribution obtained with absorbing boundary conditions and free boundary conditions. For the former, the transition times are shorter, since recrossings of the boundaries are disallowed. As a result, if one uses the distribution based on absorbing boundary conditions to fit the experimental data, one will find that the transition path barrier will be larger than the values found based on a theory with free boundary conditions. We then introduce the paradigm of a transition path barrier height, and show that one should always expect it to be much smaller than the activation energy.

Efficient evaluation of atom tunneling combined with electronic structure calculations.

PubMed

Ásgeirsson, Vilhjálmur; Arnaldsson, Andri; Jónsson, Hannes

2018-03-14

Methodology for finding optimal tunneling paths and evaluating tunneling rates for atomic rearrangements is described. First, an optimal JWKB tunneling path for a system with fixed energy is obtained using a line integral extension of the nudged elastic band method. Then, a calculation of the dynamics along the path is used to determine the temperature at which it corresponds to an optimal Feynman path for thermally activated tunneling (instanton) and a harmonic approximation is used to estimate the transition rate. The method is illustrated with calculations for a modified two-dimensional Müller-Brown surface but is efficient enough to be used in combination with electronic structure calculations of the energy and atomic forces in systems containing many atoms. An example is presented where tunneling is the dominant mechanism well above room temperature as an H 3 BNH 3 molecule dissociates to form H 2 . Also, a solid-state example is presented where density functional theory calculations of H atom tunneling in a Ta crystal give close agreement with experimental measurements on hydrogen diffusion over a wide range in temperature.

Feynman path integral application on deriving black-scholes diffusion equation for european option pricing

NASA Astrophysics Data System (ADS)

Utama, Briandhika; Purqon, Acep

2016-08-01

Path Integral is a method to transform a function from its initial condition to final condition through multiplying its initial condition with the transition probability function, known as propagator. At the early development, several studies focused to apply this method for solving problems only in Quantum Mechanics. Nevertheless, Path Integral could also apply to other subjects with some modifications in the propagator function. In this study, we investigate the application of Path Integral method in financial derivatives, stock options. Black-Scholes Model (Nobel 1997) was a beginning anchor in Option Pricing study. Though this model did not successfully predict option price perfectly, especially because its sensitivity for the major changing on market, Black-Scholes Model still is a legitimate equation in pricing an option. The derivation of Black-Scholes has a high difficulty level because it is a stochastic partial differential equation. Black-Scholes equation has a similar principle with Path Integral, where in Black-Scholes the share's initial price is transformed to its final price. The Black-Scholes propagator function then derived by introducing a modified Lagrange based on Black-Scholes equation. Furthermore, we study the correlation between path integral analytical solution and Monte-Carlo numeric solution to find the similarity between this two methods.

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

PubMed Central

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

2016-01-01

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

Wetting transitions on patterned surfaces with diffuse interaction potentials embedded in a Young-Laplace formulation

NASA Astrophysics Data System (ADS)

Pashos, G.; Kokkoris, G.; Papathanasiou, A. G.; Boudouvis, A. G.

2016-01-01

The Minimum Energy Paths (MEPs) of wetting transitions on pillared surfaces are computed with the Young-Laplace equation, augmented with a pressure term that accounts for liquid-solid interactions. The interactions are smoothed over a short range from the solid phase, therefore facilitating the numerical solution of problems concerning wetting on complex surface patterns. The patterns may include abrupt geometric features, e.g., arrays of rectangular pillars, where the application of the unmodified Young-Laplace is not practical. The MEPs are obtained by coupling the augmented Young-Laplace with the modified string method from which the energy barriers of wetting transitions are eventually extracted. We demonstrate the method on a wetting transition that is associated with the breakdown of superhydrophobic behavior, i.e., the transition from the Cassie-Baxter state to the Wenzel state, taking place on a superhydrophobic pillared surface. The computed energy barriers quantify the resistance of the system to these transitions and therefore, they can be used to evaluate superhydrophobic performance or provide guidelines for optimal pattern design.

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

Compositional and Ionic-Size Controls on the Diffusion of Divalent Cations in Garnet: Insights from Atomistic Simulations

NASA Astrophysics Data System (ADS)

Carlson, W. D.

2012-12-01

Divalent cations in garnet (Mg, Fe, Mn, Ca) diffuse at rates that depend strongly on the host-crystal composition and on the ionic radius of the diffusant. Understanding of the nanoscale basis for these behaviors comes from atomistic simulations that calculate energies in the static limit for the defects and transition-state configurations associated with each diffusive step. Diffusion of divalent cations requires (a) creation of a cation-vacancy defect in a dodecahedral site and of a charge-compensating oxygen-vacancy defect that may or may not be in close spatial association; (b) except in the case of self-diffusion, creation of an impurity defect in which a foreign atom replaces the normal atom in a dodecahedral site adjacent to the vacancy; and (c) during the diffusive process, motion of the diffusing atom to a 'saddlepoint' position that represents the transition-state configuration. Comparisons of the system's energy in these various states, in structures of different composition and for ions of different ionic size, allows assessment of the nanoscale controls on diffusion kinetics. Molecular-statics calculations quantify defect energies and identify the transition-state configuration: the maximum energy along the diffusion path between two adjacent dodecahedral sites results when the diffusing ion is surrounded symmetrically by the six oxygen atoms that lie between the two sites. Across the range of end-member compositions, self-diffusion coefficients measured at identical conditions, and the tracer diffusivity of a single ion measured at identical conditions, can each vary by five orders of magnitude or more. Measured activation energies for these motions, however, are all equivalent to within ±6%. Calculated activation energies are in agreement with observations, in that they vary by only ±10%. Calculated vacancy-formation energies, on the other hand, are significantly larger in expanded structures; for example, that energy is greater for Prp than for Grs by ~ 470 kJ/mol. Thus in expanded structures, much higher vacancy concentrations can be produced at the same energetic cost, greatly enhancing rates of diffusion. The primary explanation for the more rapid diffusion of divalent cations in structures with larger cell dimensions therefore comes not from reduced saddlepoint strain energies in more compliant structures, but instead from the smaller energy required to create vacancy defects. Diffusivities of divalent cations exhibit a curious parabolic dependence on ionic size: for each structure, an optimally-sized ion exists, close in size to the dominant ion, that exhibits the fastest diffusion. Larger ions — and enigmatically, smaller ions — both diffuse more slowly. Calculated impurity-defect energies show that undersized impurity ions are bound more tightly in their sites, but the effects are too small in comparison to corresponding reductions in strain energy for the transition-state configuration to account for observed rate differences. Calculated vacancy-association energies reveal a slight tendency for vacancies to associate preferentially with larger impurity ions, but again the effect appears to be too small to provide a full explanation for observed behaviors.

Toward Space-like Photometric Precision from the Ground with Beam-shaping Diffusers

NASA Astrophysics Data System (ADS)

Stefansson, Gudmundur; Mahadevan, Suvrath; Hebb, Leslie; Wisniewski, John; Huehnerhoff, Joseph; Morris, Brett; Halverson, Sam; Zhao, Ming; Wright, Jason; O'rourke, Joseph; Knutson, Heather; Hawley, Suzanne; Kanodia, Shubham; Li, Yiting; Hagen, Lea M. Z.; Liu, Leo J.; Beatty, Thomas; Bender, Chad; Robertson, Paul; Dembicky, Jack; Gray, Candace; Ketzeback, William; McMillan, Russet; Rudyk, Theodore

2017-10-01

We demonstrate a path to hitherto unachievable differential photometric precisions from the ground, both in the optical and near-infrared (NIR), using custom-fabricated beam-shaping diffusers produced using specialized nanofabrication techniques. Such diffusers mold the focal plane image of a star into a broad and stable top-hat shape, minimizing photometric errors due to non-uniform pixel response, atmospheric seeing effects, imperfect guiding, and telescope-induced variable aberrations seen in defocusing. This PSF reshaping significantly increases the achievable dynamic range of our observations, increasing our observing efficiency and thus better averages over scintillation. Diffusers work in both collimated and converging beams. We present diffuser-assisted optical observations demonstrating {62}-16+26 ppm precision in 30 minute bins on a nearby bright star 16 Cygni A (V = 5.95) using the ARC 3.5 m telescope—within a factor of ˜2 of Kepler's photometric precision on the same star. We also show a transit of WASP-85-Ab (V = 11.2) and TRES-3b (V = 12.4), where the residuals bin down to {180}-41+66 ppm in 30 minute bins for WASP-85-Ab—a factor of ˜4 of the precision achieved by the K2 mission on this target—and to 101 ppm for TRES-3b. In the NIR, where diffusers may provide even more significant improvements over the current state of the art, our preliminary tests demonstrated {137}-36+64 ppm precision for a K S = 10.8 star on the 200 inch Hale Telescope. These photometric precisions match or surpass the expected photometric precisions of TESS for the same magnitude range. This technology is inexpensive, scalable, easily adaptable, and can have an important and immediate impact on the observations of transits and secondary eclipses of exoplanets.

Relationship between Air Pollution and Weather Conditions under Complicated Geographical conditions

NASA Astrophysics Data System (ADS)

Cheng, Q.; Jiang, P.; Li, M.

2017-12-01

Air pollution is one of the most serious issues all over the world, especially in megacities with constrained geographical conditions for air pollution diffusion. However, the dynamic mechanism of air pollution diffusion under complicated geographical conditions is still be confused. Researches to explore relationship between air pollution and weather conditions from the perspective of local atmospheric circulations can contribute more to solve such problem. We selected three megacities (Beijing, Shanghai and Guangzhou) under different geographical condition (mountain-plain transition region, coastal alluvial plain and coastal hilly terrain) to explore the relationship between air pollution and weather conditions. RDA (Redundancy analysis) model was used to analyze how the local atmospheric circulation acts on the air pollutant diffusion. The results show that there was a positive correlation between the concentration of air pollutants and air pressure, while temperature, precipitation and wind speed have negative correlations with the concentration of air pollutants. Furthermore, geographical conditions, such as topographic relief, have significant effects on the direction, path and intensity of local atmospheric circulation. As a consequence, air pollutants diffusion modes in different cities under various geographical conditions are diverse from each other.

Parameter optimization on the convergence surface of path simulations

NASA Astrophysics Data System (ADS)

Chandrasekaran, Srinivas Niranj

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

Applicability of a diffusion model to lateral transport in the terrestrial and lunar exospheres.

NASA Technical Reports Server (NTRS)

Hodges, R. R., Jr.

1972-01-01

Kinetic theory is used to determine a series expansion of the vertical flux of particles in an exosphere in terms of time and space derivatives of particle concentration, exobase velocity, and temperature. For sufficiently large scale variations of these parameters in time and space, the series can be truncated to a form that is similar to a diffusion equation. Owing to this analogy, it is possible to unite the mathematical description of molecular diffusion, which governs thermospheric flow, and the corresponding exospheric equation by using effective transport coefficients which change smoothly with altitude through the transition from thermosphere to exosphere. A new definition of the exobase for lateral flow emerges from the analogy of exospheric and thermospheric diffusion, as the altitude where the horizontal mean free path length equals the mean horizontal extent of ballistic trajectories of the transported gas, as opposed to the scale height of the dominant gas which determines the exobase for escape. It is shown that the approximation of exospheric lateral flow as a diffusion process is applicable to global scale problems concerning terrestrial helium and heavier gases, and lunar gases heavier than helium.

Novel Diffusivity Measurement Technique

NASA Technical Reports Server (NTRS)

Rashidnia, Nasser

2001-01-01

A common-path interferometer (CPI) system was developed to measure the diffusivity of liquid pairs. The CPI is an optical technique that can be used to measure changes in the gradient of the refraction index of transparent materials. This system uses a shearing interferometer that shares the same optical path from a laser light source to the final imaging plane. Hence, the molecular diffusion coefficient of liquids can be determined using the physical relations between changes in the optical path length and the liquid phase properties. The data obtained with this interferometer were compared with similar results from other techniques and demonstrated that the instrument is superior in measuring the diffusivity of miscible liquids while keeping the system very compact and robust. CPI can also be used for studies in interface dynamics and other diffusion-dominated-process applications.

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.

Lithium diffusion at Si-C interfaces in silicon-graphene composites

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

Odbadrakh, Khorgolkhuu; McNutt, N. W.; Nicholson, D. M.

2014-08-04

Models of intercalated Li and its diffusion in Si-Graphene interfaces are investigated using density functional theory. Results suggest that the presence of interfaces alters the energetics of Li binding and diffusion significantly compared to bare Si or Graphene surfaces. Our results show that cavities along reconstructed Si surface provide diffusion paths for Li. Diffusion barriers calculated along these cavities are significantly lower than penetration barriers to bulk Si. Interaction with Si surface results in graphene defects, creating Li diffusion paths that are confined along the cavities but have still lower barrier than in bulk Si.

Cycle flux algebra for ion and water flux through the KcsA channel single-file pore links microscopic trajectories and macroscopic observables.

PubMed

Oiki, Shigetoshi; Iwamoto, Masayuki; Sumikama, Takashi

2011-01-31

In narrow pore ion channels, ions and water molecules diffuse in a single-file manner and cannot pass each other. Under such constraints, ion and water fluxes are coupled, leading to experimentally observable phenomena such as the streaming potential. Analysis of this coupled flux would provide unprecedented insights into the mechanism of permeation. In this study, ion and water permeation through the KcsA potassium channel was the focus, for which an eight-state discrete-state Markov model has been proposed based on the crystal structure, exhibiting four ion-binding sites. Random transitions on the model lead to the generation of the net flux. Here we introduced the concept of cycle flux to derive exact solutions of experimental observables from the permeation model. There are multiple cyclic paths on the model, and random transitions complete the cycles. The rate of cycle completion is called the cycle flux. The net flux is generated by a combination of cyclic paths with their own cycle flux. T.L. Hill developed a graphical method of exact solutions for the cycle flux. This method was extended to calculate one-way cycle fluxes of the KcsA channel. By assigning the stoichiometric numbers for ion and water transfer to each cycle, we established a method to calculate the water-ion coupling ratio (CR(w-i)) through cycle flux algebra. These calculations predicted that CR(w-i) would increase at low potassium concentrations. One envisions an intuitive picture of permeation as random transitions among cyclic paths, and the relative contributions of the cycle fluxes afford experimental observables.

Cycle Flux Algebra for Ion and Water Flux through the KcsA Channel Single-File Pore Links Microscopic Trajectories and Macroscopic Observables

PubMed Central

Oiki, Shigetoshi; Iwamoto, Masayuki; Sumikama, Takashi

2011-01-01

In narrow pore ion channels, ions and water molecules diffuse in a single-file manner and cannot pass each other. Under such constraints, ion and water fluxes are coupled, leading to experimentally observable phenomena such as the streaming potential. Analysis of this coupled flux would provide unprecedented insights into the mechanism of permeation. In this study, ion and water permeation through the KcsA potassium channel was the focus, for which an eight-state discrete-state Markov model has been proposed based on the crystal structure, exhibiting four ion-binding sites. Random transitions on the model lead to the generation of the net flux. Here we introduced the concept of cycle flux to derive exact solutions of experimental observables from the permeation model. There are multiple cyclic paths on the model, and random transitions complete the cycles. The rate of cycle completion is called the cycle flux. The net flux is generated by a combination of cyclic paths with their own cycle flux. T.L. Hill developed a graphical method of exact solutions for the cycle flux. This method was extended to calculate one-way cycle fluxes of the KcsA channel. By assigning the stoichiometric numbers for ion and water transfer to each cycle, we established a method to calculate the water-ion coupling ratio (CR w-i) through cycle flux algebra. These calculations predicted that CR w-i would increase at low potassium concentrations. One envisions an intuitive picture of permeation as random transitions among cyclic paths, and the relative contributions of the cycle fluxes afford experimental observables. PMID:21304994

Langevin Dynamics, Large Deviations and Instantons for the Quasi-Geostrophic Model and Two-Dimensional Euler Equations

NASA Astrophysics Data System (ADS)

Bouchet, Freddy; Laurie, Jason; Zaboronski, Oleg

2014-09-01

We investigate a class of simple models for Langevin dynamics of turbulent flows, including the one-layer quasi-geostrophic equation and the two-dimensional Euler equations. Starting from a path integral representation of the transition probability, we compute the most probable fluctuation paths from one attractor to any state within its basin of attraction. We prove that such fluctuation paths are the time reversed trajectories of the relaxation paths for a corresponding dual dynamics, which are also within the framework of quasi-geostrophic Langevin dynamics. Cases with or without detailed balance are studied. We discuss a specific example for which the stationary measure displays either a second order (continuous) or a first order (discontinuous) phase transition and a tricritical point. In situations where a first order phase transition is observed, the dynamics are bistable. Then, the transition paths between two coexisting attractors are instantons (fluctuation paths from an attractor to a saddle), which are related to the relaxation paths of the corresponding dual dynamics. For this example, we show how one can analytically determine the instantons and compute the transition probabilities for rare transitions between two attractors.

Observation of quasiperiodic dynamics in a one-dimensional quantum walk of single photons in space

NASA Astrophysics Data System (ADS)

Xue, Peng; Qin, Hao; Tang, Bao; Sanders, Barry C.

2014-05-01

We realize the quasi-periodic dynamics of a quantum walker over 2.5 quasi-periods by realizing the walker as a single photon passing through a quantum-walk optical-interferometer network. We introduce fully controllable polarization-independent phase shifters in each optical path to realize arbitrary site-dependent phase shifts, and employ large clear-aperture beam displacers, while maintaining high-visibility interference, to enable 10 quantum-walk steps to be reached. By varying the half-wave-plate setting, we control the quantum-coin bias thereby observing a transition from quasi-periodic dynamics to ballistic diffusion.

On N. Park's Analytical solution for steady state density- and mixing regime—dependent solute transport in a vertical soil column

NASA Astrophysics Data System (ADS)

Thiele, Michael

1998-04-01

Recently, Park [1996] presented an analytical solution for stationary one-dimensional solute transport in a variable-density fluid flow through a vertical soil column. He used the widespread Bear-Scheidegger dispersion model describing solute mixing as a sum of molecular diffusion and velocity-proportional mechanical dispersion effects. His closed-form implicit concentration and pressure distributions thus allow for a discussion of the combined impact of molecular diffusion and mechanical dispersion in a variable-density environment. Whereas Park only considered the example of vanishing molecular diffusion in detail, both phenomena are taken into account simultaneously in the present study in order to elucidate their different influences on concentration distribution characteristics. The boundary value problem dealt with herein is based on an upward inflow of high-density fluid of constant solute concentration and corresponding outflow of a lower constant concentration fluid at the upper end of the column when dispersivity does not change along the flow path. The thickness of the transition zone between the two fluids appeared to strongly depend on the prevailing share of the molecular diffusion and mechanical dispersion mechanisms. The latter can be characterized by a molecular Peclet number Pe, which here is defined as the ratio of the column outflow velocity multiplied by a characteristic pore size and the molecular diffusion coefficient. For very small values of Pe, when molecular diffusion represents the exclusive mixing process, density differences have no impact on transition zone thicknesses. A relative density-;dependent thickness increases with flow velocities (increasing Pe values) very rapidly compared to the density-independent case, and after having passed a maximum decreases asymptotically to a constant value for the large Peclet number limit when mechanical dispersion is the only mixing mechanism. Hence the special transport problem analyzed gives further evidence for the importance of simultaneously considering molecular diffusion and mechanical dispersion in gravity-affected solute transport in porous media.

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

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

Double diffusivity model under stochastic forcing

NASA Astrophysics Data System (ADS)

Chattopadhyay, Amit K.; Aifantis, Elias C.

2017-05-01

The "double diffusivity" model was proposed in the late 1970s, and reworked in the early 1980s, as a continuum counterpart to existing discrete models of diffusion corresponding to high diffusivity paths, such as grain boundaries and dislocation lines. It was later rejuvenated in the 1990s to interpret experimental results on diffusion in polycrystalline and nanocrystalline specimens where grain boundaries and triple grain boundary junctions act as high diffusivity paths. Technically, the model pans out as a system of coupled Fick-type diffusion equations to represent "regular" and "high" diffusivity paths with "source terms" accounting for the mass exchange between the two paths. The model remit was extended by analogy to describe flow in porous media with double porosity, as well as to model heat conduction in media with two nonequilibrium local temperature baths, e.g., ion and electron baths. Uncoupling of the two partial differential equations leads to a higher-ordered diffusion equation, solutions of which could be obtained in terms of classical diffusion equation solutions. Similar equations could also be derived within an "internal length" gradient (ILG) mechanics formulation applied to diffusion problems, i.e., by introducing nonlocal effects, together with inertia and viscosity, in a mechanics based formulation of diffusion theory. While being remarkably successful in studies related to various aspects of transport in inhomogeneous media with deterministic microstructures and nanostructures, its implications in the presence of stochasticity have not yet been considered. This issue becomes particularly important in the case of diffusion in nanopolycrystals whose deterministic ILG-based theoretical calculations predict a relaxation time that is only about one-tenth of the actual experimentally verified time scale. This article provides the "missing link" in this estimation by adding a vital element in the ILG structure, that of stochasticity, that takes into account all boundary layer fluctuations. Our stochastic-ILG diffusion calculation confirms rapprochement between theory and experiment, thereby benchmarking a new generation of gradient-based continuum models that conform closer to real-life fluctuating environments.

Stormtime transport of ring current and radiation belt ions

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Schulz, Michael; Lyons, L. R.; Gorney, David J.

1993-01-01

This is an investigation of stormtime particle transport that leads to formation of the ring current. Our method is to trace the guiding-center motion of representative ions (having selected first adiabatic invariants mu) in response to model substorm-associated impulses in the convection electric field. We compare our simulation results qualitatively with existing analytically tractable idealizations of particle transport (direct convective access and radial diffusion) in order to assess the limits of validity of these approximations. For mu approximately less than 10 MeV/G (E approximately less than 10 keV at L equivalent to 3) the ion drift period on the final (ring-current) drift shell of interest (L equivalent to 3) exceeds the duration of the main phase of our model storm, and we find that the transport of ions to this drift shell is appropriately idealized as direct convective access, typically from open drift paths. Ion transport to a final closed drift path from an open (plasma-sheet) drift trajectory is possible for those portions of that drift path that lie outside the mean stormtime separatrix between closed and open drift trajectories, For mu approximately 10-25 MeV/G (110 keV approximately less than E approximately less than 280 keV at L equivalent to 3) the drift period at L equivalent to 3 is comparable to the postulated 3-hr duration of the storm, and the mode of transport is transitional between direct convective access and transport that resembles radial diffusion. (This particle population is transitional between the ring current and radiation belt). For mu approximately greater than 25 MeV/G (radiation-belt ions having E approximately greater than 280 keV at L equivalent to 3) the ion drift period is considerably shorter than the main phase of a typical storm, and ions gain access to the ring-current region essentially via radial diffusion. By computing the mean and mean-square cumulative changes in 1/L among (in this case) 12 representative ions equally spaced in drift time around the steady-state drift shell of interest (L equivalent to 3), we have estimated (from both our forward and our time-reversed simulations) the time-integrated radial-diffusion coefficients D(sup sim)(sub LL) for particles having selected values of mu approximately greater than 15 MeV/G. The results agree surprisingly well with the predictions (D(sup ql)(sub LL)) of quasilinear radial diffusion theory, despite the rather brief duration (approximately 3 hrs) of our model storm and despite the extreme variability (with frequency) of the spectral-density function that characterizes the applied electric field during our model storm. As expected, the values of D(sup sim)(sub LL) deduced (respectively) from our forward and time-reversed simulations agree even better with each other and with D(sup sim)(sub LL) when the impulse amplitudes which characterize the individual substorms of our model storm are systematically reduced.

Transitioning to a narrow path: the impact of fear of falling in older adults.

PubMed

Dunlap, Pamela; Perera, Subashan; VanSwearingen, Jessie M; Wert, David; Brach, Jennifer S

2012-01-01

Everyday ambulation requires navigation of variable terrain, transitions from wide to narrow pathways, and avoiding obstacles. While the effect of age on the transition to a narrow path has been examined briefly, little is known about the impact of fear of falling on gait during the transition to a narrow path. The purpose was to examine the effect of age and fear of falling on gait during transition to a narrow path. In 31 young, mean age=25.3 years, and 30 older adults, mean age=79.6 years, step length, step time, step width and gait speed were examined during usual and transition to narrow pathway using an instrumented walkway. During the transition to narrow walk condition, fearful older adults compared to young had a wider step width (0.06 m vs 0.04 m) prior to the narrow path and took shorter steps (0.53 m vs 0.72 m; p<0.001). Compared to non-fearful older adults, fearful older adults walked slower and took shorter steps during narrow path walking (gait speed: 1.1m/s vs 0.82 m/s; p=0.01; step length: 0.60 m vs 0.47 m; p=0.03). In young and non-fearful older adults narrow path gait was similar to usual gait. Whereas older adults who were fearful, walked slower (0.82 m/s vs 0.91 m/s; p=0.001) and took shorter steps (0.44 m vs 0.53 m; p=0.004) during narrow path walking compared to usual walking. Changes in gait characteristics with transitioning to a narrow pathway were greater for fear of falling than for age. Copyright © 2011 Elsevier B.V. All rights reserved.

Detailed numerical investigation of the Bohm limit in cosmic ray diffusion theory

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

Hussein, M.; Shalchi, A., E-mail: m_hussein@physics.umanitoba.ca, E-mail: andreasm4@yahoo.com

2014-04-10

A standard model in cosmic ray diffusion theory is the so-called Bohm limit in which the particle mean free path is assumed to be equal to the Larmor radius. This type of diffusion is often employed to model the propagation and acceleration of energetic particles. However, recent analytical and numerical work has shown that standard Bohm diffusion is not realistic. In the present paper, we perform test-particle simulations to explore particle diffusion in the strong turbulence limit in which the wave field is much stronger than the mean magnetic field. We show that there is indeed a lower limit ofmore » the particle mean free path along the mean field. In this limit, the mean free path is directly proportional to the unperturbed Larmor radius like in the traditional Bohm limit, but it is reduced by the factor δB/B {sub 0} where B {sub 0} is the mean field and δB the turbulent field. Although we focus on parallel diffusion, we also explore diffusion across the mean field in the strong turbulence limit.« less

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.

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

PubMed

Ovchinnikov, Victor; Karplus, Martin

2012-07-26

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

Stochastic theory of photon flow in homogeneous and heterogeneous anisotropic biological and artificial material

NASA Astrophysics Data System (ADS)

Miller, Steven D.

1995-05-01

Standard Monte Carlo methods used in photon diffusion score absorbed photons or statistical weight deposited within voxels comprising a mesh. An alternative approach to a stochastic description is considered for rapid surface flux calculations and finite medias. Matrix elements are assigned to a spatial lattice whose function is to score vector intersections of scattered photons making transitions into either the forward or back solid angle half spaces. These complete matrix elements can be related to the directional fluxes within the lattice space. This model differentiates between ballistic, quasi-ballistic, and highly diffuse photon contributions, and effectively models the subsurface generation of a scattered light flux from a ballistic source. The connection between a path integral and diffusion is illustrated. Flux perturbations can be effectively illustrated for tissue-tumor-tissue and for 3 layer systems with strong absorption in one or more layers. For conditions where the diffusion theory has difficulties such as strong absorption, highly collimated sources, small finite volumes, and subsurface regions, the computation time of the algorithm is rapid with good accuracy and compliments other description of photon diffusion. The model has the potential to do computations relevant to photodynamic therapy (PDT) and analysis of laser beam interaction with tissues.

Pressure induced solid-solid reconstructive phase transition in LiGa O2 dominated by elastic strain

NASA Astrophysics Data System (ADS)

Hu, Qiwei; Yan, Xiaozhi; Lei, Li; Wang, Qiming; Feng, Leihao; Qi, Lei; Zhang, Leilei; Peng, Fang; Ohfuji, Hiroaki; He, Duanwei

2018-01-01

Pressure induced solid-solid reconstructive phase transitions for graphite-diamond, and wurtzite-rocksalt in GaN and AlN occur at significantly higher pressure than expected from equilibrium coexistence and their transition paths are always inconsistent with each other. These indicate that the underlying nucleation and growth mechanism in the solid-solid reconstructive phase transitions are poorly understood. Here, we propose an elastic-strain dominated mechanism in a reconstructive phase transition, β -LiGa O2 to γ -LiGa O2 , based on in situ high-pressure angle dispersive x-ray diffraction and single-crystal Raman scattering. This mechanism suggests that the pressure induced solid-solid reconstructive phase transition is neither purely diffusionless nor purely diffusive, as conventionally assumed, but a combination. The large elastic strains are accumulated, with the coherent nucleation, in the early stage of the transition. The elastic strains along the 〈100 〉 and 〈001 〉 directions are too large to be relaxed by the shear stress, so an intermediate structure emerges reducing the elastic strains and making the transition energetically favorable. At higher pressures, when the elastic strains become small enough to be relaxed, the phase transition to γ -LiGa O2 begins and the coherent nucleation is substituted with a semicoherent one with Li and Ga atoms disordered.

Red blood cell thickness is evolutionarily constrained by slow, hemoglobin-restricted diffusion in cytoplasm.

PubMed

Richardson, Sarah L; Swietach, Pawel

2016-10-25

During capillary transit, red blood cells (RBCs) must exchange large quantities of CO 2 and O 2 in typically less than one second, but the degree to which this is rate-limited by diffusion through cytoplasm is not known. Gas diffusivity is intuitively assumed to be fast and this would imply that the intracellular path-length, defined by RBC shape, is not a factor that could meaningfully compromise physiology. Here, we evaluated CO 2 diffusivity (D CO2 ) in RBCs and related our results to cell shape. D CO2 inside RBCs was determined by fluorescence imaging of [H + ] dynamics in cells under superfusion. This method is based on the principle that H + diffusion is facilitated by CO 2 /HCO 3 - buffer and thus provides a read-out of D CO2 . By imaging the spread of H + ions from a photochemically-activated source (6-nitroveratraldehyde), D CO2 in human RBCs was calculated to be only 5% of the rate in water. Measurements on RBCs containing different hemoglobin concentrations demonstrated a halving of D CO2 with every 75 g/L increase in mean corpuscular hemoglobin concentration (MCHC). Thus, to compensate for highly-restricted cytoplasmic diffusion, RBC thickness must be reduced as appropriate for its MCHC. This can explain the inverse relationship between MCHC and RBC thickness determined from >250 animal species.

Red blood cell thickness is evolutionarily constrained by slow, hemoglobin-restricted diffusion in cytoplasm

PubMed Central

Richardson, Sarah L.; Swietach, Pawel

2016-01-01

During capillary transit, red blood cells (RBCs) must exchange large quantities of CO2 and O2 in typically less than one second, but the degree to which this is rate-limited by diffusion through cytoplasm is not known. Gas diffusivity is intuitively assumed to be fast and this would imply that the intracellular path-length, defined by RBC shape, is not a factor that could meaningfully compromise physiology. Here, we evaluated CO2 diffusivity (DCO2) in RBCs and related our results to cell shape. DCO2 inside RBCs was determined by fluorescence imaging of [H+] dynamics in cells under superfusion. This method is based on the principle that H+ diffusion is facilitated by CO2/HCO3− buffer and thus provides a read-out of DCO2. By imaging the spread of H+ ions from a photochemically-activated source (6-nitroveratraldehyde), DCO2 in human RBCs was calculated to be only 5% of the rate in water. Measurements on RBCs containing different hemoglobin concentrations demonstrated a halving of DCO2 with every 75 g/L increase in mean corpuscular hemoglobin concentration (MCHC). Thus, to compensate for highly-restricted cytoplasmic diffusion, RBC thickness must be reduced as appropriate for its MCHC. This can explain the inverse relationship between MCHC and RBC thickness determined from >250 animal species. PMID:27777410

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.

Optical and Casimir effects in topological materials

NASA Astrophysics Data System (ADS)

Wilson, Justin H.

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

Propagation and transmission of optical vortex beams through turbid scattering wall with orbital angular momentums

NASA Astrophysics Data System (ADS)

Wang, W. B.; Gozali, Richard; Nguyen, Thien An; Alfano, R. R.

2015-03-01

Light scattering and transmission of optical Laguerre Gaussian (LG) vortex beams with different orbital angular momentum (OAM) states in turbid scattering media were investigated in comparison with Gaussian (G) beam. The scattering media used in the experiments consist of various sizes and concentrations of latex beads in water solutions. The LG beams were generated using a spatial light modulator in reflection mode. The ballistic transmissions of LG and G beams were measured with different ratios of thickness of samples (z) to scattering mean free path (ls) of the turbid media, z/ls. The results show that in the ballistic region where z/ls is small, the LG and G beams show no significant difference, while in the diffusive region where z/ls is large, LG beams show higher transmission than Gaussian beam. In the diffusive region, the LG beams with higher orbital angular momentum L values show higher transmission than the beams with lower L values. The transition points from ballistic to diffusive regions for different scattering media were studied and determined.

Focused fluorescence excitation with time-reversed ultrasonically encoded light and imaging in thick scattering media

NASA Astrophysics Data System (ADS)

Lai, Puxiang; Suzuki, Yuta; Xu, Xiao; Wang, Lihong V.

2013-07-01

Scattering dominates light propagation in biological tissue, and therefore restricts both resolution and penetration depth in optical imaging within thick tissue. As photons travel into the diffusive regime, typically 1 mm beneath human skin, their trajectories transition from ballistic to diffusive due to the increased number of scattering events, which makes it impossible to focus, much less track, photon paths. Consequently, imaging methods that rely on controlled light illumination are ineffective in deep tissue. This problem has recently been addressed by a novel method capable of dynamically focusing light in thick scattering media via time reversal of ultrasonically encoded (TRUE) diffused light. Here, using photorefractive materials as phase conjugate mirrors, we show a direct visualization and dynamic control of optical focusing with this light delivery method, and demonstrate its application for focused fluorescence excitation and imaging in thick turbid media. These abilities are increasingly critical for understanding the dynamic interactions of light with biological matter and processes at different system levels, as well as their applications for biomedical diagnosis and therapy.

Ordering kinetics in two-dimensional hexagonal pattern of cylinder-forming PS-b -PMMA block copolymer thin films: Dependence on the segregation strength

NASA Astrophysics Data System (ADS)

Seguini, Gabriele; Zanenga, Fabio; Laus, Michele; Perego, Michele

2018-05-01

This paper reports the experimental determination of the growth exponents and activation enthalpies for the ordering process of standing cylinder-forming all-organic polystyrene-block-poly (methyl methacrylate) block copolymer (BCP) thin films as a function of the BCP degree of polymerization (N). The maximum growth exponent of 1/3 is observed for the BCP with the lowest N at the border of the order-disorder transition. Both the growth exponents and the activation enthalpies exponentially decrease with the BCP segregation strength (χN) following the same path of the diffusivity.

Generating a Simulated Fluid Flow Over an Aircraft Surface Using Anisotropic Diffusion

NASA Technical Reports Server (NTRS)

Rodriguez, David L. (Inventor); Sturdza, Peter (Inventor)

2013-01-01

A fluid-flow simulation over a computer-generated aircraft surface is generated using a diffusion technique. The surface is comprised of a surface mesh of polygons. A boundary-layer fluid property is obtained for a subset of the polygons of the surface mesh. A pressure-gradient vector is determined for a selected polygon, the selected polygon belonging to the surface mesh but not one of the subset of polygons. A maximum and minimum diffusion rate is determined along directions determined using a pressure gradient vector corresponding to the selected polygon. A diffusion-path vector is defined between a point in the selected polygon and a neighboring point in a neighboring polygon. An updated fluid property is determined for the selected polygon using a variable diffusion rate, the variable diffusion rate based on the minimum diffusion rate, maximum diffusion rate, and angular difference between the diffusion-path vector and the pressure-gradient vector.

Path Finding on High-Dimensional Free Energy Landscapes

NASA Astrophysics Data System (ADS)

Díaz Leines, Grisell; Ensing, Bernd

2012-07-01

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

Computation of rare transitions in the barotropic quasi-geostrophic equations

NASA Astrophysics Data System (ADS)

Laurie, Jason; Bouchet, Freddy

2015-01-01

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

Modelling cointegration and Granger causality network to detect long-term equilibrium and diffusion paths in the financial system.

PubMed

Gao, Xiangyun; Huang, Shupei; Sun, Xiaoqi; Hao, Xiaoqing; An, Feng

2018-03-01

Microscopic factors are the basis of macroscopic phenomena. We proposed a network analysis paradigm to study the macroscopic financial system from a microstructure perspective. We built the cointegration network model and the Granger causality network model based on econometrics and complex network theory and chose stock price time series of the real estate industry and its upstream and downstream industries as empirical sample data. Then, we analysed the cointegration network for understanding the steady long-term equilibrium relationships and analysed the Granger causality network for identifying the diffusion paths of the potential risks in the system. The results showed that the influence from a few key stocks can spread conveniently in the system. The cointegration network and Granger causality network are helpful to detect the diffusion path between the industries. We can also identify and intervene in the transmission medium to curb risk diffusion.

Modelling cointegration and Granger causality network to detect long-term equilibrium and diffusion paths in the financial system

PubMed Central

Huang, Shupei; Sun, Xiaoqi; Hao, Xiaoqing; An, Feng

2018-01-01

Microscopic factors are the basis of macroscopic phenomena. We proposed a network analysis paradigm to study the macroscopic financial system from a microstructure perspective. We built the cointegration network model and the Granger causality network model based on econometrics and complex network theory and chose stock price time series of the real estate industry and its upstream and downstream industries as empirical sample data. Then, we analysed the cointegration network for understanding the steady long-term equilibrium relationships and analysed the Granger causality network for identifying the diffusion paths of the potential risks in the system. The results showed that the influence from a few key stocks can spread conveniently in the system. The cointegration network and Granger causality network are helpful to detect the diffusion path between the industries. We can also identify and intervene in the transmission medium to curb risk diffusion. PMID:29657804

Path-integral simulation of solids.

PubMed

Herrero, C P; Ramírez, R

2014-06-11

The path-integral formulation of the statistical mechanics of quantum many-body systems is described, with the purpose of introducing practical techniques for the simulation of solids. Monte Carlo and molecular dynamics methods for distinguishable quantum particles are presented, with particular attention to the isothermal-isobaric ensemble. Applications of these computational techniques to different types of solids are reviewed, including noble-gas solids (helium and heavier elements), group-IV materials (diamond and elemental semiconductors), and molecular solids (with emphasis on hydrogen and ice). Structural, vibrational, and thermodynamic properties of these materials are discussed. Applications also include point defects in solids (structure and diffusion), as well as nuclear quantum effects in solid surfaces and adsorbates. Different phenomena are discussed, as solid-to-solid and orientational phase transitions, rates of quantum processes, classical-to-quantum crossover, and various finite-temperature anharmonic effects (thermal expansion, isotopic effects, electron-phonon interactions). Nuclear quantum effects are most remarkable in the presence of light atoms, so that especial emphasis is laid on solids containing hydrogen as a constituent element or as an impurity.

A benchmark for reaction coordinates in the transition path ensemble

PubMed Central

2016-01-01

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

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

PubMed Central

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

2015-01-01

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

VQS (vapor-quasiliquid-solid, vapor-quasisolid-solid) mechanism presents a unified foundation for the syntheses of nanotubes, primarily carbon nanotubes

NASA Astrophysics Data System (ADS)

Mohammad, S. Noor

2017-09-01

Nanotubes are synthesized almost entirely by metal-catalyst-free and metal-catalyst-mediated non-eutectic mechanism(s). An investigation has been carried out to understand the basics of this mechanism. Various possible chemical and physical processes involved in nanotube synthesis have been researched. Various components and attributes of nanotube synthesis have been evaluated. Phase transitions, alloy formation, porosity, carrier transport and the fundamentals underlying them have been examined. Nanoparticle surfaces conducive to nanotube synthesis have been examined. The role of surface treatment, which includes oxidation, oxygenation, acid treatment, plasma treatment, water treatment, sputtering, etc in creating such surfaces, has been investigated. The role of surface treatment and phase transitions as functions of temperature, pressure, ambient, contaminants, surface amorphicity, etc in creating diffusion paths for the diffusion of growth species for supersaturation and nucleation has been explored. Interdiffusion of catalyst and source materials, and hence exchange of materials, on the nanoparticle surface, have been elucidated. This exchange of materials on catalyst surface appears to add a new dimension to the synthesis kinetics. Integrated together, they reveal a general mechanism for probably all metal-catalyst-free and metal-catalyst-mediated non-eutectic nanotube synthesis. Available experiments strongly support the proposed mechanism; they suggest that this mechanism has a broad appeal.

Transition of basaltic lava from pahoehoe to aa, Kilauea Volcano, Hawaii: Field observations and key factors

USGS Publications Warehouse

Peterson, Donald W.; Tilling, Robert I.

1980-01-01

Nearly all Hawaiian basaltic lava erupts as pahoehoe, and some changes to aa during flowage and cooling; factors governing the transition involve certain critical relations between viscosity and rate of shear strain. If the lava slows, cools, and stops in direct response to concomitant increase in viscosity before these critical relations are reached, it remains pahoehoe. But, if flow mechanics (flow rate, flow dimensions, slope, momentum, etc.) impel the lava to continue to move and deform even after it has become highly viscous, the critical relations may be reached and the lava changes to aa.Typical modes of transition from pahoehoe to aa include: (1) spontaneous formation of relatively stiff clots in parts of the flowing lava where shear rate is highest; these clots grow into discrete, rough, sticky masses to which the remaining fluid lava incrementally adheres; (2) fragmentation and immersion of solid or semi-solid surface crusts of pahoehoe by roiling movements of the flow, forming cores of discrete, tacky masses; (3) sudden renewed movement of lava stored and cooled within surface reservoirs to form clots. The masses, fragments, and clots in these transition modes are characterized by spinose, granulated surfaces; as flow movement continues, the masses and fragments aggregate, fracture, and grind together, completing the transition to aa.Observations show that the critical relation between viscosity and rate of shear strain is inverse: if viscosity is low, a high rate of shear is required to begin the transition to aa; conversely, if viscosity is high, a much lower rate of shear will induce the transition. These relations can be demonstrated qualitatively with simple graphs, which can be used to examine the flow history of any selected finite lava element by tracing the path represented by its changing viscosity and shear rate. A broad, diffuse “transition threshold zone” in these graphs portrays the inverse critical relation between viscosity and shear rate; the transition to aa is represented by the path of the lava element crossing this zone.Moving lava flows can be regarded as natural viscometers, by which shear stress and rate of shear strain at selected points can be determined and viscosity can be computed. By making such determinations under a wide range of conditions on pahoehoe, aa, and transitional flow types, the critical relations that control the pahoehoe-aa transition can be quantified.

On the assumptions underlying milestoning.

PubMed

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

2008-11-07

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

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

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

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

Molecular dynamics simulations of substitutional diffusion

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

Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

2016-12-18

In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less

Rotary blood pump

NASA Technical Reports Server (NTRS)

Benkowski, Robert J. (Inventor); Kiris, Cetin (Inventor); Kwak, Dochan (Inventor); Rosenbaum, Bernard J. (Inventor); Bacak, James W. (Inventor); DeBakey, Michael E. (Inventor)

1999-01-01

A blood pump that comprises a pump housing having a blood flow path therethrough, a blood inlet, and a blood outlet; a stator mounted to the pump housing, the stator having a stator field winding for producing a stator magnetic field; a flow straightener located within the pump housing, and comprising a flow straightener hub and at least one flow straightener blade attached to the flow straightener hub; a rotor mounted within the pump housing for rotation in response to the stator magnetic field, the rotor comprising an inducer and an impeller; the inducer being located downstream of the flow straightener, and comprising an inducer hub and at least one inducer blade attached to the inducer hub; the impeller being located downstream of the inducer, and comprising an impeller hub and at least one impeller blade attached to the impeller hub; and preferably also comprising a diffuser downstream of the impeller, the diffuser comprising a diffuser hub and at least one diffuser blade. Blood flow stagnation and clot formation within the pump are minimized by, among other things, providing the inducer hub with a diameter greater than the diameter of the flow straightener hub; by optimizing the axial spacing between the flow straightener hub and the inducer hub, and between the impeller hub and the diffuser hub; by optimizing the inlet angle of the diffuser blades; and by providing fillets or curved transitions between the upstream end of the inducer hub and the shaft mounted therein, and between the impeller hub and the shaft mounted therein.

Geodesic-loxodromes for diffusion tensor interpolation and difference measurement.

PubMed

Kindlmann, Gordon; Estépar, Raúl San José; Niethammer, Marc; Haker, Steven; Westin, Carl-Fredrik

2007-01-01

In algorithms for processing diffusion tensor images, two common ingredients are interpolating tensors, and measuring the distance between them. We propose a new class of interpolation paths for tensors, termed geodesic-loxodromes, which explicitly preserve clinically important tensor attributes, such as mean diffusivity or fractional anisotropy, while using basic differential geometry to interpolate tensor orientation. This contrasts with previous Riemannian and Log-Euclidean methods that preserve the determinant. Path integrals of tangents of geodesic-loxodromes generate novel measures of over-all difference between two tensors, and of difference in shape and in orientation.

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.

An isotopic and modelling study of flow paths and storage in Quaternary calcarenite, SW Australia: implications for speleothem paleoclimate records

NASA Astrophysics Data System (ADS)

Treble, Pauline C.; Bradley, Chris; Wood, Anne; Baker, Andy; Jex, Catherine N.; Fairchild, Ian J.; Gagan, Michael K.; Cowley, Joan; Azcurra, Cecilia

2013-03-01

We investigated the distinctive shallow sub-surface hydrology of the southwest Western Australia (SWWA) dune calcarenite using observed rainfall and rainfall δ18O; soil moisture, cave drip rate and dripwater δ18O over a six-year period: August 2005-March 2012. A lumped parameter hydrological model is developed to describe water fluxes and drip δ18O. Comparison of observed data and model output allow us to assess the critical non-climatic karst hydrological processes that modify the precipitation δ18O signal and discuss the implications for speleothem paleoclimate records from this cave and those with a similar karst setting. Our findings include evidence of multiple reservoirs, characterised by distinct δ18O values and recharge responses ('low' and 'high' flow sites). Dripwaters exhibit δ18O variations in wet versus dry years at low-flow sites receiving diffuse seepage from the epikarst with an attenuated isotopic composition that approximates mean rainfall. Recharge from high-magnitude rain events is stored in a secondary reservoir which is associated with high-flow dripwater that is 1‰ lower than our monitored low-flow sites (δ18O). One drip site is characterised by mixed-flow behaviour and exhibits a non-linear threshold response after the cessation of drainage from a secondary reservoir following a record dry year (2006). Additionally, our results yield a better understanding of the vadose zone hydrology and dripwater characteristics in Quaternary age dune limestones. We show that flow to our monitored sites is dominated by diffuse flow with inferred transit times of less than one year. Diffuse flow appears to follow vertical preferential paths through the limestone reflecting differences in permeability and deep recharge into the host rock.

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

PubMed Central

Ovchinnikov, Victor; Karplus, Martin; Vanden-Eijnden, Eric

2011-01-01

A set of techniques developed under the umbrella of the string method is used in combination with all-atom molecular dynamics simulations to analyze the conformation change between the prepowerstroke (PPS) and rigor (R) structures of the converter domain of myosin VI. The challenges specific to the application of these techniques to such a large and complex biomolecule are addressed in detail. These challenges include (i) identifying a proper set of collective variables to apply the string method, (ii) finding a suitable initial string, (iii) obtaining converged profiles of the free energy along the transition path, (iv) validating and interpreting the free energy profiles, and (v) computing the mean first passage time of the transition. A detailed description of the PPS↔R transition in the converter domain of myosin VI is obtained, including the transition path, the free energy along the path, and the rates of interconversion. The methodology developed here is expected to be useful more generally in studies of conformational transitions in complex biomolecules. PMID:21361558

APM_GUI: analyzing particle movement on the cell membrane and determining confinement.

PubMed

Menchón, Silvia A; Martín, Mauricio G; Dotti, Carlos G

2012-02-20

Single-particle tracking is a powerful tool for tracking individual particles with high precision. It provides useful information that allows the study of diffusion properties as well as the dynamics of movement. Changes in particle movement behavior, such as transitions between Brownian motion and temporary confinement, can reveal interesting biophysical interactions. Although useful applications exist to determine the paths of individual particles, only a few software implementations are available to analyze these data, and these implementations are generally not user-friendly and do not have a graphical interface,. Here, we present APM_GUI (Analyzing Particle Movement), which is a MatLab-implemented application with a Graphical User Interface. This user-friendly application detects confined movement considering non-random confinement when a particle remains in a region longer than a Brownian diffusant would remain. In addition, APM_GUI exports the results, which allows users to analyze this information using software that they are familiar with. APM_GUI provides an open-source tool that quantifies diffusion coefficients and determines whether trajectories have non-random confinements. It also offers a simple and user-friendly tool that can be used by individuals without programming skills.

Optical vortex beam transmission with different OAM in scattering beads and brain tissue media

NASA Astrophysics Data System (ADS)

Wang, W. B.; Shi, Lingyan; Lindwasser, Lukas; Marque, Paulo; Lavery, M. P. J.; Alfano, R. R.

2016-03-01

Light transmission of Laguerre Gaussian (LG) vortex beams with different orbital angular momentum (OAM) values (L) in scattering beads and mouse brain tissue media were experimentally investigated for the first time in comparison with Gaussian (G) beams. The LG beams with different OAM were generated using a spatial light modulator (SLM) in reflection mode. The scattering beads media consist of various sizes and concentrations of latex beads in water solutions. The transmissions of LG and G beams through scattering beads and brain tissue media were measured with different ratios of sample thicknesses (z) to scattering mean free path (ls) of the turbid media, z/ls. The results indicate that within the ballistic region where z/ls is small, the LG and G beams show no significant difference, while in the diffusive region where z/ls is higher, the vortex beams show higher transmission than G beams. In the diffusive region, the LG beams with higher L values show higher transmission than the beams with lower L values due to the eigen channels in the media. The transition points from the ballistic to diffusive regions for different scattering beads and brain tissue media were studied.

Phase transition in conservative diffusive contact processes

NASA Astrophysics Data System (ADS)

Fiore, Carlos E.; de Oliveira, Mário J.

2004-10-01

We determine the phase diagrams of conservative diffusive contact processes by means of numerical simulations. These models are versions of the ordinary diffusive single-creation, pair-creation, and triplet-creation contact processes in which the particle number is conserved. The transition between the frozen and active states was determined by studying the system in the subcritical regime, and the nature of the transition, whether continuous or first order, was determined by looking at the fractal dimension of the critical cluster. For the single-creation model the transition remains continuous for any diffusion rate. For pair- and triplet-creation models, however, the transition becomes first order for high enough diffusion rate. Our results indicate that in the limit of infinite diffusion rate the jump in density equals 2/3 for the pair-creation model and 5/6 for the triplet-creation model.

Discrete Diffusion Monte Carlo for Electron Thermal Transport

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Wollaeger, Ryan; Moses, Gregory

2014-10-01

The iSNB (implicit Schurtz Nicolai Busquet electron thermal transport method of Cao et al. is adapted to a Discrete Diffusion Monte Carlo (DDMC) solution method for eventual inclusion in a hybrid IMC-DDMC (Implicit Monte Carlo) method. The hybrid method will combine the efficiency of a diffusion method in short mean free path regions with the accuracy of a transport method in long mean free path regions. The Monte Carlo nature of the approach allows the algorithm to be massively parallelized. Work to date on the iSNB-DDMC method will be presented. This work was supported by Sandia National Laboratory - Albuquerque.

Statistical Analysis of the First Passage Path Ensemble of Jump Processes

NASA Astrophysics Data System (ADS)

von Kleist, Max; Schütte, Christof; Zhang, Wei

2018-02-01

The transition mechanism of jump processes between two different subsets in state space reveals important dynamical information of the processes and therefore has attracted considerable attention in the past years. In this paper, we study the first passage path ensemble of both discrete-time and continuous-time jump processes on a finite state space. The main approach is to divide each first passage path into nonreactive and reactive segments and to study them separately. The analysis can be applied to jump processes which are non-ergodic, as well as continuous-time jump processes where the waiting time distributions are non-exponential. In the particular case that the jump processes are both Markovian and ergodic, our analysis elucidates the relations between the study of the first passage paths and the study of the transition paths in transition path theory. We provide algorithms to numerically compute statistics of the first passage path ensemble. The computational complexity of these algorithms scales with the complexity of solving a linear system, for which efficient methods are available. Several examples demonstrate the wide applicability of the derived results across research areas.

Long-distance thermal temporal ghost imaging over optical fibers

NASA Astrophysics Data System (ADS)

Yao, Xin; Zhang, Wei; Li, Hao; You, Lixing; Wang, Zhen; Huang, Yidong

2018-02-01

A thermal ghost imaging scheme between two distant parties is proposed and experimentally demonstrated over long-distance optical fibers. In the scheme, the weak thermal light is split into two paths. Photons in one path are spatially diffused according to their frequencies by a spatial dispersion component, then illuminate the object and record its spatial transmission information. Photons in the other path are temporally diffused by a temporal dispersion component. By the coincidence measurement between photons of two paths, the object can be imaged in a way of ghost imaging, based on the frequency correlation between photons in the two paths. In the experiment, the weak thermal light source is prepared by the spontaneous four-wave mixing in a silicon waveguide. The temporal dispersion is introduced by single mode fibers of 50 km, which also could be looked as a fiber link. Experimental results show that this scheme can be realized over long-distance optical fibers.

Dynamic heterogeneity in the folding/unfolding transitions of FiP35

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

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

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

A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics.

PubMed

Hageman, Nathan S; Toga, Arthur W; Narr, Katherine L; Shattuck, David W

2009-03-01

We introduce a fluid mechanics based tractography method for estimating the most likely connection paths between points in diffusion tensor imaging (DTI) volumes. We customize the Navier-Stokes equations to include information from the diffusion tensor and simulate an artificial fluid flow through the DTI image volume. We then estimate the most likely connection paths between points in the DTI volume using a metric derived from the fluid velocity vector field. We validate our algorithm using digital DTI phantoms based on a helical shape. Our method segmented the structure of the phantom with less distortion than was produced using implementations of heat-based partial differential equation (PDE) and streamline based methods. In addition, our method was able to successfully segment divergent and crossing fiber geometries, closely following the ideal path through a digital helical phantom in the presence of multiple crossing tracts. To assess the performance of our algorithm on anatomical data, we applied our method to DTI volumes from normal human subjects. Our method produced paths that were consistent with both known anatomy and directionally encoded color images of the DTI dataset.

A Diffusion Tensor Imaging Tractography Algorithm Based on Navier-Stokes Fluid Mechanics

PubMed Central

Hageman, Nathan S.; Toga, Arthur W.; Narr, Katherine; Shattuck, David W.

2009-01-01

We introduce a fluid mechanics based tractography method for estimating the most likely connection paths between points in diffusion tensor imaging (DTI) volumes. We customize the Navier-Stokes equations to include information from the diffusion tensor and simulate an artificial fluid flow through the DTI image volume. We then estimate the most likely connection paths between points in the DTI volume using a metric derived from the fluid velocity vector field. We validate our algorithm using digital DTI phantoms based on a helical shape. Our method segmented the structure of the phantom with less distortion than was produced using implementations of heat-based partial differential equation (PDE) and streamline based methods. In addition, our method was able to successfully segment divergent and crossing fiber geometries, closely following the ideal path through a digital helical phantom in the presence of multiple crossing tracts. To assess the performance of our algorithm on anatomical data, we applied our method to DTI volumes from normal human subjects. Our method produced paths that were consistent with both known anatomy and directionally encoded color (DEC) images of the DTI dataset. PMID:19244007

High reflected cubic cavity as long path absorption cell for infrared gas sensing

NASA Astrophysics Data System (ADS)

Yu, Jia; Gao, Qiang; Zhang, Zhiguo

2014-10-01

One direct and efficient method to improve the sensitivity of infrared gas sensors is to increase the optical path length of gas cells according to Beer-Lambert Law. In this paper, cubic shaped cavities with high reflected inner coating as novel long path absorption cells for infrared gas sensing were developed. The effective optical path length (EOPL) for a single cubic cavity and tandem cubic cavities were investigated based on Tunable Diode Laser Absorption Spectroscopy (TDLAS) measuring oxygen P11 line at 763 nm. The law of EOPL of a diffuse cubic cavity in relation with the reflectivity of the coating, the port fraction and side length of the cavity was obtained. Experimental results manifested an increase of EOPL for tandem diffuse cubic cavities as the decrease of port fraction of the connecting aperture f', and the EOPL equaled to the sum of that of two single cubic cavities at f'<0.01. The EOPL spectra at infrared wavelength range for different inner coatings including high diffuse coatings and high reflected metallic thin film coatings were deduced.

Li conduction pathways in solid-state electrolytes: Insights from dynamics and polarizability

NASA Astrophysics Data System (ADS)

Takahashi, Tsukasa; Nagagiri, Koki; Iwadate, Yasuhiko; Utsuno, Futoshi; Yamaguchi, Hiroshi; Ohkubo, Takahiro

2018-04-01

We investigated the dynamical and polarizable properties of Li7P3S11, which is a fast Li-conducting material, by performing ab initio molecular dynamics simulations. A zone analysis based on Li migration highlighted the effective path along which Li diffuses in the crystal. The effective Li diffusion was analyzed in terms of the dynamics and polarizability of the sulfur surrounding the Li migration path. High flexibility and large anisotropic polarizability were the characteristics identified as necessary for the formation of an effective Li migration path. These findings provide principles for understanding Li conduction in solid-state electrolytes.

Killing (absorption) versus survival in random motion

NASA Astrophysics Data System (ADS)

Garbaczewski, Piotr

2017-09-01

We address diffusion processes in a bounded domain, while focusing on somewhat unexplored affinities between the presence of absorbing and/or inaccessible boundaries. For the Brownian motion (Lévy-stable cases are briefly mentioned) model-independent features are established of the dynamical law that underlies the short-time behavior of these random paths, whose overall lifetime is predefined to be long. As a by-product, the limiting regime of a permanent trapping in a domain is obtained. We demonstrate that the adopted conditioning method, involving the so-called Bernstein transition function, works properly also in an unbounded domain, for stochastic processes with killing (Feynman-Kac kernels play the role of transition densities), provided the spectrum of the related semigroup operator is discrete. The method is shown to be useful in the case, when the spectrum of the generator goes down to zero and no isolated minimal (ground state) eigenvalue is in existence, like in the problem of the long-term survival on a half-line with a sink at origin.

Dual control of flow field heterogeneity and immobile porosity on non-Fickian transport in Berea sandstone

NASA Astrophysics Data System (ADS)

Gjetvaj, Filip; Russian, Anna; Gouze, Philippe; Dentz, Marco

2015-10-01

Both flow field heterogeneity and mass transfer between mobile and immobile domains have been studied separately for explaining observed anomalous transport. Here we investigate non-Fickian transport using high-resolution 3-D X-ray microtomographic images of Berea sandstone containing microporous cement with pore size below the setup resolution. Transport is computed for a set of representative elementary volumes and results from advection and diffusion in the resolved macroporosity (mobile domain) and diffusion in the microporous phase (immobile domain) where the effective diffusion coefficient is calculated from the measured local porosity using a phenomenological model that includes a porosity threshold (ϕθ) below which diffusion is null and the exponent n that characterizes tortuosity-porosity power-law relationship. We show that both flow field heterogeneity and microporosity trigger anomalous transport. Breakthrough curve (BTC) tailing is positively correlated to microporosity volume and mobile-immobile interface area. The sensitivity analysis showed that the BTC tailing increases with the value of ϕθ, due to the increase of the diffusion path tortuosity until the volume of the microporosity becomes negligible. Furthermore, increasing the value of n leads to an increase in the standard deviation of the distribution of effective diffusion coefficients, which in turn results in an increase of the BTC tailing. Finally, we propose a continuous time random walk upscaled model where the transition time is the sum of independently distributed random variables characterized by specific distributions. It allows modeling a 1-D equivalent macroscopic transport honoring both the control of the flow field heterogeneity and the multirate mass transfer between mobile and immobile domains.

Workforce Development.

ERIC Educational Resources Information Center

1999

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

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

PubMed Central

Liu, Zhao; Zhu, Yunhong; Wu, Chenxue

2016-01-01

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

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

PubMed

Zheng, Jingjing; Truhlar, Donald G

2012-01-01

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

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

PubMed

Molloy, Kevin; Shehu, Amarda

2013-01-01

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

The plasma-wall transition layers in the presence of collisions with a magnetic field parallel to the wall

NASA Astrophysics Data System (ADS)

Moritz, J.; Faudot, E.; Devaux, S.; Heuraux, S.

2018-01-01

The plasma-wall transition is studied by means of a particle-in-cell (PIC) simulation in the configuration of a parallel to the wall magnetic field (B), with collisions between charged particles vs. neutral atoms taken into account. The investigated system consists of a plasma bounded by two absorbing walls separated by 200 electron Debye lengths (λd). The strength of the magnetic field is chosen such as the ratio λ d / r l , with rl being the electron Larmor radius, is smaller or larger than unity. Collisions are modelled with a simple operator that reorients randomly ion or electron velocity, keeping constant the total kinetic energy of both the neutral atom (target) and the incident charged particle. The PIC simulations show that the plasma-wall transition consists in a quasi-neutral region (pre-sheath), from the center of the plasma towards the walls, where the electric potential or electric field profiles are well described by an ambipolar diffusion model, and in a second region at the vicinity of the walls, called the sheath, where the quasi-neutrality breaks down. In this peculiar geometry of B and for a certain range of the mean-free-path, the sheath is found to be composed of two charged layers: the positive one, close to the walls, and the negative one, towards the plasma and before the neutral pre-sheath. Depending on the amplitude of B, the spatial variation of the electric potential can be non-monotonic and presents a maximum within the sheath region. More generally, the sheath extent as well as the potential drop within the sheath and the pre-sheath is studied with respect to B, the mean-free-path, and the ion and electron temperatures.

Analysis of the Yule-Nielsen effect with the multiple-path point spread function in a frequency-modulated halftone.

PubMed

Rogers, Geoffrey

2018-06-01

The Yule-Nielsen effect is an influence on halftone color caused by the diffusion of light within the paper upon which the halftone ink is printed. The diffusion can be characterized by a point spread function. In this paper, a point spread function for paper is derived using the multiple-path model of reflection. This model treats the interaction of light with turbid media as a random walk. Using the multiple-path point spread function, a general expression is derived for the average reflectance of light from a frequency-modulated halftone, in which dot size is constant and the number of dots is varied, with the arrangement of dots random. It is also shown that the line spread function derived from the multiple-path model has the form of a Lorentzian function.

A Theoretical Study of Bulk and Surface Diffusion Processes for Semiconductor Materials Using First Principles Calculations

NASA Astrophysics Data System (ADS)

Roehl, Jason L.

Diffusion of point defects on crystalline surfaces and in their bulk is an important and ubiquitous phenomenon affecting film quality, electronic properties and device functionality. A complete understanding of these diffusion processes enables one to predict and then control those processes. Such understanding includes knowledge of the structural, energetic and electronic properties of these native and non-native point defect diffusion processes. Direct experimental observation of the phenomenon is difficult and microscopic theories of diffusion mechanisms and pathways abound. Thus, knowing the nature of diffusion processes, of specific point defects in given materials, has been a challenging task for analytical theory as well as experiment. The recent advances in computing technology have been a catalyst for the rise of a third mode of investigation. The advent of tremendous computing power, breakthroughs in algorithmic development in computational applications of electronic density functional theory now enables direct computation of the diffusion process. This thesis demonstrates such a method applied to several different examples of point defect diffusion on the (001) surface of gallium arsenide (GaAs) and the bulk of cadmium telluride (CdTe) and cadmium sulfide (CdS). All results presented in this work are ab initio, total-energy pseudopotential calculations within the local density approximation to density-functional theory. Single particle wavefunctions were expanded in a plane-wave basis and reciprocal space k-point sampling was achieved by Monkhorst-Pack generated k-point grids. Both surface and bulk computations employed a supercell approach using periodic boundary conditions. Ga adatom adsorption and diffusion processes were studied on two reconstructions of the GaAs(001) surface including the c(4x4) and c(4x4)-heterodimer surface reconstructions. On the GaAs(001)- c(4x4) surface reconstruction, two distinct sets of minima and transition sites were discovered for a Ga adatom relaxing from heights of 3 and 0.5 A from the surface. These two sets show significant differences in the interaction of the Ga adatom with surface As dimers and an electronic signature of the differences in this interaction was identified. The energetic barriers to diffusion were computed between various adsorption sites. Diffusion profiles for native Cd and S, adatom and vacancy, and non-native interstitial adatoms of Te, Cu and Cl were investigated in bulk wurtzite CdS. The interstitial diffusion paths considered in this work were chosen parallel to c-axis as it represents the path encountered by defects diffusing from the CdTe layer. Because of the lattice mismatch between zinc-blende CdTe and hexagonal wurtzite CdS, the c-axis in CdS is normal to the CdTe interface. The global minimum and maximum energy positions in the bulk unit cell vary for different diffusing species. This results in a significant variation, in the bonding configurations and associated strain energies of different extrema positions along the diffusion paths for various defects. The diffusion barriers range from a low of 0.42 eV for an S interstitial to a high of 2.18 eV for a S vacancy. The computed 0.66 eV barrier for a Cu interstitial is in good agreement with experimental values in the range of 0.58 - 0.96 eV reported in the literature. There exists an electronic signature in the local density of states for the s- and d-states of the Cu interstitial at the global maximum and global minimum energy position. The work presented in this thesis is an investigation into diffusion processes for semiconductor bulk and surfaces. The work provides information about these processes at a level of control unavailable experimentally giving an elaborate description into physical and electronic properties associated with diffusion at its most basic level. Not only does this work provide information about GaAs, CdTe and CdS, it is intended to contribute to a foundation of knowledge that can be extended to other systems to expand our overall understanding into the diffusion process. (Abstract shortened by UMI.)

Atomization and dense-fluid breakup regimes in liquid rocket engines

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

Oefelein, Joseph; Dahms, Rainer Norbert Uwe

Until recently, modern theory has lacked a fundamentally based model to predict the operating pressures where classical sprays transition to dense-fluid mixing with diminished surface tension. In this paper, such a model is presented to quantify this transition for liquid-oxygen–hydrogen and n-decane–gaseous-oxygen injection processes. The analysis reveals that respective molecular interfaces break down not necessarily because of vanishing surface tension forces but instead because of the combination of broadened interfaces and a reduction in mean free molecular path. When this occurs, the interfacial structure itself enters the continuum regime, where transport processes rather than intermolecular forces dominate. Using this model,more » regime diagrams for the respective systems are constructed that show the range of operating pressures and temperatures where this transition occurs. The analysis also reveals the conditions where classical spray dynamics persists even at high supercritical pressures. As a result, it demonstrates that, depending on the composition and temperature of the injected fluids, the injection process can exhibit either classical spray atomization, dense-fluid diffusion-dominated mixing, or supercritical mixing phenomena at chamber pressures encountered in state-of-the-art liquid rocket engines.« less

Atomization and dense-fluid breakup regimes in liquid rocket engines

DOE PAGES

Oefelein, Joseph; Dahms, Rainer Norbert Uwe

2015-04-20

Until recently, modern theory has lacked a fundamentally based model to predict the operating pressures where classical sprays transition to dense-fluid mixing with diminished surface tension. In this paper, such a model is presented to quantify this transition for liquid-oxygen–hydrogen and n-decane–gaseous-oxygen injection processes. The analysis reveals that respective molecular interfaces break down not necessarily because of vanishing surface tension forces but instead because of the combination of broadened interfaces and a reduction in mean free molecular path. When this occurs, the interfacial structure itself enters the continuum regime, where transport processes rather than intermolecular forces dominate. Using this model,more » regime diagrams for the respective systems are constructed that show the range of operating pressures and temperatures where this transition occurs. The analysis also reveals the conditions where classical spray dynamics persists even at high supercritical pressures. As a result, it demonstrates that, depending on the composition and temperature of the injected fluids, the injection process can exhibit either classical spray atomization, dense-fluid diffusion-dominated mixing, or supercritical mixing phenomena at chamber pressures encountered in state-of-the-art liquid rocket engines.« less

Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam.

PubMed

Rydzewski, J; Nowak, W

2016-04-12

In this work we propose an application of a nonlinear dimensionality reduction method to represent the high-dimensional configuration space of the ligand-protein dissociation process in a manner facilitating interpretation. Rugged ligand expulsion paths are mapped into 2-dimensional space. The mapping retains the main structural changes occurring during the dissociation. The topological similarity of the reduced paths may be easily studied using the Fréchet distances, and we show that this measure facilitates machine learning classification of the diffusion pathways. Further, low-dimensional configuration space allows for identification of residues active in transport during the ligand diffusion from a protein. The utility of this approach is illustrated by examination of the configuration space of cytochrome P450cam involved in expulsing camphor by means of enhanced all-atom molecular dynamics simulations. The expulsion trajectories are sampled and constructed on-the-fly during molecular dynamics simulations using the recently developed memetic algorithms [ Rydzewski, J.; Nowak, W. J. Chem. Phys. 2015 , 143 ( 12 ), 124101 ]. We show that the memetic algorithms are effective for enforcing the ligand diffusion and cavity exploration in the P450cam-camphor complex. Furthermore, we demonstrate that machine learning techniques are helpful in inspecting ligand diffusion landscapes and provide useful tools to examine structural changes accompanying rare events.

Network of Porosity Formed in Ultrafine-Grained Copper Produced by Equal Channel Angular Pressing

NASA Astrophysics Data System (ADS)

Ribbe, Jens; Baither, Dietmar; Schmitz, Guido; Divinski, Sergiy V.

2009-04-01

Radiotracer experiments on diffusion of Ni63 and Rb86 in severely deformed commercially pure copper (8 passes of equal channel angular pressing) reveal unambiguously the existence of ultrafast transport paths. A fraction of these paths remains in the material even after complete recrystallization. Scanning electron microscopy and focused ion beam techniques are applied. Deep grooves are found which are related to original high-energy interfaces. In-depth sectioning near corresponding triple junctions reveals clearly multiple microvoids or microcracks caused by the severe deformation. Long-range tracer penetration over tens of micrometers proves that these submicrometer-large defects are connected by highly diffusive paths and that they appear with significant frequency.

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.

Diffusive and martensitic nucleation kinetics in solid-solid transitions of colloidal crystals

NASA Astrophysics Data System (ADS)

Peng, Yi; Li, Wei; Wang, Feng; Still, Tim; Yodh, Arjun G.; Han, Yilong

2017-05-01

Solid-solid transitions between crystals follow diffusive nucleation, or various diffusionless transitions, but these kinetics are difficult to predict and observe. Here we observed the rich kinetics of transitions from square lattices to triangular lattices in tunable colloidal thin films with single-particle dynamics by video microscopy. Applying a small pressure gradient in defect-free regions or near dislocations markedly transform the diffusive nucleation with an intermediate-stage liquid into a martensitic generation and oscillation of dislocation pairs followed by a diffusive nucleus growth. This transformation is neither purely diffusive nor purely martensitic as conventionally assumed but a combination thereof, and thus presents new challenges to both theory and the empirical criterion of martensitic transformations. We studied how pressure, density, grain boundary, triple junction and interface coherency affect the nucleus growth, shape and kinetic pathways. These novel microscopic kinetics cast new light on control solid-solid transitions and microstructural evolutions in polycrystals.

Diffusive and martensitic nucleation kinetics in solid-solid transitions of colloidal crystals

PubMed Central

Peng, Yi; Li, Wei; Wang, Feng; Still, Tim; Yodh, Arjun G.; Han, Yilong

2017-01-01

Solid–solid transitions between crystals follow diffusive nucleation, or various diffusionless transitions, but these kinetics are difficult to predict and observe. Here we observed the rich kinetics of transitions from square lattices to triangular lattices in tunable colloidal thin films with single-particle dynamics by video microscopy. Applying a small pressure gradient in defect-free regions or near dislocations markedly transform the diffusive nucleation with an intermediate-stage liquid into a martensitic generation and oscillation of dislocation pairs followed by a diffusive nucleus growth. This transformation is neither purely diffusive nor purely martensitic as conventionally assumed but a combination thereof, and thus presents new challenges to both theory and the empirical criterion of martensitic transformations. We studied how pressure, density, grain boundary, triple junction and interface coherency affect the nucleus growth, shape and kinetic pathways. These novel microscopic kinetics cast new light on control solid–solid transitions and microstructural evolutions in polycrystals. PMID:28504246

Graphene-based battery electrodes having continuous flow paths

DOEpatents

Zhang, Jiguang; Xiao, Jie; Liu, Jun; Xu, Wu; Li, Xiaolin; Wang, Deyu

2014-05-24

Some batteries can exhibit greatly improved performance by utilizing electrodes having randomly arranged graphene nanosheets forming a network of channels defining continuous flow paths through the electrode. The network of channels can provide a diffusion pathway for the liquid electrolyte and/or for reactant gases. Metal-air batteries can benefit from such electrodes. In particular Li-air batteries show extremely high capacities, wherein the network of channels allow oxygen to diffuse through the electrode and mesopores in the electrode can store discharge products.

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

PubMed Central

Liu, Lei; Cao, Zanxia

2013-01-01

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

Effects of amyloid and small vessel disease on white matter network disruption.

PubMed

Kim, Hee Jin; Im, Kiho; Kwon, Hunki; Lee, Jong Min; Ye, Byoung Seok; Kim, Yeo Jin; Cho, Hanna; Choe, Yearn Seong; Lee, Kyung Han; Kim, Sung Tae; Kim, Jae Seung; Lee, Jae Hong; Na, Duk L; Seo, Sang Won

2015-01-01

There is growing evidence that the human brain is a large scale complex network. The structural network is reported to be disrupted in cognitively impaired patients. However, there have been few studies evaluating the effects of amyloid and small vessel disease (SVD) markers, the common causes of cognitive impairment, on structural networks. Thus, we evaluated the association between amyloid and SVD burdens and structural networks using diffusion tensor imaging (DTI). Furthermore, we determined if network parameters predict cognitive impairments. Graph theoretical analysis was applied to DTI data from 232 cognitively impaired patients with varying degrees of amyloid and SVD burdens. All patients underwent Pittsburgh compound-B (PiB) PET to detect amyloid burden, MRI to detect markers of SVD, including the volume of white matter hyperintensities and the number of lacunes, and detailed neuropsychological testing. The whole-brain network was assessed by network parameters of integration (shortest path length, global efficiency) and segregation (clustering coefficient, transitivity, modularity). PiB retention ratio was not associated with any white matter network parameters. Greater white matter hyperintensity volumes or lacunae numbers were significantly associated with decreased network integration (increased shortest path length, decreased global efficiency) and increased network segregation (increased clustering coefficient, increased transitivity, increased modularity). Decreased network integration or increased network segregation were associated with poor performances in attention, language, visuospatial, memory, and frontal-executive functions. Our results suggest that SVD alters white matter network integration and segregation, which further predicts cognitive dysfunction.

Diffusion reordering kinetics in lattice-gas systems: Time evolution of configurational entropy and internal energy

NASA Astrophysics Data System (ADS)

Weinketz, Sieghard

1998-07-01

The reordering kinetics of a diffusion lattice-gas system of adsorbates with nearest- and next-nearest-neighbor interactions on a square lattice is studied within a dynamic Monte Carlo simulation, as it evolves towards the equilibrium from a given initial configuration, at a constant temperature. The diffusion kinetics proceeds through adsorbate hoppings to empty nearest-neighboring sites (Kawasaki dynamics). The Monte Carlo procedure allows a ``real'' time definition from the local transition rates, and the configurational entropy and internal energy can be obtained from the lattice configuration at any instant t by counting the local clusters and using the C2 approximation of the cluster variation method. These state functions are then used in their nonequilibrium form as a direct measure of reordering along the time. Different reordering processes are analyzed within this approach, presenting a rich variety of behaviors. It can also be shown that the time derivative of entropy (times temperature) is always equal to or lower than the time derivative of energy, and that the reordering path is always strongly dependent on the initial order, presenting in some cases an ``invariance'' of the entropy function to the magnitude of the interactions as far as the final order is unaltered.

Diffusing Supply Chain Innovations at Hewlett-Packard Company: Applications of Performance Technology.

ERIC Educational Resources Information Center

Cargille, Brian; Branvold, Dwight

2000-01-01

Explains how Hewlett-Packard creates supply chain management innovations and effectively diffuses new technologies. Outlines how performance technologists help accelerate the diffusion and adoption of innovations by modifying innovations, define the client adoption path, create resources to lead clients through adoption, and improve the diffusion…

Mechanisms of decoherence in electron microscopy.

PubMed

Howie, A

2011-06-01

The understanding and where possible the minimisation of decoherence mechanisms in electron microscopy were first studied in plasmon loss, diffraction contrast images but are of even more acute relevance in high resolution TEM phase contrast imaging and electron holography. With the development of phase retrieval techniques they merit further attention particularly when their effect cannot be eliminated by currently available energy filters. The roles of electronic excitation, thermal diffuse scattering, transition radiation and bremsstrahlung are examined here not only in the specimen but also in the electron optical column. Terahertz-range aloof beam electronic excitation appears to account satisfactorily for recent observations of decoherence in electron holography. An apparent low frequency divergence can emerge for the calculated classical bremsstrahlung event probability but can be ignored for photon wavelengths exceeding the required coherence distance or path lengths in the equipment. Most bremsstrahlung event probabilities are negligibly important except possibly in large-angle bending magnets or mandolin systems. A more reliable procedure for subtracting thermal diffuse scattering from diffraction pattern intensities is proposed. Copyright © 2010 Elsevier B.V. All rights reserved.

Cultural Diffusion Was the Main Driving Mechanism of the Neolithic Transition in Southern Africa

PubMed Central

Jerardino, Antonieta; Fort, Joaquim; Isern, Neus; Rondelli, Bernardo

2014-01-01

It is well known that the Neolithic transition spread across Europe at a speed of about 1 km/yr. This result has been previously interpreted as a range expansion of the Neolithic driven mainly by demic diffusion (whereas cultural diffusion played a secondary role). However, a long-standing problem is whether this value (1 km/yr) and its interpretation (mainly demic diffusion) are characteristic only of Europe or universal (i.e. intrinsic features of Neolithic transitions all over the world). So far Neolithic spread rates outside Europe have been barely measured, and Neolithic spread rates substantially faster than 1 km/yr have not been previously reported. Here we show that the transition from hunting and gathering into herding in southern Africa spread at a rate of about 2.4 km/yr, i.e. about twice faster than the European Neolithic transition. Thus the value 1 km/yr is not a universal feature of Neolithic transitions in the world. Resorting to a recent demic-cultural wave-of-advance model, we also find that the main mechanism at work in the southern African Neolithic spread was cultural diffusion (whereas demic diffusion played a secondary role). This is in sharp contrast to the European Neolithic. Our results further suggest that Neolithic spread rates could be mainly driven by cultural diffusion in cases where the final state of this transition is herding/pastoralism (such as in southern Africa) rather than farming and stockbreeding (as in Europe). PMID:25517968

Diffusion of a particle in the spatially correlated exponential random energy landscape: Transition from normal to anomalous diffusion.

PubMed

Novikov, S V

2018-01-14

Diffusive transport of a particle in a spatially correlated random energy landscape having exponential density of states has been considered. We exactly calculate the diffusivity in the nondispersive quasi-equilibrium transport regime for the 1D transport model and found that for slow decaying correlation functions the diffusivity becomes singular at some particular temperature higher than the temperature of the transition to the true non-equilibrium dispersive transport regime. It means that the diffusion becomes anomalous and does not follow the usual ∝ t 1/2 law. In such situation, the fully developed non-equilibrium regime emerges in two stages: first, at some temperature there is the transition from the normal to anomalous diffusion, and then at lower temperature the average velocity for the infinite medium goes to zero, thus indicating the development of the true dispersive regime. Validity of the Einstein relation is discussed for the situation where the diffusivity does exist. We provide also some arguments in favor of conservation of the major features of the new transition scenario in higher dimensions.

Effective optical path length for tandem diffuse cubic cavities as gas absorption cell

NASA Astrophysics Data System (ADS)

Yu, J.; Gao, Q.; Zhang, Y. G.; Zhang, Z. G.; Wu, S. H.

2014-12-01

Tandem diffuse cubic cavities designed by connecting two single diffuse cubic-shaped cavities, A and B, with an aperture (port fraction fap) in the middle of the connecting baffle was developed as a gas absorption cell. The effective optical path length (EOPL) was evaluated by comparing the oxygen absorption signal in the cavity and in air based on tunable diode laser absorption spectroscopy (TDLAS). Experimental results manifested an enhancement of EOPL for the tandem diffuse cubic cavities as the decrease of fap and can be expressed as the sum of EOPL of two single cubic cavities at fap < 0.01, which coincided well with theoretical analysis. The simulating EOPL was smaller than experimental results at fap > 0.01, which indicated that back scattering light from cavity B to cavity A cannot be ignored at this condition.

Molecular dynamics and quasidynamics simulations of the annealing of bulk and near-surface interstitials formed in molecular-beam epitaxial Si due to low-energy particle bombardment during deposition

NASA Technical Reports Server (NTRS)

Kitabatake, M.; Fons, P.; Greene, J. E.

1991-01-01

The relaxation, diffusion, and annihilation of split and hexagonal interstitials resulting from 10 eV Si irradiation of (2x1)-terminated Si(100) are investigated. Molecular dynamics and quasidynamics simulations, utilizing the Tersoff many-body potential are used in the investigation. The interstitials are created in layers two through six, and stable atomic configurations and total potential energies are derived as a function of site symmetry and layer depth. The interstitial Si atoms are allowed to diffuse, and the total potential energy changes are calculated. Lattice configurations along each path, as well as the starting configurations, are relaxed, and minimum energy diffusion paths are derived. The results show that the minimum energy paths are toward the surface and generally involved tetrahedral sites. The calculated interstitial migration activation energies are always less than 1.4 eV and are much lower in the near-surface region than in the bulk.

Defect-Tolerant Diffusion Channels for Mg 2+ Ions in Ribbon-Type Borates: Structural Insights into Potential Battery Cathodes MgVBO 4 and Mg x Fe 2–xB 2O 5

DOE PAGES

Bo, Shou-Hang; Grey, Clare P.; Khalifah, Peter G.

2015-06-10

The reversible room temperature intercalation of Mg 2+ ions is difficult to achieve, but may offer substantial advantages in the design of next-generation batteries if this electrochemical process can be successfully realized. Two types of quadruple ribbon-type transition metal borates (Mg xFe 2-xB 2O 5 and MgVBO 4) with high theoretical capacities (186 mAh/g and 360 mAh/g) have been synthesized and structurally characterized through the combined Rietveld refinement of synchrotron and time-of-flight neutron diffraction data. Neither MgVBO 4 nor Mg xFe 2-xB 2O 5 can be chemically oxidized at room temperature, though Mg can be dynamically removed from themore » latter phase at elevated temperatures (approximately 200 - 500 °C). Findings show that Mg diffusion in the Mg xFe 2-xB 2O 5 structure is more facile for the inner two octahedral sites than for the two outer octahedral sites in the ribbons, a result supported by both the refined site occupancies after Mg removal and by bond valence sum difference map calculations of diffusion paths in the pristine material. Mg diffusion in this pyroborate Mg xFe 2-xB 2O 5 framework is also found to be tolerant to the presence of Mg/Fe disorder since Mg ions can diffuse through interstitial channels which bypass Fe-containing sites.« less

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

PubMed Central

2013-01-01

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

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

NASA Technical Reports Server (NTRS)

2011-01-01

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

California PATH : 1997 annual report

DOT National Transportation Integrated Search

1997-01-01

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

California PATH : 1996 annual report

DOT National Transportation Integrated Search

1996-01-01

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

Particle model for nonlocal heat transport in fusion plasmas.

PubMed

Bufferand, H; Ciraolo, G; Ghendrih, Ph; Lepri, S; Livi, R

2013-02-01

We present a simple stochastic, one-dimensional model for heat transfer in weakly collisional media as fusion plasmas. Energies of plasma particles are treated as lattice random variables interacting with a rate inversely proportional to their energy schematizing a screened Coulomb interaction. We consider both the equilibrium (microcanonical) and nonequilibrium case in which the system is in contact with heat baths at different temperatures. The model exhibits a characteristic length of thermalization that can be associated with an interaction mean free path and one observes a transition from ballistic to diffusive regime depending on the average energy of the system. A mean-field expression for heat flux is deduced from system heat transport properties. Finally, it is shown that the nonequilibrium steady state is characterized by long-range correlations.

The diffusion of ions in unconsolidated sediments

USGS Publications Warehouse

Manheim, F.T.

1970-01-01

Diffusion in unconsolidated sediments generally proceeds at rates ranging from half to one twentieth of those applying to diffusion of ions and molecules in free solution. Diffusion rates are predictable with respect to porosity and path tortuosity in host sediments, and can be conveniently measured by determinations of electrical resistivity on bulk sediment samples. Net ion flux is further influenced by reactions of diffusing species with enclosing sediments, but such influences should not be confused with or lumped with diffusion processes. ?? 1970.

Nonequilibrium Phase Transitions in Supercooled Water

NASA Astrophysics Data System (ADS)

Limmer, David; Chandler, David

2012-02-01

We present results of a simulation study of water driven out of equilibrium. Using transition path sampling, we can probe stationary path distributions parameterize by order parameters that are extensive in space and time. We find that by coupling external fields to these parameters, we can drive water through a first order dynamical phase transition into amorphous ice. By varying the initial equilibrium distributions we can probe pathways for the creation of amorphous ices of low and high densities.

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.

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

PubMed

Bressloff, Paul C

2015-01-01

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

Predictor laws for pictorial flight displays

NASA Technical Reports Server (NTRS)

Grunwald, A. J.

1985-01-01

Two predictor laws are formulated and analyzed: (1) a circular path law based on constant accelerations perpendicular to the path and (2) a predictor law based on state transition matrix computations. It is shown that for both methods the predictor provides the essential lead zeros for the path-following task. However, in contrast to the circular path law, the state transition matrix law furnishes the system with additional zeros that entirely cancel out the higher-frequency poles of the vehicle dynamics. On the other hand, the circular path law yields a zero steady-state error in following a curved trajectory with a constant radius. A combined predictor law is suggested that utilizes the advantages of both methods. A simple analysis shows that the optimal prediction time mainly depends on the level of precision required in the path-following task, and guidelines for determining the optimal prediction time are given.

Monte Carlo Transport for Electron Thermal Transport

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Moses, Gregory

2015-11-01

The iSNB (implicit Schurtz Nicolai Busquet multigroup electron thermal transport method of Cao et al. is adapted into a Monte Carlo transport method in order to better model the effects of non-local behavior. The end goal is a hybrid transport-diffusion method that combines Monte Carlo Transport with a discrete diffusion Monte Carlo (DDMC). The hybrid method will combine the efficiency of a diffusion method in short mean free path regions with the accuracy of a transport method in long mean free path regions. The Monte Carlo nature of the approach allows the algorithm to be massively parallelized. Work to date on the method will be presented. This work was supported by Sandia National Laboratory - Albuquerque and the University of Rochester Laboratory for Laser Energetics.

Turbine exhaust diffuser flow path with region of reduced total flow area

DOEpatents

Orosa, John A.

2012-12-25

An exhaust diffuser system and method for a turbine engine includes an inner boundary and an outer boundary with a flow path defined therebetween. The inner boundary is defined at least in part by a hub that has an upstream end and a downstream end. The outer boundary has a region in which the outer boundary extends radially inward toward the hub. The region can begin at a point that is substantially aligned with the downstream end of the hub or, alternatively, at a point that is proximately upstream of the downstream end of the hub. The region directs at least a portion of an exhaust flow in the diffuser toward the hub. As a result, the exhaust diffuser system and method can achieve the performance of a long hub system while enjoying the costs of a short hub system.

Improved transition path sampling methods for simulation of rare events

NASA Astrophysics Data System (ADS)

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

2008-04-01

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

Phase Transition in Opinion Diffusion in Social Networks

DTIC Science & Technology

2012-05-01

the opinions of social agents diffuse in a network under a so-called hard-interaction model, in which the agents inter- act more strongly with...gent behavior. Index Terms— opinion diffusion , opinion dynamics, social net- works, phase transition, herding. 1. INTRODUCTION The study of the

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

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

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

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

NASA Astrophysics Data System (ADS)

Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher

2014-01-01

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

Turbine system

DOEpatents

McMahan, Kevin Weston; Dillard, Daniel Jackson

2016-05-03

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

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

PubMed

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

2018-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Unified path integral approach to theories of diffusion-influenced reactions

NASA Astrophysics Data System (ADS)

Prüstel, Thorsten; Meier-Schellersheim, Martin

2017-08-01

Building on mathematical similarities between quantum mechanics and theories of diffusion-influenced reactions, we develop a general approach for computational modeling of diffusion-influenced reactions that is capable of capturing not only the classical Smoluchowski picture but also alternative theories, as is here exemplified by a volume reactivity model. In particular, we prove the path decomposition expansion of various Green's functions describing the irreversible and reversible reaction of an isolated pair of molecules. To this end, we exploit a connection between boundary value and interaction potential problems with δ - and δ'-function perturbation. We employ a known path-integral-based summation of a perturbation series to derive a number of exact identities relating propagators and survival probabilities satisfying different boundary conditions in a unified and systematic manner. Furthermore, we show how the path decomposition expansion represents the propagator as a product of three factors in the Laplace domain that correspond to quantities figuring prominently in stochastic spatially resolved simulation algorithms. This analysis will thus be useful for the interpretation of current and the design of future algorithms. Finally, we discuss the relation between the general approach and the theory of Brownian functionals and calculate the mean residence time for the case of irreversible and reversible reactions.

A path-integral approach to the problem of time

NASA Astrophysics Data System (ADS)

Amaral, M. M.; Bojowald, Martin

2018-01-01

Quantum transition amplitudes are formulated for model systems with local internal time, using intuition from path integrals. The amplitudes are shown to be more regular near a turning point of internal time than could be expected based on existing canonical treatments. In particular, a successful transition through a turning point is provided in the model systems, together with a new definition of such a transition in general terms. Some of the results rely on a fruitful relation between the problem of time and general Gribov problems.

A satellite observation test bed for cloud parameterization development

NASA Astrophysics Data System (ADS)

Lebsock, M. D.; Suselj, K.

2015-12-01

We present an observational test-bed of cloud and precipitation properties derived from CloudSat, CALIPSO, and the the A-Train. The focus of the test-bed is on marine boundary layer clouds including stratocumulus and cumulus and the transition between these cloud regimes. Test-bed properties include the cloud cover and three dimensional cloud fraction along with the cloud water path and precipitation water content, and associated radiative fluxes. We also include the subgrid scale distribution of cloud and precipitation, and radiaitive quantities, which must be diagnosed by a model parameterization. The test-bed further includes meterological variables from the Modern Era Retrospective-analysis for Research and Applications (MERRA). MERRA variables provide the initialization and forcing datasets to run a parameterization in Single Column Model (SCM) mode. We show comparisons of an Eddy-Diffusivity/Mass-FLux (EDMF) parameterization coupled to micorphsycis and macrophysics packages run in SCM mode with observed clouds. Comparsions are performed regionally in areas of climatological subsidence as well stratified by dynamical and thermodynamical variables. Comparisons demonstrate the ability of the EDMF model to capture the observed transitions between subtropical stratocumulus and cumulus cloud regimes.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States

NASA Astrophysics Data System (ADS)

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M.

2018-03-01

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

PubMed

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M

2018-03-23

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

SIEST-A-RT: a study of vacancy diffusion in crystalline silicon using a local-basis first-principle (SIESTA) activation technique (ART).

NASA Astrophysics Data System (ADS)

El Mellouhi, Fedwa; Mousseau, Normand; Ordejón, Pablo

2003-03-01

We report on a first-principle study of vacancy-induced self-diffusion in crystalline silicon. Our simulations are performed on supercells containing 63 and 215 atoms. We generate the diffusion paths using the activation-relaxation technique (ART) [1], which can sample efficiently the energy landscape of complex systems. The forces and energy are evaluated using SIESTA [2], a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible numerical linear combination of atomic orbitals basis set. Combining these two methods allows us to identify diffusion paths that would not be reachable with this degree of accuracy, using other methods. After a full relaxation of the neutral vacancy, we proceed to search for local diffusion paths. We identify various mechanisms like the formation of the four fold coordinated defect, and the recombination of dangling bonds by WWW process. The diffusion of the vacancy proceeds by hops to first nearest neighbor with an energy barrier of 0.69 eV. This work is funded in part by NSERC and NATEQ. NM is a Cottrell Scholar of the Research Corporation. [1] G. T. Barkema and N. Mousseau, Event-based relaxation of continuous disordered systems, Phys. Rev. Lett. 77, 4358 (1996); N. Mousseau and G. T. Barkema, Traveling through potential energy landscapes of disordered materials: ART, Phys. Rev. E 57, 2419 (1998). [2] Density functional method for very large systems with LCAO basis sets D. Sánchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quant. Chem. 65, 453 (1997).

Evolution of Edge Pedestal Profiles Over the L-H Transition

NASA Astrophysics Data System (ADS)

Sayer, M. S.; Stacey, W. M.; Floyd, J. P.; Groebner, R. J.

2012-10-01

The detailed time evolution of thermal diffusivities, electromagnetic forces, pressure gradients, particle pinch and momentum transport frequencies (which determine the diffusion coefficient) have been analyzed during the L-H transition in a DIII-D discharge. Density, temperature, rotation velocity and electric field profiles at times just before and after the L-H transition are analyzed in terms of these quantities. The analysis is based on the fluid particle balance, energy balance, force balance and heat conduction equations, as in Ref. [1], but with much greater time resolution and with account for thermal ion orbit loss. The variation of diffusive and non-diffusive transport over the L-H transition is determined from the variation in the radial force balance (radial electric field, VxB force, and pressure gradient) and the variation in the interpreted diffusive transport coefficients. 6pt [1] W.M. Stacey and R.J. Groebner, Phys. Plasmas 17, 112512 (2010).

Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition.

PubMed

Molchanov, Stanislav; Faizullin, Dzhigangir A; Nesmelova, Irina V

2016-10-06

Translational diffusion is the most fundamental form of transport in chemical and biological systems. The diffusion coefficient is highly sensitive to changes in the size of the diffusing species; hence, it provides important information on the variety of macromolecular processes, such as self-assembly or folding-unfolding. Here, we investigate the behavior of the diffusion coefficient of a macromolecule in the vicinity of heat-induced transition from folded to unfolded state. We derive the equation that describes the diffusion coefficient of the macromolecule in the vicinity of the transition and use it to fit the experimental data from pulsed-field-gradient nuclear magnetic resonance (PFG NMR) experiments acquired for two globular proteins, lysozyme and RNase A, undergoing temperature-induced unfolding. A very good qualitative agreement between the theoretically derived diffusion coefficient and experimental data is observed.

Thermal Evolution of Diapirs with Complex Mantle Wedge Flow

NASA Astrophysics Data System (ADS)

Sylvia, R. T.; Kincaid, C.

2016-12-01

Subduction of oceanic lithosphere drives heat and mass exchange between Earth's interior and surface. One proposed transport mechanism for thermally and chemically distinct material through the wedge is the diapir model. The dominant driver of flow in the upper mantle is a mode of forced convection responding to motion of a tabular slab. A set of 4D laboratory experiments was conducted exploring the relationship between buoyancy flux and subduction parameters and subsequent effects on diapir transport. Variable subduction styles tested include downdip and rollback motion, slab gaps, slab steepening and backarc extension. The mantle is modeled using viscous glucose syrup with an Arrhenius type temperature dependent viscosity. Diapirs representing homogeneous mechanically mixed melange layer are introduced as buoyant fluid injected at multiple point sources situated along the surface of the sinking slab. Laboratory data is collected using high definition time-lapse photography and quantified using image velocimetry techniques. Here we present results from numerical simulation of the thermal evolution of spherical mantle wedge diapirs using 2D axisymmetric advection-diffusion model with internal diapir flow described by an analytic potential flow solution. A suite of wedge temperature profiles are used as thermal forcing on diapirs traversing the wedge along experimentally observed 4D ascent pathways. Scaling arguments suggest that for systems with Péclet number on the order of 15 advective heat transport is expected to dominate over diffusive heat transport, but the range of observed P-T-t paths and vigorous internal flow complicate this assumption. Interactions between modes of free (diapiric) and forced (wedge) convection lead to complex spatio-temporal variability in slab-to-arc connectivity patterns. Rollback induced toroidal flow, along trench changes in dip, convergence rate and backarc extension all produce a significant ( 500 km) trench-parallel transport component. Combined with diapir-diapir interactions these factors produce a spectrum of transit times and pathlengths, ranging from much shorter to much longer than those from simple 2D model estimates. Results highlight the broad range of expected internal temperature distributions derived from variable transit paths.

Method for applying a diffusion barrier interlayer for high temperature components

DOEpatents

Wei, Ronghua; Cheruvu, Narayana S.

2016-03-08

A coated substrate and a method of forming a diffusion barrier coating system between a substrate and a MCrAl coating, including a diffusion barrier coating deposited onto at least a portion of a substrate surface, wherein the diffusion barrier coating comprises a nitride, oxide or carbide of one or more transition metals and/or metalloids and a MCrAl coating, wherein M includes a transition metal or a metalloid, deposited on at least a portion of the diffusion barrier coating, wherein the diffusion barrier coating restricts the inward diffusion of aluminum of the MCrAl coating into the substrate.

Longitudinal distribution of ozone and chlorine in the human respiratory tract: simulation of nasal and oral breathing with the single-path diffusion model.

PubMed

Bush, M L; Zhang, W; Ben-Jebria, A; Ultman, J S

2001-06-15

In the single-path model of the respiratory system, gas transport occurs within a conduit of progressively increasing cross-sectional and surface areas by a combination of flow, longitudinal dispersion, and lateral absorption. The purpose of this study was to use bolus inhalation data previously obtained for chlorine (Cl(2)) and for ozone (O(3)) to test the predictive capability of the single-path model and to adjust input parameters for applying the model to other exposure conditions. The data, consisting of uptake fraction as a function of bolus penetration volume, were recorded on 10 healthy nonsmokers breathing orally as well as nasally at alternative air flows of 150, 250, and 1000 ml/s. By employing published data for airway anatomy, gas-phase dispersion coefficients, and gas-phase mass transfer coefficients while neglecting diffusion limitations in the mucus phase, the single-path model was capable of predicting the uptake distribution for O(3) but not the steeper distribution that was observed for Cl(2). To simultaneously explain the data for these two gases, it was necessary to increase gas-phase mass transfer coefficients and to include a finite diffusion resistance of O(3) within the mucous layer. The O(3) reaction rate constants that accounted for this diffusion resistance, 2 x 10(6) s(-1) in the mouth and 8 x 10(6) s(-1) in the nose and lower airways, were much greater than previously reported reactivities of individual substrates found in mucus. Copyright 2001 Academic Press.

Characteristics of transitional and turbulent jet diffusion flames in microgravity

NASA Technical Reports Server (NTRS)

Bahadori, Yousef M.; Small, James F., Jr.; Hegde, Uday G.; Zhou, Liming; Stocker, Dennis P.

1995-01-01

This paper presents the ground-based results obtained to date in preparation of a proposed space experiment to study the role of large-scale structures in microgravity transitional and turbulent gas-jet diffusion flames by investigating the dynamics of vortex/flame interactions and their influence on flame characteristics. The overall objective is to gain an understanding of the fundamental characteristics of transitional and turbulent gas-jet diffusion flames. Understanding of the role of large-scale structures on the characteristics of microgravity transitional and turbulent flames will ultimately lead to improved understanding of normal-gravity turbulent combustion.

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

PubMed

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

2016-09-07

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

ICF target 2D modeling using Monte Carlo SNB electron thermal transport in DRACO

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Moses, Gregory

2016-10-01

The iSNB (implicit Schurtz Nicolai Busquet multigroup diffusion electron thermal transport method is adapted into a Monte Carlo (MC) transport method to better model angular and long mean free path non-local effects. The MC model was first implemented in the 1D LILAC code to verify consistency with the iSNB model. Implementation of the MC SNB model in the 2D DRACO code enables higher fidelity non-local thermal transport modeling in 2D implosions such as polar drive experiments on NIF. The final step is to optimize the MC model by hybridizing it with a MC version of the iSNB diffusion method. The hybrid method will combine the efficiency of a diffusion method in intermediate mean free path regions with the accuracy of a transport method in long mean free path regions allowing for improved computational efficiency while maintaining accuracy. Work to date on the method will be presented. This work was supported by Sandia National Laboratories and the Univ. of Rochester Laboratory for Laser Energetics.

Formation of Anionic C, N-bearing Chains in the Interstellar Medium via Reactions of H- with HC x N for Odd-valued x from 1 to 7

NASA Astrophysics Data System (ADS)

Gianturco, F. A.; Satta, M.; Yurtsever, E.; Wester, R.

2017-11-01

We investigate the relative efficiencies of low-temperature chemical reactions in the interstellar medium with H- anion reacting in the gas phase with cyanopolyyne neutral molecules, leading to the formation of anionic {{{C}}}x{{{N}}}- linear chains of different lengths and of H2. All the reactions turn out to be without barriers, highly exothermic reactions that provide a chemical route to the formation of anionic chains of the same length. Some of the anions have been observed in the dark molecular clouds and in the diffuse interstellar envelopes. Quantum calculations are carried out for the corresponding reactive potential energy surfaces for all the odd-numbered members of the series (x = 1, 3, 5, 7). We employ the minimum energy paths to obtain the relevant transition state configurations and use the latter within the variational transition state model to obtain the chemical rates. The present results indicate that at typical temperatures around 100 K, a set of significantly larger rate values exists for x = 3 and x = 5, while the rate values are smaller for CN- and {{{C}}}7{{{N}}}-. At those temperatures, however, all the rates turn out to be larger than the estimates in the current literature for the radiative electron attachment (REA) rates, thus indicating the greater importance of the present chemical path with respect to REA processes at those temperatures. The physical reasons for our findings are discussed in detail and linked with the existing observational findings.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

PubMed

Pool, René; Bolhuis, Peter G

2007-06-28

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

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

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

Wiebe, David J.

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

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

PubMed Central

Zhao, Shuo; Huang, Jie; Shan, Xinghua

2017-01-01

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

Mnemonic discrimination relates to perforant path integrity: An ultra-high resolution diffusion tensor imaging study.

PubMed

Bennett, Ilana J; Stark, Craig E L

2016-03-01

Pattern separation describes the orthogonalization of similar inputs into unique, non-overlapping representations. This computational process is thought to serve memory by reducing interference and to be mediated by the dentate gyrus of the hippocampus. Using ultra-high in-plane resolution diffusion tensor imaging (hrDTI) in older adults, we previously demonstrated that integrity of the perforant path, which provides input to the dentate gyrus from entorhinal cortex, was associated with mnemonic discrimination, a behavioral outcome designed to load on pattern separation. The current hrDTI study assessed the specificity of this perforant path integrity-mnemonic discrimination relationship relative to other cognitive constructs (identified using a factor analysis) and white matter tracts (hippocampal cingulum, fornix, corpus callosum) in 112 healthy adults (20-87 years). Results revealed age-related declines in integrity of the perforant path and other medial temporal lobe (MTL) tracts (hippocampal cingulum, fornix). Controlling for global effects of brain aging, perforant path integrity related only to the factor that captured mnemonic discrimination performance. Comparable integrity-mnemonic discrimination relationships were also observed for the hippocampal cingulum and fornix. Thus, whereas perforant path integrity specifically relates to mnemonic discrimination, mnemonic discrimination may be mediated by a broader MTL network. Copyright © 2015 Elsevier Inc. All rights reserved.

Computational characterization of lightweight multilayer MXene Li-ion battery anodes

NASA Astrophysics Data System (ADS)

Ashton, Michael; Hennig, Richard G.; Sinnott, Susan B.

2016-01-01

MXenes, a class of two-dimensional transition metal carbides and nitrides, have shown promise experimentally and computationally for use in energy storage applications. In particular, the most lightweight members of the monolayer MXene family (M = Sc, Ti, V, or Cr) are predicted to have gravimetric capacities above 400 mAh/g, higher than graphite. Additionally, intercalation of ions into multilayer MXenes can be accomplished at low voltages, and low diffusion barriers exist for Li diffusing across monolayer MXenes. However, large discrepancies have been observed between the calculated and experimental reversible capacities of MXenes. Here, dispersion-corrected density functional theory calculations are employed to predict reversible capacities and other battery-related properties for six of the most promising members of the MXene family (O-functionalized Ti- and V-based carbide MXenes) as bilayer structures. The calculated reversible capacities of the V2CO2 and Ti2CO2 bilayers agree more closely with experiment than do previous calculations for monolayers. Additionally, the minimum energy paths and corresponding energy barriers along the in-plane [1000] and [0100] directions for Li travelling between neighboring MXene layers are determined. V4C3O2 exhibits the lowest diffusion barrier of the compositions considered, at 0.42 eV, but its reversible capacity (148 mAh/g) is dragged down by its heavy formula unit. Conversely, the V2CO2 MXene shows good reversible capacity (276 mAh/g), but a high diffusion barrier (0.82 eV). We show that the diffusion barriers of all bilayer structures are significantly higher than those calculated for the corresponding monolayers, advocating the use of dispersed monolayer MXenes instead of multilayers in high performance anodes.

Contrasting Diffusion Patterns for PC and Mobile Videos: A User-Centric View of the Influencing Factors

ERIC Educational Resources Information Center

Wu, Baixue

2010-01-01

As both computer and mobile phone reach nearly ubiquity in the U.S. market, the slow uptake of mobile video, in contrast to the thriving usage of PC-based video, warrants a deeper understanding of user-oriented factors contributing to the two diffusion paths. Unlike the majority of existing diffusion research practices, the dissertation…

Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

PubMed

Cendagorta, Joseph R; Powers, Anna; Hele, Timothy J H; Marsalek, Ondrej; Bačić, Zlatko; Tuckerman, Mark E

2016-11-30

Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H 2 and D 2 diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H 2 and D 2 as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H 2 and D 2 diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are strongly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as a result the quantum rate is greater than the classical rate.

Changes in diffusion path length with old age in diffuse optical tomography

NASA Astrophysics Data System (ADS)

Bonnéry, Clément; Leclerc, Paul-Olivier; Desjardins, Michèle; Hoge, Rick; Bherer, Louis; Pouliot, Philippe; Lesage, Frédéric

2012-05-01

Diffuse, optical near infrared imaging is increasingly being used in various neurocognitive contexts where changes in optical signals are interpreted through activation maps. Statistical population comparison of different age or clinical groups rely on the relative homogeneous distribution of measurements across subjects in order to infer changes in brain function. In the context of an increasing use of diffuse optical imaging with older adult populations, changes in tissue properties and anatomy with age adds additional confounds. Few studies investigated these changes with age. Duncan et al. measured the so-called diffusion path length factor (DPF) in a large population but did not explore beyond the age of 51 after which physiological and anatomical changes are expected to occur [Pediatr. Res. 39(5), 889-894 (1996)]. With increasing interest in studying the geriatric population with optical imaging, we studied changes in tissue properties in young and old subjects using both magnetic resonance imaging (MRI)-guided Monte-Carlo simulations and time-domain diffuse optical imaging. Our results, measured in the frontal cortex, show changes in DPF that are smaller than previously measured by Duncan et al. in a younger population. The origin of these changes are studied using simulations and experimental measures.

Conservative Diffusions: a Constructive Approach to Nelson's Stochastic Mechanics.

NASA Astrophysics Data System (ADS)

Carlen, Eric Anders

In Nelson's stochastic mechanics, quantum phenomena are described in terms of diffusions instead of wave functions; this thesis is a study of that description. We emphasize that we are concerned here with the possibility of describing, as opposed to explaining, quantum phenomena in terms of diffusions. In this direction, the following questions arise: "Do the diffusions of stochastic mechanics--which are formally given by stochastic differential equations with extremely singular coefficients--really exist?" Given that they exist, one can ask, "Do these diffusions have physically reasonable sample path behavior, and can we use information about sample paths to study the behavior of physical systems?" These are the questions we treat in this thesis. In Chapter I we review stochastic mechanics and diffusion theory, using the Guerra-Morato variational principle to establish the connection with the Schroedinger equation. This chapter is largely expository; however, there are some novel features and proofs. In Chapter II we settle the first of the questions raised above. Using PDE methods, we construct the diffusions of stochastic mechanics. Our result is sufficiently general to be of independent mathematical interest. In Chapter III we treat potential scattering in stochastic mechanics and discuss direct probabilistic methods of studying quantum scattering problems. Our results provide a solid "Yes" in answer to the second question raised above.

A diffusivity model for predicting VOC diffusion in porous building materials based on fractal theory.

PubMed

Liu, Yanfeng; Zhou, Xiaojun; Wang, Dengjia; Song, Cong; Liu, Jiaping

2015-12-15

Most building materials are porous media, and the internal diffusion coefficients of such materials have an important influences on the emission characteristics of volatile organic compounds (VOCs). The pore structure of porous building materials has a significant impact on the diffusion coefficient. However, the complex structural characteristics bring great difficulties to the model development. The existing prediction models of the diffusion coefficient are flawed and need to be improved. Using scanning electron microscope (SEM) observations and mercury intrusion porosimetry (MIP) tests of typical porous building materials, this study developed a new diffusivity model: the multistage series-connection fractal capillary-bundle (MSFC) model. The model considers the variable-diameter capillaries formed by macropores connected in series as the main mass transfer paths, and the diameter distribution of the capillary bundles obeys a fractal power law in the cross section. In addition, the tortuosity of the macrocapillary segments with different diameters is obtained by the fractal theory. Mesopores serve as the connections between the macrocapillary segments rather than as the main mass transfer paths. The theoretical results obtained using the MSFC model yielded a highly accurate prediction of the diffusion coefficients and were in a good agreement with the VOC concentration measurements in the environmental test chamber. Copyright © 2015 Elsevier B.V. All rights reserved.

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

ERIC Educational Resources Information Center

Furstenau, Sara

2005-01-01

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

Modeling Particle Acceleration and Transport at a 2-D CME-Driven Shock

NASA Astrophysics Data System (ADS)

Hu, Junxiang; Li, Gang; Ao, Xianzhi; Zank, Gary P.; Verkhoglyadova, Olga

2017-11-01

We extend our earlier Particle Acceleration and Transport in the Heliosphere (PATH) model to study particle acceleration and transport at a coronal mass ejection (CME)-driven shock. We model the propagation of a CME-driven shock in the ecliptic plane using the ZEUS-3D code from 20 solar radii to 2 AU. As in the previous PATH model, the initiation of the CME-driven shock is simplified and modeled as a disturbance at the inner boundary. Different from the earlier PATH model, the disturbance is now longitudinally dependent. Particles are accelerated at the 2-D shock via the diffusive shock acceleration mechanism. The acceleration depends on both the parallel and perpendicular diffusion coefficients κ|| and κ⊥ and is therefore shock-obliquity dependent. Following the procedure used in Li, Shalchi, et al. (k href="#jgra53857-bib-0045"/>), we obtain the particle injection energy, the maximum energy, and the accelerated particle spectra at the shock front. Once accelerated, particles diffuse and convect in the shock complex. The diffusion and convection of these particles are treated using a refined 2-D shell model in an approach similar to Zank et al. (k href="#jgra53857-bib-0089"/>). When particles escape from the shock, they propagate along and across the interplanetary magnetic field. The propagation is modeled using a focused transport equation with the addition of perpendicular diffusion. We solve the transport equation using a backward stochastic differential equation method where adiabatic cooling, focusing, pitch angle scattering, and cross-field diffusion effects are all included. Time intensity profiles and instantaneous particle spectra as well as particle pitch angle distributions are shown for two example CME shocks.

Liquid-liquid phase transition and anomalous diffusion in simulated liquid GeO 2

NASA Astrophysics Data System (ADS)

Hoang, Vo Van; Anh, Nguyen Huynh Tuan; Zung, Hoang

2007-03-01

We perform molecular dynamics (MD) simulation of diffusion in liquid GeO 2 at the temperatures ranged from 3000 to 5000 K and densities ranged from 3.65 to 7.90 g/cm 3. Simulations were done in a model containing 3000 particles with the new interatomic potentials for liquid and amorphous GeO 2, which have weak Coulomb interaction and Morse-type short-range interaction. We found a liquid-liquid phase transition in simulated liquid GeO 2 from a tetrahedral to an octahedral network structure upon compression. Moreover, such phase transition accompanied with an anomalous diffusion of particles in liquid GeO 2 that the diffusion constant of both Ge and O particles strongly increases with increasing density (e.g. with increasing pressure) and it shows a maximum at the density around 4.95 g/cm 3. The possible relation between anomalous diffusion of particles and structural phase transition in the system has been discussed.

Effects of spin transition on diffusion of Fe2+ in ferropericlase in Earth's lower mantle

NASA Astrophysics Data System (ADS)

Saha, Saumitra; Bengtson, Amelia; Crispin, Katherine L.; van Orman, James A.; Morgan, Dane

2011-11-01

Knowledge of Fe composition in lower-mantle minerals (primarily perovskite and ferropericlase) is essential to a complete understanding of the Earth's interior. Fe cation diffusion potentially controls many aspects of the distribution of Fe in the Earth's lower mantle, including mixing of chemical heterogeneities, element partitioning, and the extent of core-mantle communications. Fe in ferropericlase has been shown to undergo a spin transition starting at about 40 GPa and exists in a mixture of high-spin and low-spin states over a wide range of pressures. Present experimental data on Fe transport in ferropericlase is limited to pressures below 35 GPa and provides little information on the pressure dependence of the activation volume and none on the impact of the spin transition on diffusion. Therefore, known experimental data on Fe diffusion cannot be reliably extrapolated to predict diffusion throughout the lower mantle. Here, first-principles and statistical modeling are combined to predict diffusion of Fe in ferropericlase over the entire lower mantle, including the effects of the Fe spin transition. A thorough statistical thermodynamic treatment is given to fully incorporate the coexistence of high- and low-spin Fe in the model of overall Fe diffusion in the lower mantle. Pure low-spin Fe diffuses approximately 104 times slower than high-spin Fe in ferropericlase but Fe diffusion of the mixed-spin state is only about 10 times slower than that of high-spin Fe. The predicted Fe diffusivities demonstrate that ferropericlase is unlikely to be rate limiting in transporting Fe in deep earth since much slower Fe diffusion in perovskite is predicted.

Retention and diffusion of H, He, O, C impurities in Be

NASA Astrophysics Data System (ADS)

Zhang, Pengbo; Zhao, Jijun; Wen, Bin

2012-04-01

We report the energetics and diffusion behavior of H, He, O, and C impurities in beryllium as fusion materials from first-principles calculations. Among the six interstitial sites in Be, the basal tetrahedral one is most stable for H, He, O, while C prefers to occupy an octahedral site. Solution of O impurity in Be is an exothermic process with solution energy of -2.37 eV, whereas solution of H, C and He is an endothermic process (solution energy: 1.55 eV, 2.46 eV, and 5.70 eV, respectively). Overall speaking, these impurities prefer to diffuse along longer paths. The H and O impurities share the same out-of-plane diffusion path via basal tetrahedral sites, while the He and C impurities in Be mainly diffuse via basal tetrahedral and octahedral sites along the (0 0 1) plane. Diffusion of He in Be is easiest with a lowest barrier of 0.14 eV; whereas H diffusion in Be is also rather fast with migration energies of 0.4 eV. On the contrary, diffusion of C and O impurities is more difficult because of strong bonding with lattice atoms and high energy barriers of 0.42 and 1.63 eV, respectively. Our theoretical results provide the fundamental parameters for understanding the impurity aggregation and bubble formation in early stage of irradiation damage.

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

PubMed Central

Ovchinnikov, Victor; Karplus, Martin

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

Ovchinnikov, Victor; Karplus, Martin

2014-05-01

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

What sets the minimum tokamak scrape-off layer width?

NASA Astrophysics Data System (ADS)

Joseph, Ilon

2016-10-01

The heat flux width of the tokamak scrape-off layer is on the order of the poloidal ion gyroradius, but the ``heuristic drift'' physics model is still not completely understood. In the absence of anomalous transport, neoclassical transport sets the minimum width. For plateau collisionality, the ion temperature width is set by qρi , while the electron temperature width scales as the geometric mean q(ρeρi) 1 / 2 and is close to qρi in magnitude. The width is enhanced because electrons are confined by the sheath potential and have a much longer time to radially diffuse before escaping to the wall. In the Pfirsch-Schluter regime, collisional diffusion increases the width by the factor (qR / λ) 1 / 2 where qR is the connection length and λ is the mean free path. This qualitatively agrees with the observed transition in the scaling law for detached plasmas. The radial width of the SOL electric field is determined by Spitzer parallel and ``neoclassical'' radial electric conductivity and has a similar scaling to that for thermal transport. Prepared under US DOE contract DE-AC52-07NA27344.

Liquid jet breakup regimes at supercritical pressures

DOE PAGES

Oefelein, Joseph C.; Dahms, Rainer Norbert Uwe

2015-07-23

Previously, a theory has been presented that explains how discrete vapor–liquid interfaces become diminished at certain high-pressure conditions in a manner that leads to well known qualitative trends observed from imaging in a variety of experiments. Rather than surface tension forces, transport processes can dominate over relevant ranges of conditions. In this paper, this framework is now generalized to treat a wide range of fuel-oxidizer combinations in a manner consistent with theories of capillary flows and extended corresponding states theory. Different flow conditions and species-specific molecular properties are shown to produce distinct variations of interfacial structures and local free molecularmore » paths. These variations are shown to occur over the operating ranges in a variety of propulsion and power systems. Despite these variations, the generalized analysis reveals that the envelope of flow conditions at which the transition from classical sprays to diffusion-dominated mixing occurs exhibits a characteristic shape for all liquid–gas combinations. As a result, for alkane-oxidizer mixtures, it explains that these conditions shift to higher pressure flow conditions with increasing carbon number and demonstrates that, instead of widely assumed classical spray atomization, diffusion-dominated mixing may occur under relevant high-pressure conditions in many modern devices.« less

Diffusive shock acceleration - Acceleration rate, magnetic-field direction and the diffusion limit

NASA Technical Reports Server (NTRS)

Jokipii, J. R.

1992-01-01

This paper reviews the concept of diffusive shock acceleration, showing that the acceleration of charged particles at a collisionless shock is a straightforward consequence of the standard cosmic-ray transport equation, provided that one treats the discontinuity at the shock correctly. This is true for arbitrary direction of the upstream magnetic field. Within this framework, it is shown that acceleration at perpendicular or quasi-perpendicular shocks is generally much faster than for parallel shocks. Paradoxically, it follows also that, for a simple scattering law, the acceleration is faster for less scattering or larger mean free path. Obviously, the mean free path can not become too large or the diffusion limit becomes inapplicable. Gradient and curvature drifts caused by the magnetic-field change at the shock play a major role in the acceleration process in most cases. Recent observations of the charge state of the anomalous component are shown to require the faster acceleration at the quasi-perpendicular solar-wind termination shock.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

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

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

Wiebe, David J.

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

Flow field investigation in a bulb turbine diffuser

NASA Astrophysics Data System (ADS)

Pereira, M.; Duquesne, P.; Aeschlimann, V.; Deschênes, C.

2017-04-01

An important drop in turbine performances has been measured in a bulb turbine model operated at overload. Previous investigations have correlated the performance drop with diffuser losses, and particularly to the flow separation zone at the diffuser wall. The flow has been investigated in the transition part of the diffuser using two LDV measurement sections. The transition part is a diffuser section that transforms from a circular to a rectangular section. The two measurement sections are at the inlet and outlet of the diffuser transition part. The turbine has been operated at three operating points, which are representative of different flow patterns at the diffuser exit at overload. In addition to the average velocity field, the analysis is conducted based on a backflow occurrence function and on the swirl level. Results reveal a counter-rotating zone in the diffuser, which intensifies with the guide vanes opening. The guide vanes opening induces a modification of the flow phenomena: from a central backflow recirculation zone at the lowest flowrate to a backflow zone induced by flow separation at the wall at the highest flowrate.

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.

Dynamics and diffusion mechanism of low-density liquid silicon

DOE PAGES

Shen, B.; Wang, Z. Y.; Dong, F.; ...

2015-11-05

A first-order phase transition from a high-density liquid to a low-density liquid has been proposed to explain the various thermodynamic anomies of water. It also has been proposed that such liquid–liquid phase transition would exist in supercooled silicon. Computer simulation studies show that, across the transition, the diffusivity drops roughly 2 orders of magnitude, and the structures exhibit considerable tetrahedral ordering. The resulting phase is a highly viscous, low-density liquid silicon. Investigations on the atomic diffusion of such a novel form of liquid silicon are of high interest. Here we report such diffusion results from molecular dynamics simulations using themore » classical Stillinger–Weber (SW) potential of silicon. We show that the atomic diffusion of the low-density liquid is highly correlated with local tetrahedral geometries. We also show that atoms diffuse through hopping processes within short ranges, which gradually accumulate to an overall random motion for long ranges as in normal liquids. There is a close relationship between dynamical heterogeneity and hopping process. We point out that the above diffusion mechanism is closely related to the strong directional bonding nature of the distorted tetrahedral network. Here, our work offers new insights into the complex behavior of the highly viscous low density liquid silicon, suggesting similar diffusion behaviors in other tetrahedral coordinated liquids that exhibit liquid–liquid phase transition such as carbon and germanium.« less

Optimal resource diffusion for suppressing disease spreading in multiplex networks

NASA Astrophysics Data System (ADS)

Chen, Xiaolong; Wang, Wei; Cai, Shimin; Stanley, H. Eugene; Braunstein, Lidia A.

2018-05-01

Resource diffusion is a ubiquitous phenomenon, but how it impacts epidemic spreading has received little study. We propose a model that couples epidemic spreading and resource diffusion in multiplex networks. The spread of disease in a physical contact layer and the recovery of the infected nodes are both strongly dependent upon resources supplied by their counterparts in the social layer. The generation and diffusion of resources in the social layer are in turn strongly dependent upon the state of the nodes in the physical contact layer. Resources diffuse preferentially or randomly in this model. To quantify the degree of preferential diffusion, a bias parameter that controls the resource diffusion is proposed. We conduct extensive simulations and find that the preferential resource diffusion can change phase transition type of the fraction of infected nodes. When the degree of interlayer correlation is below a critical value, increasing the bias parameter changes the phase transition from double continuous to single continuous. When the degree of interlayer correlation is above a critical value, the phase transition changes from multiple continuous to first discontinuous and then to hybrid. We find hysteresis loops in the phase transition. We also find that there is an optimal resource strategy at each fixed degree of interlayer correlation under which the threshold reaches a maximum and the disease can be maximally suppressed. In addition, the optimal controlling parameter increases as the degree of inter-layer correlation increases.

Transition density of one-dimensional diffusion with discontinuous drift

NASA Technical Reports Server (NTRS)

Zhang, Weijian

1990-01-01

The transition density of a one-dimensional diffusion process with a discontinuous drift coefficient is studied. A probabilistic representation of the transition density is given, illustrating the close connections between discontinuities of the drift and Brownian local times. In addition, some explicit results are obtained based on the trivariate density of Brownian motion, its occupation, and local times.

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

PubMed

Preto, Jordane; Clementi, Cecilia

2014-09-28

The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-directed Molecular Dynamics (extended DM-d-MD) used to enhance the sampling of MD trajectories in such a way as to rapidly cover all important regions of the free energy landscape including deep metastable states and critical transition paths. Moreover, extended DM-d-MD was combined with a reweighting scheme enabling to save on-the-fly information about the Boltzmann distribution. Our algorithm was successfully applied to two systems, alanine dipeptide and alanine-12. Due to the enhanced sampling, the Boltzmann distribution is recovered much faster than in plain MD simulations. For alanine dipeptide, we report a speedup of one order of magnitude with respect to plain MD simulations. For alanine-12, our algorithm allows us to highlight all important unfolded basins in several days of computation when one single misfolded event is barely observable within the same amount of computational time by plain MD simulations. Our method is reaction coordinate free, shows little dependence on the a priori knowledge of the system, and can be implemented in such a way that the biased steps are not computationally expensive with respect to MD simulations thus making our approach well adapted for larger complex systems from which little information is known.

A theoretical model of grain boundary self-diffusion in metals with phase transitions (case study into titanium and zirconium)

NASA Astrophysics Data System (ADS)

Semenycheva, Alexandra V.; Chuvil'deev, Vladimir N.; Nokhrin, Aleksey V.

2018-05-01

The paper offers a model describing the process of grain boundary self-diffusion in metals with phase transitions in the solid state. The model is based on ideas and approaches found in the theory of non-equilibrium grain boundaries. The range of application of basic relations contained in this theory is shown to expand, as they can be used to calculate the parameters of grain boundary self-diffusion in high-temperature and low-temperature phases of metals with a phase transition. The model constructed is used to calculate grain boundary self-diffusion activation energy in titanium and zirconium and an explanation is provided as to their abnormally low values in the low-temperature phase. The values of grain boundary self-diffusion activation energy are in good agreement with the experiment.

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.

Clustering and optimal arrangement of enzymes in reaction-diffusion systems.

PubMed

Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

2013-05-17

Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.

Systematic derivation of reaction-diffusion equations with distributed delays and relations to fractional reaction-diffusion equations and hyperbolic transport equations: application to the theory of Neolithic transition.

PubMed

Vlad, Marcel Ovidiu; Ross, John

2002-12-01

We introduce a general method for the systematic derivation of nonlinear reaction-diffusion equations with distributed delays. We study the interactions among different types of moving individuals (atoms, molecules, quasiparticles, biological organisms, etc). The motion of each species is described by the continuous time random walk theory, analyzed in the literature for transport problems, whereas the interactions among the species are described by a set of transformation rates, which are nonlinear functions of the local concentrations of the different types of individuals. We use the time interval between two jumps (the transition time) as an additional state variable and obtain a set of evolution equations, which are local in time. In order to make a connection with the transport models used in the literature, we make transformations which eliminate the transition time and derive a set of nonlocal equations which are nonlinear generalizations of the so-called generalized master equations. The method leads under different specified conditions to various types of nonlocal transport equations including a nonlinear generalization of fractional diffusion equations, hyperbolic reaction-diffusion equations, and delay-differential reaction-diffusion equations. Thus in the analysis of a given problem we can fit to the data the type of reaction-diffusion equation and the corresponding physical and kinetic parameters. The method is illustrated, as a test case, by the study of the neolithic transition. We introduce a set of assumptions which makes it possible to describe the transition from hunting and gathering to agriculture economics by a differential delay reaction-diffusion equation for the population density. We derive a delay evolution equation for the rate of advance of agriculture, which illustrates an application of our analysis.

Construction of nanostructures for selective lithium ion conduction using self-assembled molecular arrays in supramolecular solids

NASA Astrophysics Data System (ADS)

Moriya, Makoto

2017-12-01

In the development of innovative molecule-based materials, the identification of the structural features in supramolecular solids and the understanding of the correlation between structure and function are important factors. The author investigated the development of supramolecular solid electrolytes by constructing ion conduction paths using a supramolecular hierarchical structure in molecular crystals because the ion conduction path is an attractive key structure due to its ability to generate solid-state ion diffusivity. The obtained molecular crystals exhibited selective lithium ion diffusion via conduction paths consisting of lithium bis(trifluoromethanesulfonyl)amide (LiTFSA) and small molecules such as ether or amine compounds. In the present review, the correlation between the crystal structure and ion conductivity of the obtained molecular crystals is addressed based on the systematic structural control of the ionic conduction paths through the modification of the component molecules. The relationship between the crystal structure and ion conductivity of the molecular crystals provides a guideline for the development of solid electrolytes based on supramolecular solids exhibiting rapid and selective lithium ion conduction.

Diffusing-wave spectroscopy in a standard dynamic light scattering setup

NASA Astrophysics Data System (ADS)

Fahimi, Zahra; Aangenendt, Frank J.; Voudouris, Panayiotis; Mattsson, Johan; Wyss, Hans M.

2017-12-01

Diffusing-wave spectroscopy (DWS) extends dynamic light scattering measurements to samples with strong multiple scattering. DWS treats the transport of photons through turbid samples as a diffusion process, thereby making it possible to extract the dynamics of scatterers from measured correlation functions. The analysis of DWS data requires knowledge of the path length distribution of photons traveling through the sample. While for flat sample cells this path length distribution can be readily calculated and expressed in analytical form; no such expression is available for cylindrical sample cells. DWS measurements have therefore typically relied on dedicated setups that use flat sample cells. Here we show how DWS measurements, in particular DWS-based microrheology measurements, can be performed in standard dynamic light scattering setups that use cylindrical sample cells. To do so we perform simple random-walk simulations that yield numerical predictions of the path length distribution as a function of both the transport mean free path and the detection angle. This information is used in experiments to extract the mean-square displacement of tracer particles in the material, as well as the corresponding frequency-dependent viscoelastic response. An important advantage of our approach is that by performing measurements at different detection angles, the average path length through the sample can be varied. For measurements performed on a single sample cell, this gives access to a wider range of length and time scales than obtained in a conventional DWS setup. Such angle-dependent measurements also offer an important consistency check, as for all detection angles the DWS analysis should yield the same tracer dynamics, even though the respective path length distributions are very different. We validate our approach by performing measurements both on aqueous suspensions of tracer particles and on solidlike gelatin samples, for which we find our DWS-based microrheology data to be in good agreement with rheological measurements performed on the same samples.

Thermal diffusivity of electrical insulators at high temperatures: Evidence for diffusion of bulk phonon-polaritons at infrared frequencies augmenting phonon heat conduction

NASA Astrophysics Data System (ADS)

Hofmeister, Anne M.; Dong, Jianjun; Branlund, Joy M.

2014-04-01

We show that laser-flash analysis measurements of the temperature (T) dependence of thermal diffusivity (D) for diverse non-metallic (e.g., silicates) single-crystals is consistently represented by D(T) = FT-G + HT above 298 K, with G ranging from 0.3 to 2, depending on structure, and H being ˜10-4 K-1 for 51 single-crystals, 3 polycrystals, and two glasses unaffected by disorder or reconstructive phase transitions. Materials exhibiting this behavior include complex silicates with variable amounts of cation disorder, perovskite structured materials, and graphite. The high-temperature term HT becomes important by ˜1300 K, above which temperature its contribution to D(T) exceeds that of the FT-G term. The combination of the FT-G and HT terms produces the nearly temperature independent high-temperature region of D previously interpreted as the minimal phonon mean free path being limited by the finite interatomic spacing. Based on the simplicity of the fit and large number of materials it represents, this finding has repercussions for high-temperature models of heat transport. One explanation is that the two terms describing D(T) are associated with two distinct microscopic mechanisms; here, we explore the possibility that the thermal diffusivity of an electrical insulator could include both a contribution of lattice phonons (the FT-G term) and a contribution of diffusive bulk phonon-polaritons (BPP) at infrared (IR) frequencies (the HT term). The proposed BPP diffusion exists over length scales smaller than the laboratory sample sizes, and transfers mixed light and vibrational energy at a speed significantly smaller than the speed of light. Our diffusive IR-BPP hypothesis is consistent with other experimental observations such as polarization behavior, dependence of D on the number of IR peaks, and H = 0 for Ge and Si, which lack IR fundamentals. A simple quasi-particle thermal diffusion model is presented to begin understanding the contribution from bulk phonon-polaritons to overall heat conduction.

3He Diffusion MRI of the Lung

PubMed Central

Conradi, Mark S.; Yablonskiy, Dmitriy A.; Woods, Jason C.; Gierada, David S.; Jacob, Richard E.; Chang, Yulin V.; Choong, Cliff K.; Sukstanskii, Alex L.; Tanoli, Tariq; Lefrak, Stephen S.; Cooper, Joel D.

2007-01-01

Rationale and Objectives MR imaging of the restricted diffusion of laser-polarized 3He gas provides unique insights into the changes in lung microstructure in emphysema. Results We discuss measurements of ventilation (spin density), mean diffusivity, and the anisotropy of diffusion, which yields the mean acinar airway radius. In addition, the use of spatially modulated longitudinal magnetization allows diffusion to be measured over longer distances and times, with sensitivity to collateral ventilation paths. Early results are also presented for spin density and diffusivity maps made with a perfluorinated inert gas, C3F8. Methods Techniques for purging and imaging excised lungs are discussed. PMID:16253852

A study of interdiffusion in beta + gamma/gamma + gamma prime Ni-Cr-Al. M.S. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Carol, L. A.

1985-01-01

Ternary diffusion in the NiCrAl system at 1200 C was studied with beta + gamma/gamma + gamma prime infinite diffusion couples. Interdiffusion resulted in the formation of complex, multiphase diffusion zones. Concentration/distance profiles for Cr and Al in the phases present in the diffusion zone were measured after 200 hr. The Ni-rich portion of the NiCrAl phase diagram (1200 C) was also determined. From these data, bulk Cr and Al profiles were calculated and translated to diffusion paths on the ternary isotherm. Growth layer kinetics of the layers present in the diffusion zone were also measured.

Numerical Test of Analytical Theories for Perpendicular Diffusion in Small Kubo Number Turbulence

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

Heusen, M.; Shalchi, A., E-mail: husseinm@myumanitoba.ca, E-mail: andreasm4@yahoo.com

In the literature, one can find various analytical theories for perpendicular diffusion of energetic particles interacting with magnetic turbulence. Besides quasi-linear theory, there are different versions of the nonlinear guiding center (NLGC) theory and the unified nonlinear transport (UNLT) theory. For turbulence with high Kubo numbers, such as two-dimensional turbulence or noisy reduced magnetohydrodynamic turbulence, the aforementioned nonlinear theories provide similar results. For slab and small Kubo number turbulence, however, this is not the case. In the current paper, we compare different linear and nonlinear theories with each other and test-particle simulations for a noisy slab model corresponding to smallmore » Kubo number turbulence. We show that UNLT theory agrees very well with all performed test-particle simulations. In the limit of long parallel mean free paths, the perpendicular mean free path approaches asymptotically the quasi-linear limit as predicted by the UNLT theory. For short parallel mean free paths we find a Rechester and Rosenbluth type of scaling as predicted by UNLT theory as well. The original NLGC theory disagrees with all performed simulations regardless what the parallel mean free path is. The random ballistic interpretation of the NLGC theory agrees much better with the simulations, but compared to UNLT theory the agreement is inferior. We conclude that for this type of small Kubo number turbulence, only the latter theory allows for an accurate description of perpendicular diffusion.« less

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

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

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less

Feynman-Kac formula for stochastic hybrid systems.

PubMed

Bressloff, Paul C

2017-01-01

We derive a Feynman-Kac formula for functionals of a stochastic hybrid system evolving according to a piecewise deterministic Markov process. We first derive a stochastic Liouville equation for the moment generator of the stochastic functional, given a particular realization of the underlying discrete Markov process; the latter generates transitions between different dynamical equations for the continuous process. We then analyze the stochastic Liouville equation using methods recently developed for diffusion processes in randomly switching environments. In particular, we obtain dynamical equations for the moment generating function, averaged with respect to realizations of the discrete Markov process. The resulting Feynman-Kac formula takes the form of a differential Chapman-Kolmogorov equation. We illustrate the theory by calculating the occupation time for a one-dimensional velocity jump process on the infinite or semi-infinite real line. Finally, we present an alternative derivation of the Feynman-Kac formula based on a recent path-integral formulation of stochastic hybrid systems.

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

Wang, Yujie; Gong, Sha; Wang, Zhen

The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption ofmore » hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.« less

Competition among networks highlights the power of the weak

PubMed Central

Iranzo, Jaime; Buldú, Javier M.; Aguirre, Jacobo

2016-01-01

The unpreventable connections between real networked systems have recently called for an examination of percolation, diffusion or synchronization phenomena in multilayer networks. Here we use network science and game theory to explore interactions in networks-of-networks and model these as a game for gaining importance. We propose a viewpoint where networks choose the connection strategies, in contrast with classical approaches where nodes are the active players. Specifically, we investigate how creating paths between networks leads to different Nash equilibria that determine their structural and dynamical properties. In a wide variety of cases, selecting adequate connections leads to a cooperative solution that allows weak networks to overcome the strongest opponent. Counterintuitively, each weak network can induce a global transition to such cooperative configuration regardless of the actions of the strongest network. This power of the weak reveals a critical dominance of the underdogs in the fate of networks-of-networks. PMID:27841258

De novo design of a transmembrane Zn²⁺-transporting four-helix bundle.

PubMed

Joh, Nathan H; Wang, Tuo; Bhate, Manasi P; Acharya, Rudresh; Wu, Yibing; Grabe, Michael; Hong, Mei; Grigoryan, Gevorg; DeGrado, William F

2014-12-19

The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn(2+) and Co(2+), but not Ca(2+), across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn(2+) ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties. Copyright © 2014, American Association for the Advancement of Science.

Complex Diffusion Mechanisms for Li in Feldspar: Re-thinking Li-in-Plag Geospeedometry

NASA Astrophysics Data System (ADS)

Holycross, M.; Watson, E. B.

2017-12-01

In recent years, the lithium isotope system has been applied to model processes in a wide variety of terrestrial environments. In igneous settings, Li diffusion gradients have been frequently used to time heating episodes. Lithium partitioning behavior during decompression or cooling events drives Li transfer between phases, but the extent of Li exchange may be limited by its diffusion rate in geologic materials. Lithium is an exceptionally fast diffuser in silicate media, making it uniquely suited to record short-lived volcanic phenomena. The Li-in-plagioclase geospeedometer is often used to time explosive eruptions by applying laboratory-calibrated Li diffusion coefficients to model concentration profiles in magmatic feldspar samples. To quantify Li transport in natural scenarios, experimental measurements are needed that account for changing temperature and oxygen fugacity as well as different feldspar compositions and crystallographic orientation. Ambient pressure experiments were run at RPI to diffuse Li from a powdered spodumene source into polished sanidine, albite, oligoclase or anorthite crystals over the temperature range 500-950 ºC. The resulting 7Li concentration gradients developed in the mineral specimens were evaluated using laser ablation ICP-MS. The new data show that Li diffusion in all feldspar compositions simultaneously operates by both a "fast" and "slow" diffusion mechanism. Fast path diffusivities are similar to those found by Giletti and Shanahan [1997] for Li diffusion in plagioclase and are typically 10 to 20 times greater than slow path diffusivities. Lithium concentration gradients in the feldspar experiments plot in the shape of two superimposed error function curves with the slow diffusion regime in the near-surface of the crystal. Lithium diffusion is most sluggish in sanidine and is significantly faster in the plagioclase feldspars. It is still unclear what diffusion mechanism operates in nature, but the new measurements may impact how Li-in-plagioclase geospeedometry is used to time igneous processes. Giletti, B.J., and T.M. Shanahan (1997) Alkali diffusion in plagioclase feldspar, Chem. Geol., 139, 3-20

Sign phase transition in the problem of interfering directed paths

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Carbon Chemistry in Transitional Clouds from the GOT C+ Survey of CII 158 micron Emission in the Galactic Plane

NASA Astrophysics Data System (ADS)

Langer, W. D.; Velusamy, T.; Pineda, J.; Willacy, K.; Goldsmith, P. F.

2011-05-01

In understanding the lifecycle and chemistry of the interstellar gas, the transition from diffuse atomic to molecular gas clouds is a very important stage. The evolution of carbon from C+ to C0 and CO is a fundamental part of this transition, and C+ along with its carbon chemistry is a key diagnostic. Until now our knowledge of interstellar gas has been limited primarily to the diffuse atomic phase traced by HI and the dense molecular H2 phase traced by CO. However, we have generally been missing an important layer in diffuse and transition clouds, which is denoted by the warm "dark gas'', that is mostly H2 and little HI and CO, and is best traced with C+. Here, we discuss the chemistry in the transition from C+ to C0 and CO in these clouds as understood by a survey of the CII 1.9 THz (158 micron) line from a sparse survey of the inner galaxy over about 40 degrees in longitude as part of the Galactic Observations of Terahertz C+ (GOT C+) program, a Herschel Space Observatory Open Time Key Program to study interstellar clouds by sampling ionized carbon. Using the first results from GOT C+ along 11 LOSs, in a sample of 53 transition clouds, Velusamy, Langer et al. (A&A 521, L18, 2010) detected an excess of CII intensities indicative of a thick H2 layer (a significant warm H2, "dark gas'' component) around the 12CO core. Here we present a much larger, statistically significant sample of a few hundred diffuse and transition clouds traced by CII, along with auxiliary HI and CO data in the inner Galaxy between l=-30° and +30°. Our new and more extensive sample of transition clouds is used to elucidate the time dependent physical and carbon chemical evolution of diffuse to transition clouds, and transition layers. We consider the C+ to CO conversion pathways such as H++ O and C+ + H2 chemistry for CO production to constrain the physical parameters such as the FUV intensity and cosmic ray ionization rate that drive the CO chemistry in the diffuse transition clouds.

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

Sanz, Alejandro; Ezquerra, Tiberio A.; Nogales, Aurora, E-mail: aurora.nogales@csic.es

The dynamics of lower disorder-order temperature diblock copolymer leading to phase separation has been observed by X ray photon correlation spectroscopy. Two different modes have been characterized. A non-diffusive mode appears at temperatures below the disorder to order transition, which can be associated to compositional fluctuations, that becomes slower as the interaction parameter increases, in a similar way to the one observed for diblock copolymers exhibiting phase separation upon cooling. At temperatures above the disorder to order transition T{sub ODT}, the dynamics becomes diffusive, indicating that after phase separation in Lower Disorder-Order Transition (LDOT) diblock copolymers, the diffusion of chainmore » segments across the interface is the governing dynamics. As the segregation is stronger, the diffusive process becomes slower. Both observed modes have been predicted by the theory describing upper order-disorder transition systems, assuming incompressibility. However, the present results indicate that the existence of these two modes is more universal as they are present also in compressible diblock copolymers exhibiting a lower disorder-order transition. No such a theory describing the dynamics in LDOT block copolymers is available, and these experimental results may offer some hints to understanding the dynamics in these systems. The dynamics has also been studied in the ordered state, and for the present system, the non-diffusive mode disappears and only a diffusive mode is observed. This mode is related to the transport of segment in the interphase, due to the weak segregation on this system.« less

Serpentine Diffuser Performance with Emphasis on Future Introduction to a Transonic Fan (Postprint)

DTIC Science & Technology

2013-01-01

conditioning barrel . The velocity distribution across the flow conditioning barrel was measured at the same axial location of inlet temperature and...rakes at the same axial plane (AIP) of the total pressure probe tips. The probes were constructed from stainless steel tubing with 0.027 inch inside...numbers with 195 axial and circumferential static pressure measurements within the diffuser flow path. Pressure distortion at the diffuser discharge

Diffusive transport of energetic electrons in the solar corona: X-ray and radio diagnostics

NASA Astrophysics Data System (ADS)

Musset, S.; Kontar, E. P.; Vilmer, N.

2018-02-01

Context. Imaging spectroscopy in X-rays with RHESSI provides the possibility to investigate the spatial evolution of X-ray emitting electron distribution and therefore, to study transport effects on energetic electrons during solar flares. Aims: We study the energy dependence of the scattering mean free path of energetic electrons in the solar corona. Methods: We used imaging spectroscopy with RHESSI to study the evolution of energetic electrons distribution in various parts of the magnetic loop during the 2004 May 21 flare. We compared these observations with the radio observations of the gyrosynchrotron radiation of the same flare and with the predictions of a diffusive transport model. Results: X-ray analysis shows a trapping of energetic electrons in the corona and a spectral hardening of the energetic electron distribution between the top of the loop and the footpoints. Coronal trapping of electrons is stronger for radio-emitting electrons than for X-ray-emitting electrons. These observations can be explained by a diffusive transport model. Conclusions: We show that the combination of X-ray and radio diagnostics is a powerful tool to study electron transport in the solar corona in different energy domains. We show that the diffusive transport model can explain our observations, and in the range 25-500 keV, the scattering mean free path of electrons decreases with electron energy. We can estimate for the first time the scattering mean free path dependence on energy in the corona.

Disentangling the stochastic behavior of complex time series

NASA Astrophysics Data System (ADS)

Anvari, Mehrnaz; Tabar, M. Reza Rahimi; Peinke, Joachim; Lehnertz, Klaus

2016-10-01

Complex systems involving a large number of degrees of freedom, generally exhibit non-stationary dynamics, which can result in either continuous or discontinuous sample paths of the corresponding time series. The latter sample paths may be caused by discontinuous events - or jumps - with some distributed amplitudes, and disentangling effects caused by such jumps from effects caused by normal diffusion processes is a main problem for a detailed understanding of stochastic dynamics of complex systems. Here we introduce a non-parametric method to address this general problem. By means of a stochastic dynamical jump-diffusion modelling, we separate deterministic drift terms from different stochastic behaviors, namely diffusive and jumpy ones, and show that all of the unknown functions and coefficients of this modelling can be derived directly from measured time series. We demonstrate appli- cability of our method to empirical observations by a data-driven inference of the deterministic drift term and of the diffusive and jumpy behavior in brain dynamics from ten epilepsy patients. Particularly these different stochastic behaviors provide extra information that can be regarded valuable for diagnostic purposes.

The Role of Collateral Paths in Long-Range Diffusion of 3He in Lungs

PubMed Central

Conradi, Mark S.; Yablonskiy, Dmitriy A.; Woods, Jason C.; Gierada, David S.; Bartel, Seth-Emil T.; Haywood, Susan E.; Menard, Christopher

2008-01-01

Rationale and Objectives The hyperpolarized 3He long-range diffusion coefficient (LRDC) in lungs is sensitive to changes in lung structure due to emphysema, reflecting the increase in collateral paths resulting from tissue destruction. However, no clear understanding of LRDC in healthy lungs has emerged. Here we compare LRDC measured in healthy lungs with computer simulations of diffusion along the airway tree with no collateral connections. Materials and Methods Computer simulations of diffusion of spatially modulated spin magnetization were performed in computer generated, symmetric-branching models of lungs and compared with existing LRDC measurements in canine and human lungs. Results The simulations predict LRDC values of order 0.001 cm2/s, approximately 20 times smaller than the measured LRDC. We consider and rule out possible mechanisms for LRDC not included in the simulations: incomplete breath hold, cardiac motion, and passage of dissolved 3He through airway walls. However, a very low density of small (micron) holes in the airways is shown to account for the observed LRDC. Conclusion It is proposed that LRDC in healthy lungs is determined by small collateral pathways. PMID:18486004

Study of Diffusion Bonding of 45 Steel through the Compacted Nickel Powder Layer

NASA Astrophysics Data System (ADS)

Zeer, G. M.; Zelenkova, E. G.; Temnykh, V. I.; Tokmin, A. M.; Shubin, A. A.; Koroleva, Yu. P.; Mikheev, A. A.

2018-02-01

The microstructure of the transition zone and powder spacer, the concentration distribution of chemical elements over the width of the diffusion-bonded joint, and microhardness of 45 steel-compacted Ni powder spacer-45 steel layered composites formed by diffusion bonding have been investigated. It has been shown that the relative spacer thickness χ < 0.06 is optimal for obtaining a high-quality joint has been formed under a compacting pressure of 500 MPa. The solid-state diffusion bonding is accompanied by sintering the nickel powder spacer and the formation of the transition zone between the spacer and steel. The transition zone consists of solid solution of nickel in the α-Fe phase and ordered solid solution of iron in nickel (FeNi3).

Diffuse phase ferroelectric vs. Polomska transition in (1-x) BiFeO3-(x) Ba Zr0.025Ti0.975O3 (0.1 ≤ x ≤ 0.3) solid solutions

NASA Astrophysics Data System (ADS)

Jha, Pardeep K.; Jha, Priyanka A.; Singh, Vikash; Kumar, Pawan; Asokan, K.; Dwivedi, R. K.

2015-01-01

Investigations on the solid solutions (1-x) BiFeO3 - (x) Ba Zr0.025Ti0.975O3 (0.1 ≤ x ≤ 0.3) in the temperature range 300-750 K show colossal permittivity behavior and the occurrence of diffuse phase ferroelectric transition along with frequency dependent anomaly which disappears at temperature ˜450 K. For x = 0.3, these anomalies have been verified through differential scanning calorimetry and dielectric/impedance/conductivity measurements. The occurrence of peak in pyrocurrent (dPs/dT) vs. T plots also supports phase transition. With the increasing x, transition temperature decreases and diffusivity increases. This anomaly is absent at high frequencies (>100 kHz) in conductivity plots, indicating Polomska like surface phase transition, which is supported by modulus study.

Phase transition of traveling waves in bacterial colony pattern

NASA Astrophysics Data System (ADS)

Wakano, Joe Yuichiro; Komoto, Atsushi; Yamaguchi, Yukio

2004-05-01

Depending on the growth condition, bacterial colonies can exhibit different morphologies. Many previous studies have used reaction diffusion equations to reproduce spatial patterns. They have revealed that nonlinear reaction term can produce diverse patterns as well as nonlinear diffusion coefficient. Typical reaction term consists of nutrient consumption, bacterial reproduction, and sporulation. Among them, the functional form of sporulation rate has not been biologically investigated. Here we report experimentally measured sporulation rate. Then, based on the result, a reaction diffusion model is proposed. One-dimensional simulation showed the existence of traveling wave solution. We study the wave form as a function of the initial nutrient concentration and find two distinct types of solution. Moreover, transition between them is very sharp, which is analogous to phase transition. The velocity of traveling wave also shows sharp transition in nonlinear diffusion model, which is consistent with the previous experimental result. The phenomenon can be explained by separatrix in reaction term dynamics. Results of two-dimensional simulation are also shown and discussed.

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

NASA Technical Reports Server (NTRS)

Thomas, Randy; Stueber, Thomas J.

2013-01-01

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

Realization of a multipath ultrasonic gas flowmeter based on transit-time technique.

PubMed

Chen, Qiang; Li, Weihua; Wu, Jiangtao

2014-01-01

A microcomputer-based ultrasonic gas flowmeter with transit-time method is presented. Modules of the flowmeter are designed systematically, including the acoustic path arrangement, ultrasound emission and reception module, transit-time measurement module, the software and so on. Four 200 kHz transducers forming two acoustic paths are used to send and receive ultrasound simultaneously. The synchronization of the transducers can eliminate the influence caused by the inherent switch time in simple chord flowmeter. The distribution of the acoustic paths on the mechanical apparatus follows the Tailored integration, which could reduce the inherent error by 2-3% compared with the Gaussian integration commonly used in the ultrasonic flowmeter now. This work also develops timing modules to determine the flight time of the acoustic signal. The timing mechanism is different from the traditional method. The timing circuit here adopts high capability chip TDC-GP2, with the typical resolution of 50 ps. The software of Labview is used to receive data from the circuit and calculate the gas flow value. Finally, the two paths flowmeter has been calibrated and validated on the test facilities for air flow in Shaanxi Institute of Measurement & Testing. Copyright © 2013 Elsevier B.V. All rights reserved.

Constraining Thermal Histories by Monte Carlo Simulation of Mg-Fe Isotopic Profiles in Olivine

NASA Astrophysics Data System (ADS)

Sio, C. K. I.; Dauphas, N.

2016-12-01

In thermochronology, random time-temperature (t-T) paths are generated and used as inputs to model fission track data. This random search method is used to identify a range of acceptable thermal histories that can describe the data. We have extended this modeling approach to magmatic systems. This approach utilizes both the chemical and stable isotope profiles measured in crystals as model constraints. Specifically, the isotopic profiles are used to determine the relative contribution of crystal growth vs. diffusion in generating chemical profiles, and to detect changes in melt composition. With this information, tighter constraints can be placed on the thermal evolution of magmatic bodies. We use an olivine phenocryst from the Kilauea Iki lava lake, HI, to demonstrate proof of concept. We treat this sample as one with little geologic context, then compare our modeling results to the known thermal history experienced by that sample. To complete forward modeling, we use MELTS to estimate the boundary condition, initial and quench temperatures. We also assume a simple relationship between crystal growth and cooling rate. Another important parameter is the isotopic effect for diffusion (i.e., the relative diffusivity of the light vs. heavy isotope of an element). The isotopic effects for Mg and Fe diffusion in olivine have been estimated based on natural samples; experiments to better constrain these parameters are underway. We find that 40% of the random t-T paths can be used to fit the Mg-Fe chemical profiles. However, only a few can be used to simultaneously fit the Mg-Fe isotopic profiles. These few t-T paths are close to the independently determined t-T history of the sample. This modeling approach can be further extended other igneous and metamorphic systems where data exist for diffusion rates, crystal growth rates, and isotopic effects for diffusion.

Off-great-circle paths in transequatorial propagation: 2. Nonmagnetic-field-aligned reflections

NASA Astrophysics Data System (ADS)

Tsunoda, Roland T.; Maruyama, Takashi; Tsugawa, Takuya; Yokoyama, Tatsuhiro; Ishii, Mamoru; Nguyen, Trang T.; Ogawa, Tadahiko; Nishioka, Michi

2016-11-01

There is considerable evidence that plasma structure in nighttime equatorial F layer develops from large-scale wave structure (LSWS) in bottomside F layer. However, crucial details of how this process proceeds, from LSWS to equatorial plasma bubbles (EPBs), remain to be sorted out. A major obstacle to success is the paucity of measurements that provide a space-time description of the bottomside F layer over a broad geographical region. The transequatorial propagation (TEP) experiment is one of few methods that can do so. New findings using a TEP experiment, between Shepparton (SHP), Australia, and Oarai (ORI), Japan, are presented in two companion papers. In Paper 1 (P1), (1) off-great-circle (OGC) paths are described in terms of discrete and diffuse types, (2) descriptions of OGC paths are generalized from a single-reflection to a multiple-reflection process, and (3) discrete type is shown to be associated with an unstructured but distorted upwelling, whereas the diffuse type is shown to be associated with EPBs. In Paper 2 (P2), attention is placed on differences in east-west (EW) asymmetry, found between OGC paths from the SHP-ORI experiment and those from another near-identical TEP experiment. Differences are reconciled by allowing three distinct sources for the EW asymmetries: (1) reflection properties within an upwelling (see P1), (2) OGC paths that depend on magnetic declination of geomagnetic field (B), and (3) OGC paths supported by non-B-aligned reflectors at latitudes where inclination of B is finite.

Scaling Laws in Arctic Permafrost River Basins: Statistical Signature in Transition

NASA Astrophysics Data System (ADS)

Rowland, J. C.; Gangodagamage, C.; Wilson, C. J.; Prancevic, J. P.; Brumby, S. P.; Marsh, P.; Crosby, B. T.

2011-12-01

The Arctic landscape has been shown to be fundamentally different from the temperate landscape in many ways. Long winters and cold temperatures have led to the development of permafrost, perennially frozen ground, that controls geomorphic processes and the structure of the Arctic landscape. Climate warming is causing changes in permafrost and the active layer (the seasonally thawed surface layer) that is driving an increase in thermal erosion including thermokarst (collapsed soil), retrogressive thaw slumps, and gullies. These geomorphic anomalies in the arctic landscapes have not been well quantified, even though some of the landscape geomorphic and hydrologic characteristics and changes are detectable by our existing sensor networks. We currently lack understanding of the fundamental fluvio-thermal-erosional processes that underpin Arctic landscape structure and form, which limits our ability to develop models to predict the landscape response to current and future climate change. In this work, we seek a unified framework that can explain why permafrost landscapes are different from temperate landscapes. We use high resolution LIDAR data to analyze arctic geomorphic processes at a scale of less than a 1 m and demonstrate our ability to quantify the fundamental difference in the arctic landscape. We first simulate the arctic hillslopes from a stochastic space-filling network and demonstrate that the flow-path convergent properties of arctic landscape can be effectively captured from this simple model, where the simple model represents a landscape flowpath arrangement on a relatively impervious frozen soil layer. Further, we use a novel data processing algorithm to analyze landscape attributes such as slope, curvature, flow-accumulation, elevation-drops and other geomorphic properties, and show that the pattern of diffusion and advection dominated soil transport processes (diffusion/advection regime transition) in the arctic landscape is substantially different from the pattern in temperate landscapes. Our results suggest that Arctic landscapes are characterized by relatively undissected, long planar hillslopes, which convey sediment to quasi-fluvial valleys through long (~ 1 km) flow-paths. Further, we also document that broad planar hillslopes abruptly converge, forcing rapid subsurface flow accumulation at channel heads. This topographic characteristic can successfully be used to explain the position of erosion features. Finally we estimate the landscape model parameters for the arctic landscape that can be successfully used to model development and validation purposes.

C+/CO Transitions in the Diffuse ISM: Transitional Cloud Sample from the GOT C+ Survey of [CII] in the inner Galaxy at l = -30deg to 30deg

NASA Astrophysics Data System (ADS)

Velusamy, T.; Pineda, J. L.; Langer, W. D.; Willacy, K.; Goldsmith, P. F.

2011-05-01

Our knowledge of interstellar gas has been limited primarily to the diffuse atomic phase traced by HI and the well-shielded molecular phase traced by CO. Recently, using the first results of the Herschel Key Project GOT C+, a HIFI C+ survey of the Galactic plane, Velusamy, Langer, Pineda et al. (A&A 521, L18, 2010) have shown that in the diffuse interstellar transition clouds a significant fraction of the carbon exists primarily as C^+ with little C^0 and CO in a warm 'dark gas' layer in which hydrogen is mostly H_2 with little atomic H, surrounding a modest 12CO-emitting core. The [CII] fine structure transition, at 1.9 THz (158 μm) is the best tracer of this component of the interstellar medium, which is critical to our understanding of the atomic to molecular cloud transitions. The Herschel Key Project GOT C+ is designed to study such clouds by observing with HIFI the [CII] line emission along 500 lines of sight (LOSs) throughout the Galactic disk. Here we present the identification and chemical status of a few hundred diffuse and transition clouds traced by [CII], along with auxiliary HI and CO data covering ~100 LOSs in the inner Galaxy between l= -30° and 30°. We identify transition clouds as [CII] components that are characterized by the presence of both HI and 12CO, but no 13CO emission. The intensities, I(CII) and I(HI), are used as measures of the visual extinction, AV, in the cloud up to the C^+/C^0/CO transition layer and a comparison with I(12CO) yields a more complete H_2 molecular inventory. Our results show that [CII] emission is an excellent tool to study transition clouds and their carbon chemistry in the ISM, in particular as a unique tracer of molecular H_2, which is not easily observed by other means. The large sample presented here will serve as a resource to study the chemical and physical status of diffuse transition clouds in a wide range of Galactic environments and constrain the physical parameters such as the FUV intensity and cosmic ray ionization rate that drive the CO chemistry in the diffuse ISM.

Translational diffusion coefficients of volatile compounds in various aqueous solutions at low and subzero temperatures.

PubMed

Covarrubias-Cervantes, Marco; Champion, Dominique; Debeaufort, Frédéric; Voilley, Andrée

2005-08-24

Translational diffusion coefficients (D(12)) of volatile compounds were measured in model media with the profile concentration method. The influence of sample temperature (from 25 to -10 degrees C) was studied on translational diffusion in sucrose or maltodextrin solutions at various concentrations. Results show that diffusivity of volatile compounds in sucrose solutions is controlled by temperature, molecule size, and the viscosity of the liquid phase as expected with the Stokes-Einstein equation; moreover, physicochemical interactions between volatile compounds and the medium are determinant for diffusion estimation. At negative temperature, the winding path induced by an ice crystal content of >70% lowered volatile compound diffusion. On the contrary, no influence on translational diffusion coefficients was observed for lower ice content.

Evaluation of Rutter Sigma S6 Ice Navigation Radar on USCGC Healy during Arctic Shield 2014

DTIC Science & Technology

2015-03-01

useful in making decisions about the pressure ridges ahead of time instead of making an immediate decision. Figure 33. CG radar display of... use the radar to help chart an efficient path through an ice field to reduce transit time and fuel expenses. This includes a clear picture of the ice...a ship would be able to use the radar to help chart an efficient path through an ice field to reduce transit time and fuel expenses. This includes

Monte Carlo simulation of the mixed alkali effect with cooperative jumps

NASA Astrophysics Data System (ADS)

Habasaki, Junko; Hiwatari, Yasuaki

2000-12-01

In our previous works on molecular dynamics (MD) simulations of lithium metasilicate (Li2SiO3), it has been shown that the long time behavior of the lithium ions in Li2SiO3 has been characterized by the component showing the enhanced diffusion (Lévy flight) due to cooperative jumps. It has also been confirmed that the contribution of such component decreases by interception of the paths in the mixed alkali silicate (LiKSiO3). Namely, cooperative jumps of like ions are much decreased in number owing to the interception of the path for unlike alkali-metal ions. In the present work, we have performed a Monte Carlo simulation using a cubic lattice in order to establish the role of the cooperative jumps in the transport properties in a mixed alkali glass. Fixed particles (blockage) were introduced instead of the interception of the jump paths for unlike alkali-metal ions. Two types of cooperative motions (a pull type and a push type) were taken into account. Low-dimensionality of the jump path caused by blockage resulted in a decrease of a diffusion coefficient of the particles. The effect of blockage is enhanced when the cooperative motions were introduced.

Toward the existence of ultrafast diffusion paths in Cu with a gradient microstructure: Room temperature diffusion of Ni

NASA Astrophysics Data System (ADS)

Wang, Z. B.; Lu, K.; Wilde, G.; Divinski, S.

2008-09-01

Room temperature diffusion of Ni63 in Cu with a gradient microstructure prepared by surface mechanical attrition treatment (SMAT) was investigated by applying the radiotracer technique. The results reveal significant penetration of Ni into the nanostructured layer. The relevant diffusivity is higher than that along the conventional high-angle grain boundaries by about six orders of magnitude. This behavior is associated with a higher energy state of internal interfaces produced via plastic deformation. The diffusivity in the top surface layer is somewhat smaller than that in the subsurface layer. This fact is related to nanotwin formation in the former during SMAT.

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

PubMed

Ren, Weiqing

2014-03-18

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

Modelling the Composition of Outgassing Bubbles at Basaltic Open Vent Volcanoes

NASA Astrophysics Data System (ADS)

Edmonds, M.; Clements, N.; Houghton, B. F.; Oppenheimer, C.; Jones, R. L.; Burton, M. R.

2015-12-01

Basaltic open vent volcanoes exhibit a wide range in eruption styles, from passive outgassing to Strombolian and Hawaiian explosive activity. Transitions between these styles are linked to contrasting two-phase (melt and gas) flow regimes in the conduit system. A wealth of data now exists characterising the fluxes and compositions of gases emitted from these volcanoes, alongside detailed observations of patterns of outgassing at the magma free surfaces. Complex variations in gas composition are apparent from high temporal resolution measurement techniques such as open path spectroscopy. This variability with time is likely a function of individual bubbles' histories of growth during ascent, with variable degrees of kinetic inhibition. Our previous studies at Kilauea and Stromboli have, for example, linked CO2-rich gases with the bursting of bubbles that last equilibrated at some depth beneath the surface. However, very few studies have attempted to reconcile such observations with quantitative models of diffusion-limited bubble growth in magmas prior to eruption. We present here an analytical model that simulates the growth of populations of bubbles by addition of volatile mass during decompression, with growth limited by diffusion. The model simulates a range of behaviors between the end members of separated two-phase flow and homogeneous bubbly flow in the conduit, tied to thermodynamic models of solubility and partitioning of volatile species (carbon, water, sulfur). We explore the effects of the form of bubble populations at depth, melt viscosity, total volatile content, magma decompression rate and other intrinsic parameters on expected gas compositions at the surface and consider implications for transitions between eruption styles. We compare the the model to data suites from Stromboli and Kilauea.

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.

An asymptotic preserving unified gas kinetic scheme for frequency-dependent 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

This paper presents an extension of previous work (Sun et al., 2015 [22]) of the unified gas kinetic scheme (UGKS) for the gray radiative transfer equations to the frequency-dependent (multi-group) radiative transfer system. Different from the gray radiative transfer equations, where the optical opacity is only a function of local material temperature, the simulation of frequency-dependent radiative transfer is associated with additional difficulties from the frequency-dependent opacity. For the multiple frequency radiation, the opacity depends on both the spatial location and the frequency. For example, the opacity is typically a decreasing function of frequency. At the same spatial region themore » transport physics can be optically thick for the low frequency photons, and optically thin for high frequency ones. Therefore, the optical thickness is not a simple function of space location. In this paper, the UGKS for frequency-dependent radiative system is developed. The UGKS is a finite volume method and the transport physics is modeled according to the ratio of the cell size to the photon's frequency-dependent mean free path. When the cell size is much larger than the photon's mean free path, a diffusion solution for such a frequency radiation will be obtained. On the other hand, when the cell size is much smaller than the photon's mean free path, a free transport mechanism will be recovered. In the regime between the above two limits, with the variation of the ratio between the local cell size and photon's mean free path, the UGKS provides a smooth transition in the physical and frequency space to capture the corresponding transport physics accurately. The seemingly straightforward extension of the UGKS from the gray to multiple frequency radiation system is due to its intrinsic consistent multiple scale transport modeling, but it still involves lots of work to properly discretize the multiple groups in order to design an asymptotic preserving (AP) scheme in all regimes. The current scheme is tested in a few frequency-dependent radiation problems, and the results are compared with the solutions from the well-defined implicit Monte Carlo (IMC) method. The UGKS is much more efficient than IMC, and the computational times of both schemes for all test cases are listed. The UGKS seems to be the first discrete ordinate method (DOM) for the accurate capturing of multiple frequency radiative transport physics from ballistic particle motion to the diffusive wave propagation.« less

Simulation of adsorbed hydrogen on tungsten surface

NASA Astrophysics Data System (ADS)

Degtyarenko, N. N.; Pisarev, A. A.

2017-12-01

Calculations of the energy of the H-W system were performed using DFT method based on plane waves. Adsorption energies, equilibrium states, vibration spectra, saddle points, activation energies of jumps, and diffusion paths have been analyzed for H atom on W(100) and W(110). Diffusion coefficient for H on W(110) agrees very well with experimental data.

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

Quantum fluctuations increase the self-diffusive motion of para-hydrogen in narrow carbon nanotubes.

PubMed

Kowalczyk, Piotr; Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester

2011-05-28

Quantum fluctuations significantly increase the self-diffusive motion of para-hydrogen adsorbed in narrow carbon nanotubes at 30 K comparing to its classical counterpart. Rigorous Feynman's path integral calculations reveal that self-diffusive motion of para-hydrogen in a narrow (6,6) carbon nanotube at 30 K and pore densities below ∼29 mmol cm(-3) is one order of magnitude faster than the classical counterpart. We find that the zero-point energy and tunneling significantly smoothed out the free energy landscape of para-hydrogen molecules adsorbed in a narrow (6,6) carbon nanotube. This promotes a delocalization of the confined para-hydrogen at 30 K (i.e., population of unclassical paths due to quantum effects). Contrary the self-diffusive motion of classical para-hydrogen molecules in a narrow (6,6) carbon nanotube at 30 K is very slow. This is because classical para-hydrogen molecules undergo highly correlated movement when their collision diameter approached the carbon nanotube size (i.e., anomalous diffusion in quasi-one dimensional pores). On the basis of current results we predict that narrow single-walled carbon nanotubes are promising nanoporous molecular sieves being able to separate para-hydrogen molecules from mixtures of classical particles at cryogenic temperatures. This journal is © the Owner Societies 2011

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Decoupling of rotational and translational diffusion in supercooled colloidal fluids

PubMed Central

Edmond, Kazem V.; Elsesser, Mark T.; Hunter, Gary L.; Pine, David J.; Weeks, Eric R.

2012-01-01

We use confocal microscopy to directly observe 3D translational and rotational diffusion of tetrahedral clusters, which serve as tracers in colloidal supercooled fluids. We find that as the colloidal glass transition is approached, translational and rotational diffusion decouple from each other: Rotational diffusion remains inversely proportional to the growing viscosity whereas translational diffusion does not, decreasing by a much lesser extent. We quantify the rotational motion with two distinct methods, finding agreement between these methods, in contrast with recent simulation results. The decoupling coincides with the emergence of non-Gaussian displacement distributions for translation whereas rotational displacement distributions remain Gaussian. Ultimately, our work demonstrates that as the glass transition is approached, the sample can no longer be approximated as a continuum fluid when considering diffusion. PMID:23071311

Reliable Transition State Searches Integrated with the Growing String Method.

PubMed

Zimmerman, Paul

2013-07-09

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

Foundations and latest advances in replica exchange transition interface sampling.

PubMed

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

2017-10-21

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

Foundations and latest advances in replica exchange transition interface sampling

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Effect of measurement on the ballistic-diffusive transition in turbid media.

PubMed

Glasser, Ziv; Yaroshevsky, Andre; Barak, Bavat; Granot, Er'el; Sternklar, Shmuel

2013-10-01

The dependence of the transition between the ballistic and the diffusive regimes of turbid media on the experimental solid angle of the detection system is analyzed theoretically and experimentally. A simple model is developed which shows the significance of experimental conditions on the location of the ballistic-diffusive transition. It is demonstrated that decreasing the solid angle expands the ballistic regime; however, this benefit is bounded by the initial Gaussian beam diffraction. In addition, choosing the appropriate wavelength according to the model's principles provides another means of expanding the ballistic regime. Consequently, by optimizing the experimental conditions, it should be possible to extract the ballistic image of a tissue with a thickness of 1 cm.

Linear response theory and transient fluctuation relations for diffusion processes: a backward point of view

NASA Astrophysics Data System (ADS)

Liu, Fei; Tong, Huan; Ma, Rui; Ou-Yang, Zhong-can

2010-12-01

A formal apparatus is developed to unify derivations of the linear response theory and a variety of transient fluctuation relations for continuous diffusion processes from a backward point of view. The basis is a perturbed Kolmogorov backward equation and the path integral representation of its solution. We find that these exact transient relations could be interpreted as a consequence of a generalized Chapman-Kolmogorov equation, which intrinsically arises from the Markovian characteristic of diffusion processes.

Modeling a Single SEP Event from Multiple Vantage Points Using the iPATH Model

NASA Astrophysics Data System (ADS)

Hu, Junxiang; Li, Gang; Fu, Shuai; Zank, Gary; Ao, Xianzhi

2018-02-01

Using the recently extended 2D improved Particle Acceleration and Transport in the Heliosphere (iPATH) model, we model an example gradual solar energetic particle event as observed at multiple locations. Protons and ions that are energized via the diffusive shock acceleration mechanism are followed at a 2D coronal mass ejection-driven shock where the shock geometry varies across the shock front. The subsequent transport of energetic particles, including cross-field diffusion, is modeled by a Monte Carlo code that is based on a stochastic differential equation method. Time intensity profiles and particle spectra at multiple locations and different radial distances, separated in longitudes, are presented. The results shown here are relevant to the upcoming Parker Solar Probe mission.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Formation of alternating interfacial layers in Au-12Ge/Ni joints

PubMed Central

Lin, Shih-kang; Tsai, Ming-yueh; Tsai, Ping-chun; Hsu, Bo-hsun

2014-01-01

Au-Ge alloys are promising materials for high-power and high-frequency packaging, and Ni is frequently used as diffusion barriers. This study investigates interfacial reactions in Au-12Ge/Ni joints at 300°C and 400°C. For the reactions at 300°C, typical interfacial morphology was observed and the diffusion path was (Au) + (Ge)/NiGe/Ni5Ge3/Ni. However, an interesting phenomenon – the formation of (Au,Ni,Ge)/NiGe alternating layers – was observed for the reactions at 400°C. The diffusion path across the interface was liquid/(Au,Ni,Ge)/NiGe/···/(Au,Ni,Ge)/NiGe/Ni2Ge/Ni. The periodic thermodynamic instability at the NiGe/Ni2Ge interface caused the subsequent nucleation of new (Au,Ni,Ge)/NiGe pairs. The thermodynamic foundation and mechanism of formation of the alternating layers are elaborated in this paper. PMID:24690992

Tortuosity Computations of Porous Materials using the Direct Simulation Monte Carlo

NASA Technical Reports Server (NTRS)

Borner, A.; Ferguson, C.; Panerai, F.; Mansour, Nagi N.

2017-01-01

Low-density carbon fiber preforms, used as thermal protection systems (TPS) materials for planetary entry systems, have permeable, highly porous microstructures consisting of interlaced fibers. Internal gas transport in TPS is important in modeling the penetration of hot boundary-layer gases and the in-depth transport of pyrolysis and ablation products. The gas effective diffusion coefficient of a porous material must be known before the gas transport can be modeled in material response solvers; however, there are very little available data for rigid fibrous insulators used in heritage TPS.The tortuosity factor, which reflects the efficiency of the percolation paths, can be computed from the effective diffusion coefficient of a gas inside a porous material and is based on the micro-structure of the material. It is well known, that the tortuosity factor is a strong function of the Knudsen number. Due to the small characteristic scales of porous media used in TPS applications (typical pore size of the order of 50 micron), the transport of gases can occur in the rarefied and transitional regimes, at Knudsen numbers above 1. A proper way to model the gas dynamics at these conditions consists in solving the Boltzmann equation using particle-based methods that account for movement and collisions of atoms and molecules.In this work we adopt, for the first time, the Direct Simulation Monte Carlo (DSMC) method to compute the tortuosity factor of fibrous media in the rarefied regime. To enable realistic simulations of the actual transport of gases in the porous medium, digitized computational grids are obtained from X-ray micro-tomography imaging of real TPS materials. The SPARTA DSMC solver is used for simulations. Effective diffusion coefficients and tortuosity factors are obtained by computing the mean-square displacement of diffusing particles.We first apply the method to compute the tortuosity factors as a function of the Knudsen number for computationally designed materials such as random cylindrical fibers and packed bed of spheres with prescribed porosity. Results are compared to literature values obtained using random walk methods in the rarefied and transitional regime and a finite-volume method for the continuum regime. We then compute tortuosity factors for a real carbon fiber material with a transverse isotropic structure (FiberForm), quantifying differences between through-thickness and in-plain tortuosities at various Knudsen regimes.

Generating a Simulated Fluid Flow over a Surface Using Anisotropic Diffusion

NASA Technical Reports Server (NTRS)

Rodriguez, David L. (Inventor); Sturdza, Peter (Inventor)

2016-01-01

A fluid-flow simulation over a computer-generated surface is generated using a diffusion technique. The surface is comprised of a surface mesh of polygons. A boundary-layer fluid property is obtained for a subset of the polygons of the surface mesh. A gradient vector is determined for a selected polygon, the selected polygon belonging to the surface mesh but not one of the subset of polygons. A maximum and minimum diffusion rate is determined along directions determined using the gradient vector corresponding to the selected polygon. A diffusion-path vector is defined between a point in the selected polygon and a neighboring point in a neighboring polygon. An updated fluid property is determined for the selected polygon using a variable diffusion rate, the variable diffusion rate based on the minimum diffusion rate, maximum diffusion rate, and the gradient vector.

Dynamical transition for a particle in a squared Gaussian potential

NASA Astrophysics Data System (ADS)

Touya, C.; Dean, D. S.

2007-02-01

We study the problem of a Brownian particle diffusing in finite dimensions in a potential given by ψ = phi2/2 where phi is Gaussian random field. Exact results for the diffusion constant in the high temperature phase are given in one and two dimensions and it is shown to vanish in a power-law fashion at the dynamical transition temperature. Our results are confronted with numerical simulations where the Gaussian field is constructed, in a standard way, as a sum over random Fourier modes. We show that when the number of Fourier modes is finite the low temperature diffusion constant becomes non-zero and has an Arrhenius form. Thus we have a simple model with a fully understood finite size scaling theory for the dynamical transition. In addition we analyse the nature of the anomalous diffusion in the low temperature regime and show that the anomalous exponent agrees with that predicted by a trap model.

Transition fronts of time periodic bistable reaction-diffusion equations in RN

NASA Astrophysics Data System (ADS)

Sheng, Wei-Jie; Guo, Hong-Jun

2018-09-01

This paper is concerned with the existence and qualitative properties of transition fronts for time periodic bistable reaction-diffusion equations in RN. We first show that any almost-planar transition front is actually planar, regardless of the number of transition layers. Then we prove that all transition fronts admit a global mean speed γ and it holds γ = | c |, where c is the speed of the planar traveling front. Finally we establish the existence of a transition front in RN that is not a standard traveling front. Such a front behaves like three moving time periodic planar fronts as time goes to -∞ and like a time periodic V-shaped traveling front as time goes to ∞.

Combining phase-field crystal methods with a Cahn-Hilliard model for binary alloys

NASA Astrophysics Data System (ADS)

Balakrishna, Ananya Renuka; Carter, W. Craig

2018-04-01

Diffusion-induced phase transitions typically change the lattice symmetry of the host material. In battery electrodes, for example, Li ions (diffusing species) are inserted between layers in a crystalline electrode material (host). This diffusion induces lattice distortions and defect formations in the electrode. The structural changes to the lattice symmetry affect the host material's properties. Here, we propose a 2D theoretical framework that couples a Cahn-Hilliard (CH) model, which describes the composition field of a diffusing species, with a phase-field crystal (PFC) model, which describes the host-material lattice symmetry. We couple the two continuum models via coordinate transformation coefficients. We introduce the transformation coefficients in the PFC method to describe affine lattice deformations. These transformation coefficients are modeled as functions of the composition field. Using this coupled approach, we explore the effects of coarse-grained lattice symmetry and distortions on a diffusion-induced phase transition process. In this paper, we demonstrate the working of the CH-PFC model through three representative examples: First, we describe base cases with hexagonal and square symmetries for two composition fields. Next, we illustrate how the CH-PFC method interpolates lattice symmetry across a diffuse phase boundary. Finally, we compute a Cahn-Hilliard type of diffusion and model the accompanying changes to lattice symmetry during a phase transition process.

Pyridine adsorption and diffusion on Pt(111) investigated with density functional theory

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

Kolsbjerg, Esben L.; Groves, Michael N.; Hammer, Bjørk, E-mail: hammer@phys.au.dk

2016-04-28

The adsorption, diffusion, and dissociation of pyridine, C{sub 5}H{sub 5}N, on Pt(111) are investigated with van der Waals-corrected density functional theory. An elaborate search for local minima in the adsorption potential energy landscape reveals that the intact pyridine adsorbs with the aromatic ring parallel to the surface. Piecewise interconnections of the local minima in the energy landscape reveal that the most favourable diffusion path for pyridine has a barrier of 0.53 eV. In the preferred path, the pyridine remains parallel to the surface while performing small single rotational steps with a carbon-carbon double bond hinged above a single Pt atom.more » The origin of the diffusion pathway is discussed in terms of the C{sub 2}–Pt π-bond being stronger than the corresponding CN–Pt π-bond. The energy barrier and reaction enthalpy for dehydrogenation of adsorbed pyridine into an adsorbed, upright bound α-pyridyl species are calculated to 0.71 eV and 0.18 eV, respectively (both zero-point energy corrected). The calculations are used to rationalize previous experimental observations from the literature for pyridine on Pt(111).« less

Diffusive and localization behavior of electromagnetic waves in a two-dimensional random medium

NASA Astrophysics Data System (ADS)

Wang, Ken Kang-Hsin; Ye, Zhen

2003-10-01

In this paper, we discuss the transport phenomena of electromagnetic waves in a two-dimensional random system which is composed of arrays of electrical dipoles, following the model presented earlier by Erdogan et al. [J. Opt. Soc. Am. B 10, 391 (1993)]. A set of self-consistent equations is presented, accounting for the multiple scattering in the system, and is then solved numerically. A strong localization regime is discovered in the frequency domain. The transport properties within, near the edge of, and nearly outside the localization regime are investigated for different parameters such as filling factor and system size. The results show that within the localization regime, waves are trapped near the transmitting source. Meanwhile, the diffusive waves follow an intuitive but expected picture. That is, they increase with traveling path as more and more random scattering incurs, followed by a saturation, then start to decay exponentially when the travelling path is large enough, signifying the localization effect. For the cases where the frequencies are near the boundary of or outside the localization regime, the results of diffusive waves are compared with the diffusion approximation, showing less encouraging agreement as in other systems [Asatryan et al., Phys. Rev. E 67, 036605 (2003)].

Ab initio study of novel carbon nanofoam structure as an anode material for Li secondary battery

NASA Astrophysics Data System (ADS)

Park, Hanjin; Park, Sora; Kang, Seoung-Hun; Kwon, Young-Kyun

2014-03-01

Using ab inito density functional theory, we investigate the adsorption and diffusion properties of Li atoms on a new carbon nanostructure, which may be used as an anode of Li secondary battery. We focus on a special carbon nanofoam structure consisting of Schwarzite structures with negative Gaussian curvature as core parts, which are interconnected through (4,4) CNT segments. Considering the symmetry of the nanofoam structure, we find various Li adsorption sites exhibiting relatively large binding energies (>= 2 . 00 eV). Based on these adsorption sites, we identify several diffusion paths on the outside or inside surface of the nanofoam structure and examine the diffusion barriers along the paths. Our results show that Li atom can diffuse almost freely due to its low energy barriers on both outside and inside surfaces. Finally, we also evaluate the energy gain tendency and the volume expansion as well as the average binding energy while adding Li atoms to estimate the Li-capacity and recyclability of the system, which are important characterisitics for anode materials. We conclude that the carbon nanofoam structure would be better as an anode material than graphite in Li capacity and volume expansion.

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

NASA Astrophysics Data System (ADS)

Wainwright, Carroll L.

2012-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Variational transition state theory: theoretical framework and recent developments.

PubMed

Bao, Junwei Lucas; Truhlar, Donald G

2017-12-11

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

Improving Upon String Methods for Transition State Discovery.

PubMed

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

2012-02-14

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

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

Feynman-Kac equations for reaction and diffusion processes

NASA Astrophysics Data System (ADS)

Hou, Ru; Deng, Weihua

2018-04-01

This paper provides a theoretical framework for deriving the forward and backward Feynman-Kac equations for the distribution of functionals of the path of a particle undergoing both diffusion and reaction processes. Once given the diffusion type and reaction rate, a specific forward or backward Feynman-Kac equation can be obtained. The results in this paper include those for normal/anomalous diffusions and reactions with linear/nonlinear rates. Using the derived equations, we apply our findings to compute some physical (experimentally measurable) statistics, including the occupation time in half-space, the first passage time, and the occupation time in half-interval with an absorbing or reflecting boundary, for the physical system with anomalous diffusion and spontaneous evanescence.

Fick's second law transformed: one path to cloaking in mass diffusion.

PubMed

Guenneau, S; Puvirajesinghe, T M

2013-06-06

Here, we adapt the concept of transformational thermodynamics, whereby the flux of temperature is controlled via anisotropic heterogeneous diffusivity, for the diffusion and transport of mass concentration. The n-dimensional, time-dependent, anisotropic heterogeneous Fick's equation is considered, which is a parabolic partial differential equation also applicable to heat diffusion, when convection occurs, for example, in fluids. This theory is illustrated with finite-element computations for a liposome particle surrounded by a cylindrical multi-layered cloak in a water-based environment, and for a spherical multi-layered cloak consisting of layers of fluid with an isotropic homogeneous diffusivity, deduced from an effective medium approach. Initial potential applications could be sought in bioengineering.

Interstitial diffusion in lithium-ion battery electrodes and structural phase transitions in crystalline solids from first principles

NASA Astrophysics Data System (ADS)

Bhattacharya, Jishnu

We perform first-principles investigations of thermally activated phase transitions and diffusion in solids. The atomic scale energy landscapes are evaluated with first-principles total energy calculations for different structural and configurational microstates. Effective Hamiltonians constructed from the total energies are subjected to Monte Carlo simulations to study thermodynamic and kinetic properties of the solids at finite temperatures. Cubic to tetragonal martensitic phase transitions are investigated beyond the harmonic approximation. As an example, stoichiometric TiH2 is studied where a cubic phase becomes stable at high temperature while ab-initio energy calculations predict the cubic phase to be mechanically unstable with respect to tetragonal distortions at zero Kelvin. An anharmonic Hamiltonian is used to explain the stability of the cubic phase at higher temperature. The importance of anharmonic terms is emphasized and the true nature of the high temperature phase is elucidated beyond the traditional Landau-like explanation. In Li-ion battery electrodes, phase transitions due to atomic redistribution with changes in Li concentration occur with insertion (removal) of Li-ions during discharge (charge). A comprehensive study of the thermodynamics and the non-dilute Li-diffusion mechanisms in spinel-Li1+xTi2 O4 is performed. Two distinct phases are predicted at different lithium compositions. The predicted voltage curve qualitatively matches with experimental observation. The predicted fast diffusion arises from crystallographic features unique to the spinel crystal structure elucidating the crucial role of crystal structure on Li diffusion in intercalation compounds. Effects of anion and guest species on diffusion are elucidated with Li- and Cu-diffusion in spinel-LixTiS2. We predict strong composition dependence of the diffusion coefficients. A unique feature about spinel-LixTiS2 is that the intermediate site of a Li-hop is coordinated by four Li-sites. This results in di- and triple-vacancy mechanisms at non-dilute concentrations with very different migration barriers. The strong dependence of hop mechanisms on local Li-arrangement is at the origin of large concentration dependence of the diffusion coefficients. This contrasts with spinel-Li xTiO2 where the transition states are coordinated only by the end states of the hop, thereby restricting hops to a single vacancy mechanism. Cu ions are predicted to have much slower diffusion rate in TiS 2 host compared to Li ions.

Growth and melting of droplets in cold vapors.

PubMed

L'Hermite, Jean-Marc

2009-11-01

A model has been developed to investigate the growth of droplets in a supersaturated cold vapor taking into account their possible solid-liquid phase transition. It is shown that the solid-liquid phase transition is nontrivially coupled, through the energy released in attachment, to the nucleation process. The model is based on the one developed by J. Feder, K. C. Russell, J. Lothe, and G. M. Pound [Adv. Phys. 15, 111 (1966)], where the nucleation process is described as a thermal diffusion motion in a two-dimensional field of force given by the derivatives of a free-energy surface. The additional dimension accounts for droplets internal energy. The solid-liquid phase transition is introduced through a bimodal internal energy distribution in a Gaussian approximation derived from small clusters physics. The coupling between nucleation and melting results in specific nonequilibrium thermodynamical properties, exemplified in the case of water droplets. Analyzing the free-energy landscapes gives an insight into the nucleation dynamics. This landscape can be complex but generally exhibits two paths: the first one can generally be ascribed to the solid state, while the other to the liquid state. Especially at high supersaturation, the growth in the liquid state is often favored, which is not unexpected since in a supersaturated vapor the droplets can stand higher internal energy than at equilibrium. From a given critical temperature that is noticeably lower than the bulk melting temperature, nucleation may end in very large liquid droplets. These features can be qualitatively generalized to systems other than water.

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

NASA Technical Reports Server (NTRS)

Crouch, Roger

2004-01-01

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

International Space Station: Transitional Platform for Moon and Mars

NASA Technical Reports Server (NTRS)

Greeniesen, Michael C.

2006-01-01

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

Structural abnormality of the corticospinal tract in major depressive disorder

PubMed Central

2014-01-01

Background Scientists are beginning to document abnormalities in white matter connectivity in major depressive disorder (MDD). Recent developments in diffusion-weighted image analyses, including tractography clustering methods, may yield improved characterization of these white matter abnormalities in MDD. In this study, we acquired diffusion-weighted imaging data from MDD participants and matched healthy controls. We analyzed these data using two tractography clustering methods: automated fiber quantification (AFQ) and the maximum density path (MDP) procedure. We used AFQ to compare fractional anisotropy (FA; an index of water diffusion) in these two groups across major white matter tracts. Subsequently, we used the MDP procedure to compare FA differences in fiber paths related to the abnormalities in major fiber tracts that were identified using AFQ. Results FA was higher in the bilateral corticospinal tracts (CSTs) in MDD (p’s < 0.002). Secondary analyses using the MDP procedure detected primarily increases in FA in the CST-related fiber paths of the bilateral posterior limbs of the internal capsule, right superior corona radiata, and the left external capsule. Conclusions This is the first study to implicate the CST and several related fiber pathways in MDD. These findings suggest important new hypotheses regarding the role of CST abnormalities in MDD, including in relation to explicating CST-related abnormalities to depressive symptoms and RDoC domains and constructs. PMID:25295159

Algal ancestor of land plants was preadapted for symbiosis.

PubMed

Delaux, Pierre-Marc; Radhakrishnan, Guru V; Jayaraman, Dhileepkumar; Cheema, Jitender; Malbreil, Mathilde; Volkening, Jeremy D; Sekimoto, Hiroyuki; Nishiyama, Tomoaki; Melkonian, Michael; Pokorny, Lisa; Rothfels, Carl J; Sederoff, Heike Winter; Stevenson, Dennis W; Surek, Barbara; Zhang, Yong; Sussman, Michael R; Dunand, Christophe; Morris, Richard J; Roux, Christophe; Wong, Gane Ka-Shu; Oldroyd, Giles E D; Ané, Jean-Michel

2015-10-27

Colonization of land by plants was a major transition on Earth, but the developmental and genetic innovations required for this transition remain unknown. Physiological studies and the fossil record strongly suggest that the ability of the first land plants to form symbiotic associations with beneficial fungi was one of these critical innovations. In angiosperms, genes required for the perception and transduction of diffusible fungal signals for root colonization and for nutrient exchange have been characterized. However, the origin of these genes and their potential correlation with land colonization remain elusive. A comprehensive phylogenetic analysis of 259 transcriptomes and 10 green algal and basal land plant genomes, coupled with the characterization of the evolutionary path leading to the appearance of a key regulator, a calcium- and calmodulin-dependent protein kinase, showed that the symbiotic signaling pathway predated the first land plants. In contrast, downstream genes required for root colonization and their specific expression pattern probably appeared subsequent to the colonization of land. We conclude that the most recent common ancestor of extant land plants and green algae was preadapted for symbiotic associations. Subsequent improvement of this precursor stage in early land plants through rounds of gene duplication led to the acquisition of additional pathways and the ability to form a fully functional arbuscular mycorrhizal symbiosis.

Flow Through a Rectangular-to-Semiannular Diffusing Transition Duct

NASA Technical Reports Server (NTRS)

Foster, Jeff; Wendt, Bruce J.; Reichert, Bruce A.; Okiishi, Theodore H.

1997-01-01

Rectangular-to-semiannular diffusing transition ducts are critical inlet components on supersonic airplanes having bifucated engine inlets. This paper documents measured details of the flow through a rectangular-to-semiannular transition duct having an expansion area ratio of 1.53. Three-dimensional velocity vectors and total pressures at the exit plane of the diffuser are presented. Surface oil-flow visualization and surface static pressure data are shown. The tests were conducted with an inlet Mach number of 0.786 and a Reynolds number based on the inlet centerline velocity and exit diameter of 3.2 x 10(exp 6). The measured data are compared with previously published computational results. The ability of vortex generators to reduce circumferential total pressure distortion is demonstrated.

Site reactivity in the free radicals induced damage to leucine residues: a theoretical study.

PubMed

Medina, M E; Galano, A; Alvarez-Idaboy, J R

2015-02-21

Several recent computational studies have tried to explain the observed selectivity in radical damage to proteins. In this work we use Density Functional Theory and Transition State Theory including tunnelling corrections, reaction path degeneracy, the effect of diffusion, and the role of free radicals to get further insights into this important topic. The reaction between a leucine derivative and free radicals of biological significance, in aqueous and lipid media, has been investigated. Both thermochemical and kinetic analyses, in both hydrophilic and hydrophobic environments, have been carried out. DPPH, ˙OOH, ˙OOCH3, ˙OOCH2Cl, ˙OOCHCl2 and ˙OOCHCH2 radicals do not react with the target molecule. The reactions are proposed to be kinetically controlled. The leucine gamma site was the most reactive for the reactions with ˙N3, ˙OOCCl3, ˙OCH3, ˙OCH2Cl, and ˙OCHCl2 radicals, with rate constants equal to 1.97 × 10(5), 3.24 × 10(4), 6.68 × 10(5), 5.98 × 10(6) and 8.87 × 10(8) M(-1) s(-1), respectively, in aqueous solution. The ˙Cl, ˙OH and ˙OCCl3 radicals react with leucine at the beta, gamma, and delta positions at rates close to the diffusion limit with the alpha position which is the slowest path and the most thermodynamically favored. The presented results confirm that the Bell-Evans-Polanyi principle does not apply for the reactions between amino acid residues and free radicals. Regarding the influence of the environment on the reactivity of the studied series of free radicals towards leucine residues, it is concluded that hydrophilic media slightly lower the reactivity of the studied radicals, compared to hydrophobic ones, albeit the trends in reactivity are very similar.

A new regime of nanoscale thermal transport: Collective diffusion increases dissipation efficiency

DOE PAGES

Hoogeboom-Pot, Kathleen M.; Hernandez-Charpak, Jorge N.; Gu, Xiaokun; ...

2015-03-23

Understanding thermal transport from nanoscale heat sources is important for a fundamental description of energy flow in materials, as well as for many technological applications including thermal management in nanoelectronics and optoelectronics, thermoelectric devices, nanoenhanced photovoltaics, and nanoparticle-mediated thermal therapies. Thermal transport at the nanoscale is fundamentally different from that at the macroscale and is determined by the distribution of carrier mean free paths and energy dispersion in a material, the length scales of the heat sources, and the distance over which heat is transported. Past work has shown that Fourier’s law for heat conduction dramatically overpredicts the rate ofmore » heat dissipation from heat sources with dimensions smaller than the mean free path of the dominant heat-carrying phonons. In this work, we uncover a new regime of nanoscale thermal transport that dominates when the separation between nanoscale heat sources is small compared with the dominant phonon mean free paths. Surprisingly, the interaction of phonons originating from neighboring heat sources enables more efficient diffusive-like heat dissipation, even from nanoscale heat sources much smaller than the dominant phonon mean free paths. This finding suggests that thermal management in nanoscale systems including integrated circuits might not be as challenging as previously projected. In conclusion, we demonstrate a unique capability to extract differential conductivity as a function of phonon mean free path in materials, allowing the first (to our knowledge) experimental validation of predictions from the recently developed first-principles calculations.« less

A new regime of nanoscale thermal transport: Collective diffusion increases dissipation efficiency

NASA Astrophysics Data System (ADS)

Hoogeboom-Pot, Kathleen M.; Hernandez-Charpak, Jorge N.; Gu, Xiaokun; Frazer, Travis D.; Anderson, Erik H.; Chao, Weilun; Falcone, Roger W.; Yang, Ronggui; Murnane, Margaret M.; Kapteyn, Henry C.; Nardi, Damiano

2015-04-01

Understanding thermal transport from nanoscale heat sources is important for a fundamental description of energy flow in materials, as well as for many technological applications including thermal management in nanoelectronics and optoelectronics, thermoelectric devices, nanoenhanced photovoltaics, and nanoparticle-mediated thermal therapies. Thermal transport at the nanoscale is fundamentally different from that at the macroscale and is determined by the distribution of carrier mean free paths and energy dispersion in a material, the length scales of the heat sources, and the distance over which heat is transported. Past work has shown that Fourier's law for heat conduction dramatically overpredicts the rate of heat dissipation from heat sources with dimensions smaller than the mean free path of the dominant heat-carrying phonons. In this work, we uncover a new regime of nanoscale thermal transport that dominates when the separation between nanoscale heat sources is small compared with the dominant phonon mean free paths. Surprisingly, the interaction of phonons originating from neighboring heat sources enables more efficient diffusive-like heat dissipation, even from nanoscale heat sources much smaller than the dominant phonon mean free paths. This finding suggests that thermal management in nanoscale systems including integrated circuits might not be as challenging as previously projected. Finally, we demonstrate a unique capability to extract differential conductivity as a function of phonon mean free path in materials, allowing the first (to our knowledge) experimental validation of predictions from the recently developed first-principles calculations.

The path to COVIS: A review of acoustic imaging of hydrothermal flow regimes

NASA Astrophysics Data System (ADS)

Bemis, Karen G.; Silver, Deborah; Xu, Guangyu; Light, Russ; Jackson, Darrell; Jones, Christopher; Ozer, Sedat; Liu, Li

2015-11-01

Acoustic imaging of hydrothermal flow regimes started with the incidental recognition of a plume on a routine sonar scan for obstacles in the path of the human-occupied submersible ALVIN. Developments in sonar engineering, acoustic data processing and scientific visualization have been combined to develop technology which can effectively capture the behavior of focused and diffuse hydrothermal discharge. This paper traces the development of these acoustic imaging techniques for hydrothermal flow regimes from their conception through to the development of the Cabled Observatory Vent Imaging Sonar (COVIS). COVIS has monitored such flow eight times a day for several years. Successful acoustic techniques for estimating plume entrainment, bending, vertical rise, volume flux, and heat flux are presented as is the state-of-the-art in diffuse flow detection.

Clouding tracing: Visualization of the mixing of fluid elements in convection-diffusion systems

NASA Technical Reports Server (NTRS)

Ma, Kwan-Liu; Smith, Philip J.

1993-01-01

This paper describes a highly interactive method for computer visualization of the basic physical process of dispersion and mixing of fluid elements in convection-diffusion systems. It is based on transforming the vector field from a traditionally Eulerian reference frame into a Lagrangian reference frame. Fluid elements are traced through the vector field for the mean path as well as the statistical dispersion of the fluid elements about the mean position by using added scalar information about the root mean square value of the vector field and its Lagrangian time scale. In this way, clouds of fluid elements are traced and are not just mean paths. We have used this method to visualize the simulation of an industrial incinerator to help identify mechanisms for poor mixing.

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.

Diffuse Scattering Investigations of Orientational Pair Potentials in C_60

NASA Astrophysics Data System (ADS)

Wochner, Peter

1996-03-01

Premonitory orientational fluctuations above the first order phase transition of C_60 at 260K have been studied by diffuse X-ray scattering experiments. These experiments probe the orientational pair correlations between C_60 molecules as a function of their separation and therefore the orientational pair potential. In addition to the diffuse scattering due to the orientational disorder of single molecules, we have observed zone boundary diffuse scattering at the X-points related to the Pabar 3 low temperature structure up to 300K. An additional set of diffuse peaks, which are even at room temperature comparable in intensity to the former ones, have been found at (0.5,0.5,0.5) positions (L-point). Similar results have recently been reported by P. Launois et al. (P. Launois, S. Ravy, R. Moret, PRB 52), 5414 (1995) and L. Pintschovius et al. (L. Pintschovius, S.L. Chaplot, G. Roth, G. Heger, PRL 75), 2843 (1995) The temperature dependence of the integrated intensity of both sets of diffuse peaks shows only a weak increase in approaching T_c, indicative of a strongly first order transition. Additional intensity with a very weak temperature dependence but similar correlation length has also been found at (0.5,0.5,0) and (0.5,0,0) positions. The diffuse intensity at the L, Σ and Δ points has probably its origin in competing phases which are not stabilized at low temperatures. Recent DSC measurements show close lying transitions at 260K with a separation of ~= 0.2-0.3K which might be related to these competing phases footnote J. Fischer, private communication. The data will be compared with model calculations using orientational pair potentials which have been used in literature to describe the orientational phase transition in C_60.

Diffusive dynamics during the high-to-low density transition in amorphous ice

DOE PAGES

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkuhler, Felix; ...

2017-06-26

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distributionmore » function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. In conclusion, the diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid–liquid transition in the ultraviscous regime.« less

Diffusive dynamics during the high-to-low density transition in amorphous ice

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

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkuhler, Felix

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distributionmore » function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. In conclusion, the diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid–liquid transition in the ultraviscous regime.« less

Diffusive dynamics during the high-to-low density transition in amorphous ice

NASA Astrophysics Data System (ADS)

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkühler, Felix; Sprung, Michael; Mariedahl, Daniel; Sellberg, Jonas A.; Pathak, Harshad; Späh, Alexander; Cavalca, Filippo; Schlesinger, Daniel; Ricci, Alessandro; Jain, Avni; Massani, Bernhard; Aubree, Flora; Benmore, Chris J.; Loerting, Thomas; Grübel, Gerhard; Pettersson, Lars G. M.; Nilsson, Anders

2017-08-01

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distribution function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. The diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid-liquid transition in the ultraviscous regime.

First-principles study of transition-metal nitrides as diffusion barriers against Al

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

Mei, Zhi-Gang; Yacout, Abdellatif M.; Kim, Yeon Soo

2016-04-01

Using density-functional theory based first-principles calculations we provided a comparative study of the diffusion barrier properties of TiN, ZrN, and HfN against Al for U-Mo dispersion fuel applications. We firstly examined the thermodynamic stability of these transition-metal nitrides with Al. The calculated heats of reaction show that both TiN and ZrN are thermodynamically unstable diffusion barrier materials, which might be decomposed by Al at relatively high temperatures. As a comparison, HfN is a stable diffusion barrier material for Al. To evaluate the kinetic stability of these nitride systems against Al diffusion, we investigated the diffusion mechanisms of Al in TiN,more » ZrN and HfN using atomic scale simulations. The effect of non-stoichiometry on the defect formation and Al migration was systematically studied. (C) 2015 ELSEVIER B.V. All rights reserved« less

Localization and Ballistic Diffusion for the Tempered Fractional Brownian-Langevin Motion

NASA Astrophysics Data System (ADS)

Chen, Yao; Wang, Xudong; Deng, Weihua

2017-10-01

This paper discusses the tempered fractional Brownian motion (tfBm), its ergodicity, and the derivation of the corresponding Fokker-Planck equation. Then we introduce the generalized Langevin equation with the tempered fractional Gaussian noise for a free particle, called tempered fractional Langevin equation (tfLe). While the tfBm displays localization diffusion for the long time limit and for the short time its mean squared displacement (MSD) has the asymptotic form t^{2H}, we show that the asymptotic form of the MSD of the tfLe transits from t^2 (ballistic diffusion for short time) to t^{2-2H}, and then to t^2 (again ballistic diffusion for long time). On the other hand, the overdamped tfLe has the transition of the diffusion type from t^{2-2H} to t^2 (ballistic diffusion). The tfLe with harmonic potential is also considered.

Diffusion and interactions of interstitials in hard-sphere interstitial solid solutions

NASA Astrophysics Data System (ADS)

van der Meer, Berend; Lathouwers, Emma; Smallenburg, Frank; Filion, Laura

2017-12-01

Using computer simulations, we study the dynamics and interactions of interstitial particles in hard-sphere interstitial solid solutions. We calculate the free-energy barriers associated with their diffusion for a range of size ratios and densities. By applying classical transition state theory to these free-energy barriers, we predict the diffusion coefficients, which we find to be in good agreement with diffusion coefficients as measured using event-driven molecular dynamics simulations. These results highlight that transition state theory can capture the interstitial dynamics in the hard-sphere model system. Additionally, we quantify the interactions between the interstitials. We find that, apart from excluded volume interactions, the interstitial-interstitial interactions are almost ideal in our system. Lastly, we show that the interstitial diffusivity can be inferred from the large-particle fluctuations alone, thus providing an empirical relationship between the large-particle fluctuations and the interstitial diffusivity.

Radiative recombination in GaN/InGaN heterojunction bipolar transistors

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

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

2015-12-14

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

Influence of La/W ratio on electrical conductivity of lanthanum tungstate with high La/W ratio

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

Kojo, Gen; Shono, Yohei; Ushiyama, Hiroshi

The proton-conducting properties of lanthanum tungstates (LWOs) with high La/W ratios were investigated using electrochemical measurements and quantum chemical calculations. Single phases of LWOs with high La/W ratios (6.3≤La/W≤6.7) were synthesized by high-temperature sintering at around 1700 °C. The electrical conductivity of LWO increased with increasing La/W ratio in the single-phase region. The LWO synthesized at the optimum sintering temperature and time, and with the optimum La/W ratio gave the maximum conductivity, i.e., 2.7×10{sup −3} S cm{sup −1} with La/W=6.7 at 500 °C. Density functional theory calculations, using the nudged elastic band method, were performed to investigate the proton diffusionmore » barrier. The results suggest that the proton diffusion paths around La sites have the lowest proton diffusion barrier. These findings improve our understanding of LWO synthesis and the proton-conducting mechanism and provide a strategy for improving proton conduction in LWOs. - Graphical abstract: The LWOs with high La/W ratios were synthesized for the first time. The optimum La/W ratio gave the maximum conductivity with La/W=6.7 at 500 °C. The proton diffusion paths were also considered with density functional theory calculations. - Highlights: • The proton-conducting properties of lanthanum tungstates (LWOs) were investigated. • Single phase LWOs with high La/W ratios (6.3≤La/W≤6.7) were synthesized successfully. • LWOs with the high La/W ratios showed high proton conductivity. • The DFT calculation suggested the lowest proton diffusion barrier in the path around La sites.« less

Mixed-order phase transition in a minimal, diffusion-based spin model.

PubMed

Fronczak, Agata; Fronczak, Piotr

2016-07-01

In this paper we exactly solve, within the grand canonical ensemble, a minimal spin model with the hybrid phase transition. We call the model diffusion based because its Hamiltonian can be recovered from a simple dynamic procedure, which can be seen as an equilibrium statistical mechanics representation of a biased random walk. We outline the derivation of the phase diagram of the model, in which the triple point has the hallmarks of the hybrid transition: discontinuity in the average magnetization and algebraically diverging susceptibilities. At this point, two second-order transition curves meet in equilibrium with the first-order curve, resulting in a prototypical mixed-order behavior.

Infrared spectroscopic characterization of dehydration and accompanying phase transition behaviors in NAT-topology zeolites

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

Wang, Hsiu-Wen; Bishop, David

2012-01-01

Relative humidity (PH2O, partial pressure of water)-dependent dehydration and accompanying phase transitions in NAT-topology zeolites (natrolite, scolecite, and mesolite) were studied under controlled temperature and known PH2O conditions by in situ diffuse-reflectance infrared Fourier transform spectroscopy and parallel X-ray powder diffraction. Dehydration was characterized by the disappearance of internal H2O vibrational modes. The loss of H2O molecules caused a sequence of structural transitions in which the host framework transformation path was coupled primarily via the thermal motion of guest Na?/Ca2? cations and H2O molecules. The observation of different interactions of H2O molecules and Na?/Ca2? cations with host aluminosilicate frameworks undermore » highand low-PH2O conditions indicated the development of different local strain fields, arising from cation H2O interactions in NAT-type channels. These strain fields influence the Si O/Al O bond strength and tilting angles within and between tetrahedra as the dehydration temperature is approached. The newly observed infrared bands (at 2,139 cm-1 in natrolite, 2,276 cm-1 in scolecite, and 2,176 and 2,259 cm-1 in mesolite) result from strong cation H2O Al Si framework interactions in NAT-type channels, and these bands can be used to evaluate the energetic evolution of Na?/Ca2? cations before and after phase transitions, especially for scolecite and mesolite. The 2,176 and 2,259 cm-1 absorption bands in mesolite also appear to be related to Na?/Ca2? order disorder that occur when mesolite loses its Ow4 H2O molecules.« less

Transition from diffuse to self-organized discharge in a high frequency dielectric barrier discharge

NASA Astrophysics Data System (ADS)

Belinger, Antoine; Naudé, Nicolas; Gherardi, Nicolas

2017-05-01

Depending on the operating conditions, different regimes can be obtained in a dielectric barrier discharge (DBD): filamentary, diffuse (also called homogeneous) or self-organized. For a plane-to-plane DBD operated at high frequency (160 kHz) and at atmospheric pressure in helium gas, we show that the addition of a small amount of nitrogen induces a transition from the diffuse regime to a self-organized regime characterized by the appearance of filaments at the exit of the discharge. In this paper, we detail mechanisms that could be responsible of the transition from diffuse mode to this self-organized mode. We point out the critical role of the power supply and the importance of the gas memory effect from one discharge to the following one on the transition to the self-organised mode. The self-organized mode is usually attributed to a surface memory effect. In this work, we show an additional involvement of the gas memory effect on the self-organized mode. Contribution to the topical issue "The 15th International Symposium on High Pressure Low Temperature Plasma Chemistry (HAKONE XV)", edited by Nicolas Gherardi and Tomáš Hoder

Importance sampling large deviations in nonequilibrium steady states. I.

PubMed

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T

2018-03-28

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Ballistic phonon transport in holey silicon.

PubMed

Lee, Jaeho; Lim, Jongwoo; Yang, Peidong

2015-05-13

When the size of semiconductors is smaller than the phonon mean free path, phonons can carry heat with no internal scattering. Ballistic phonon transport has received attention for both theoretical and practical aspects because Fourier's law of heat conduction breaks down and the heat dissipation in nanoscale transistors becomes unpredictable in the ballistic regime. While recent experiments demonstrate room-temperature evidence of ballistic phonon transport in various nanomaterials, the thermal conductivity data for silicon in the length scale of 10-100 nm is still not available due to experimental challenges. Here we show ballistic phonon transport prevails in the cross-plane direction of holey silicon from 35 to 200 nm. The thermal conductivity scales linearly with the length (thickness) even though the lateral dimension (neck) is as narrow as 20 nm. We assess the impact of long-wavelength phonons and predict a transition from ballistic to diffusive regime using scaling models. Our results support strong persistence of long-wavelength phonons in nanostructures and are useful for controlling phonon transport for thermoelectrics and potential phononic applications.

Hydrogen migration modeling in a symmetric tilt boundary of the Iron-Chromium system

NASA Astrophysics Data System (ADS)

Ramunni, V. P.

2018-03-01

Previous experimental studies of H permeation in 9%Cr-Fe alloys have found a permeation coefficient 10 times lower and a diffusion coefficient 200 times lower than in pure annealed Fe. In an effort to shed some light on the microscopic origin of these findings, we perform an extensive study of Fe, Cr, and H migration in a high-angle symmetric tilt grain boundary in bcc Fe, both via vacancy and interstitial mechanism. This is undertaken in the framework of transition state theory with the relevant energies obtained from classical interatomic potentials, and partially from Density Functional Theory calculations, in order to check the consistency of structures. Trapping sites for H and possible migration paths are explored. We find that the presence of Cr and its migration via vacancy and interstitials creates the conditions in produce stable preferential trapping sites for H in the grain boundary, that delay the H migration, thereby explaining the experimental results.

Importance sampling large deviations in nonequilibrium steady states. I

NASA Astrophysics Data System (ADS)

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.

2018-03-01

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Some TEM observations of Al2O3 scales formed on NiCrAl alloys

NASA Technical Reports Server (NTRS)

Smialek, J.; Gibala, R.

1979-01-01

The microstructural development of Al2O3 scales on NiCrAl alloys has been examined by transmission electron microscopy. Voids were observed within grains in scales formed on a pure NiCrAl alloy. Both voids and oxide grains grew measurably with oxidation time at 1100 C. The size and amount of porosity decreased towards the oxide-metal growth interface. The voids resulted from an excess number of oxygen vacancies near the oxidemetal interface. Short-circuit diffusion paths were discussed in reference to current growth stress models for oxide scales. Transient oxidation of pure, Y-doped, and Zr-doped NiCrAl was also examined. Oriented alpha-(Al, Cr)2O3 and Ni(Al, Cr)2O4 scales often coexisted in layered structures on all three alloys. Close-packed oxygen planes and directions in the corundum and spinel layers were parallel. The close relationship between oxide layers provided a gradual transition from initial transient scales to steady state Al2O3 growth.

Minority carrier diffusion and defects in InGaAsN grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kurtz, Steven R.; Klem, J. F.; Allerman, A. A.; Sieg, R. M.; Seager, C. H.; Jones, E. D.

2002-02-01

To gain insight into the nitrogen-related defects of InGaAsN, nitrogen vibrational mode spectra, Hall mobilities, and minority carrier diffusion lengths are examined for InGaAsN (1.1 eV band gap) grown by molecular beam epitaxy (MBE). Annealing promotes the formation of In-N bonding, and lateral carrier transport is limited by large scale (≫mean free path) material inhomogeneities. Comparing solar cell quantum efficiencies with our earlier results for devices grown by metalorganic chemical vapor deposition (MOCVD), we find significant electron diffusion in the MBE material (reversed from the hole diffusion in MOCVD material), and minority carrier diffusion in InGaAsN cannot be explained by a "universal," nitrogen-related defect.

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

PubMed

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

2012-11-26

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

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

NASA Astrophysics Data System (ADS)

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

2007-05-01

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

Graph transformation method for calculating waiting times in Markov chains.

PubMed

Trygubenko, Semen A; Wales, David J

2006-06-21

We describe an exact approach for calculating transition probabilities and waiting times in finite-state discrete-time Markov processes. All the states and the rules for transitions between them must be known in advance. We can then calculate averages over a given ensemble of paths for both additive and multiplicative properties in a nonstochastic and noniterative fashion. In particular, we can calculate the mean first-passage time between arbitrary groups of stationary points for discrete path sampling databases, and hence extract phenomenological rate constants. We present a number of examples to demonstrate the efficiency and robustness of this approach.

Ultrafast electron crystallography of the cooperative reaction path in vanadium dioxide

PubMed Central

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

2016-01-01

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

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

USDA-ARS?s Scientific Manuscript database

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

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.

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

NASA Astrophysics Data System (ADS)

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

2008-06-01

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

Low carbon transition and sustainable development path of tourism industry

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

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

DOT National Transportation Integrated Search

2014-07-01

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

TIME-DOMAIN METHODS FOR DIFFUSIVE TRANSPORT IN SOFT MATTER

PubMed Central

Fricks, John; Yao, Lingxing; Elston, Timothy C.; Gregory Forest, And M.

2015-01-01

Passive microrheology [12] utilizes measurements of noisy, entropic fluctuations (i.e., diffusive properties) of micron-scale spheres in soft matter to infer bulk frequency-dependent loss and storage moduli. Here, we are concerned exclusively with diffusion of Brownian particles in viscoelastic media, for which the Mason-Weitz theoretical-experimental protocol is ideal, and the more challenging inference of bulk viscoelastic moduli is decoupled. The diffusive theory begins with a generalized Langevin equation (GLE) with a memory drag law specified by a kernel [7, 16, 22, 23]. We start with a discrete formulation of the GLE as an autoregressive stochastic process governing microbead paths measured by particle tracking. For the inverse problem (recovery of the memory kernel from experimental data) we apply time series analysis (maximum likelihood estimators via the Kalman filter) directly to bead position data, an alternative to formulas based on mean-squared displacement statistics in frequency space. For direct modeling, we present statistically exact GLE algorithms for individual particle paths as well as statistical correlations for displacement and velocity. Our time-domain methods rest upon a generalization of well-known results for a single-mode exponential kernel [1, 7, 22, 23] to an arbitrary M-mode exponential series, for which the GLE is transformed to a vector Ornstein-Uhlenbeck process. PMID:26412904

Effect of Isothermal Hold on the Microstructural Evolution of the Stainless Steel 304L/Zircaloy-4 Interface

NASA Astrophysics Data System (ADS)

Lebaili, A.; Taouinet, M.; Nibou, D.; Lebaili, S.; Hodaj, F.

2017-07-01

The transition from solid-state bonding of the stainless steel 304L/Zircaloy-4 diffusion couple to a partial liquid-phase bonding is important for the bonding process at temperatures ranging from 950 to 1050 °C. In this study, the temperature at which a melting process occurs at the interface after 45 min of isothermal holdings is determined experimentally. This melting process leads to a drastic change in the thickness of the reaction products zone (RPZ) as well as on its microstructure. Diffusion couples were characterized by SEM-EDS, and quantitative chemical analyses of different phases are performed by EPMA. The RPZ consists of three layers: the (α-Fe-Cr) phase layer and two layers consisting of Zr(Fe,Cr)2 (ɛ), Zr2(Fe,Ni) and (α-Zr) phases. The thickness of these layers strongly depends on the holding temperature. The analysis allowed the description of the physicochemical phenomena occurring during isothermal holding as well as during cooling. The solidification paths are determined at 1000, 1020 and 1050 °C. Hardness tests are performed on the bonded samples in order to qualify the mechanical properties of different phases of the RPZ. This study leads to a better understanding of the complex phenomena intervening in the joining process which is very useful for applications in industrial scale.

Engineering amorphous-crystalline interfaces in TiO2-x/TiO2-y-based bilayer structures for enhanced resistive switching and synaptic properties

NASA Astrophysics Data System (ADS)

Bousoulas, P.; Asenov, P.; Karageorgiou, I.; Sakellaropoulos, D.; Stathopoulos, S.; Tsoukalas, D.

2016-10-01

The operating principle of resistive random access memories (RRAMs) relies on the distribution of ionic species and their influence on the electron transport. Taking into account that formation and annihilation of conducting filaments (CFs) is the driving mechanism for the switching effect, it is very important to control the regions where these filaments will evolve. Thus, homolayers of titanium oxide with different oxygen contents were fabricated in order to tune the local electrical and thermal properties of the CFs and narrow down the potential percolation paths. We show that the oxygen content in the top layer of the TiO2-x/TiO2-y bilayer memristors can directly influence the morphology of the layers which affect the diffusion barrier and consequently the diffusivity and drift velocity of oxygen vacancies, yielding in important enhancement of switching characteristics, in terms of spatial uniformity (σ/μ < 0.2), enlarged switching ratio (˜104), and synaptic learning. In order to address the experimental data, a physical model was applied, divulging the crucial role of temperature, electric potential and oxygen vacancy density on the switching effect and offering physical insights to the SET/RESET transitions and the analog switching. The forming free nature of all the devices in conjunction with the self-rectifying behavior, should also be regarded as important assets towards RRAM device optimization.

Pedestrian paths: why path-dependence theory leaves health policy analysis lost in space.

PubMed

Brown, Lawrence D

2010-08-01

Path dependence, a model first advanced to explain puzzles in the diffusion of technology, has lately won allegiance among analysts of the politics of public policy, including health care policy. Though the central premise of the model--that past events and decisions shape options for innovation in the present and future--is indisputable (indeed path dependence is, so to speak, too shallow to be false), the approach, at least as applied to health policy, suffers from ambiguities that undercut its claims to illuminate policy projects such as managed care, on which this article focuses. Because path dependence adds little more than marginal value to familiar images of the politics of policy--incrementalism, for one--analysts might do well to put it on the back burner and pursue instead "thick descriptions" that help them to distinguish different degrees of openness to exogenous change among diverse policy arenas.

Vacancies in MgO at ultrahigh pressure: About mantle rheology of super-Earths

NASA Astrophysics Data System (ADS)

Ritterbex, Sebastian; Harada, Takafumi; Tsuchiya, Taku

2018-05-01

First-principles calculations are performed to investigate vacancy formation and migration in the B2 phase of MgO. Defect energetics suggest the importance of intrinsic non-interacting vacancy pairs, even though the extrinsic vacancy concentration might govern atomic diffusion in the B2 phase of MgO. The enthalpies of ionic vacancy migration are generally found to decrease across the B1-B2 phase transition around a pressure of 500 GPa. It is shown that this enthalpy change induces a substantial increase in the rate of vacancy diffusion in MgO of almost four orders of magnitude (∼104) when the B1 phase transforms into the B2 phase with increasing pressure. If plastic deformation is controlled by vacancy diffusion, mantle viscosity is expected to decrease in relation to this enhanced diffusion rate in MgO across the B1-B2 transition in the interior of Earth-like large exoplanets. Our results of atomic relaxations near the defects suggest that diffusion controlled creep viscosity may generally decrease across high-pressure phase transitions with increasing coordination number. Plastic flow and resulting mantle convection in the interior of these super-Earths may be therefore less sluggish than previously thought.

Pretransitional diffuse neutron scattering in the mixed perovskite relaxor K1-xLixTaO3

NASA Astrophysics Data System (ADS)

Yong, Grace; Toulouse, Jean; Erwin, Ross; Shapiro, Stephen M.; Hennion, Bernard

2000-12-01

Several previous studies of K1-xLixTaO3 (KLT) have revealed the presence, above the structural transition, of polar nanoregions. Recently, these have been shown to play an essential role in the relaxor behavior of KLT. In order to characterize these regions, we have performed a neutron-scattering study of KLT crystals with different lithium concentrations, both above and below the critical concentration. This study reveals the existence of diffuse scattering that appears upon formation of these regions. The rodlike distribution of the diffuse scattering along cubic directions indicates that the regions form in the shape of discs in the various cubic planes. From the width of the diffuse scattering we extract values for a correlation length or size of the regions as a function of temperature. Finally, on the basis of the reciprocal lattice points around which the diffuse scattering is most intense, we conclude that the regions have tetragonal symmetry. The large increase in Bragg intensities at the first-order transition suggests that the polar regions freeze to form large structural domains and the transition is triggered by the percolation of strain fields through the crystals.

Nonequilibrium transition and pattern formation in a linear reaction-diffusion system with self-regulated kinetics

NASA Astrophysics Data System (ADS)

Paul, Shibashis; Ghosh, Shyamolina; Ray, Deb Shankar

2018-02-01

We consider a reaction-diffusion system with linear, stochastic activator-inhibitor kinetics where the time evolution of concentration of a species at any spatial location depends on the relative average concentration of its neighbors. This self-regulating nature of kinetics brings in spatial correlation between the activator and the inhibitor. An interplay of this correlation in kinetics and disparity of diffusivities of the two species leads to symmetry breaking non-equilibrium transition resulting in stationary pattern formation. The role of initial noise strength and the linear reaction terms has been analyzed for pattern selection.

Cortico-Cortical, Cortico-Striatal, and Cortico-Thalamic White Matter Fiber Tracts Generated in the Macaque Brain via Dynamic Programming

PubMed Central

Lal, Rakesh M.; An, Michael; Poynton, Clare B.; Li, Muwei; Jiang, Hangyi; Oishi, Kenichi; Selemon, Lynn D.; Mori, Susumu; Miller, Michael I.

2013-01-01

Abstract Probabilistic methods have the potential to generate multiple and complex white matter fiber tracts in diffusion tensor imaging (DTI). Here, a method based on dynamic programming (DP) is introduced to reconstruct fibers pathways whose complex anatomical structures cannot be resolved beyond the resolution of standard DTI data. DP is based on optimizing a sequentially additive cost function derived from a Gaussian diffusion model whose covariance is defined by the diffusion tensor. DP is used to determine the optimal path between initial and terminal nodes by efficiently searching over all paths, connecting the nodes, and choosing the path in which the total probability is maximized. An ex vivo high-resolution scan of a macaque hemi-brain is used to demonstrate the advantages and limitations of DP. DP can generate fiber bundles between distant cortical areas (superior longitudinal fasciculi, arcuate fasciculus, uncinate fasciculus, and fronto-occipital fasciculus), neighboring cortical areas (dorsal and ventral banks of the principal sulcus), as well as cortical projections to the hippocampal formation (cingulum bundle), neostriatum (motor cortical projections to the putamen), thalamus (subcortical bundle), and hippocampal formation projections to the mammillary bodies via the fornix. Validation is established either by comparison with in vivo intracellular transport of horseradish peroxidase in another macaque monkey or by comparison with atlases. DP is able to generate known pathways, including crossing and kissing tracts. Thus, DP has the potential to enhance neuroimaging studies of cortical connectivity. PMID:23879573

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.

Stochastic Cell Fate Progression in Embryonic Stem Cells

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Photon diffusion coefficient in scattering and absorbing media.

PubMed

Pierrat, Romain; Greffet, Jean-Jacques; Carminati, Rémi

2006-05-01

We present a unified derivation of the photon diffusion coefficient for both steady-state and time-dependent transport in disordered absorbing media. The derivation is based on a modal analysis of the time-dependent radiative transfer equation. This approach confirms that the dynamic diffusion coefficient is given by the random-walk result D = cl(*)/3, where l(*) is the transport mean free path and c is the energy velocity, independent of the level of absorption. It also shows that the diffusion coefficient for steady-state transport, often used in biomedical optics, depends on absorption, in agreement with recent theoretical and experimental works. These two results resolve a recurrent controversy in light propagation and imaging in scattering media.

Using selection bias to explain the observed structure of Internet diffusions

PubMed Central

Golub, Benjamin; Jackson, Matthew O.

2010-01-01

Recently, large datasets stored on the Internet have enabled the analysis of processes, such as large-scale diffusions of information, at new levels of detail. In a recent study, Liben-Nowell and Kleinberg [(2008) Proc Natl Acad Sci USA 105:4633–4638] observed that the flow of information on the Internet exhibits surprising patterns whereby a chain letter reaches its typical recipient through long paths of hundreds of intermediaries. We show that a basic Galton–Watson epidemic model combined with the selection bias of observing only large diffusions suffices to explain these patterns. Thus, selection biases of which data we observe can radically change the estimation of classical diffusion processes. PMID:20534439

Transition Specialists Partner with Students to Turn Dreams into Reality

ERIC Educational Resources Information Center

Flannery, Ann

2013-01-01

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

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

ERIC Educational Resources Information Center

Tchalakov, Ivan; Mitev, Tihomir; Petrov, Venelin

2010-01-01

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

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

ERIC Educational Resources Information Center

Lyons, Guy Kevin

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

Kiyokawa, Shuji

2018-05-01

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

Comparison of active-set method deconvolution and matched-filtering for derivation of an ultrasound transit time spectrum.

PubMed

Wille, M-L; Zapf, M; Ruiter, N V; Gemmeke, H; Langton, C M

2015-06-21

The quality of ultrasound computed tomography imaging is primarily determined by the accuracy of ultrasound transit time measurement. A major problem in analysis is the overlap of signals making it difficult to detect the correct transit time. The current standard is to apply a matched-filtering approach to the input and output signals. This study compares the matched-filtering technique with active set deconvolution to derive a transit time spectrum from a coded excitation chirp signal and the measured output signal. The ultrasound wave travels in a direct and a reflected path to the receiver, resulting in an overlap in the recorded output signal. The matched-filtering and deconvolution techniques were applied to determine the transit times associated with the two signal paths. Both techniques were able to detect the two different transit times; while matched-filtering has a better accuracy (0.13 μs versus 0.18 μs standard deviations), deconvolution has a 3.5 times improved side-lobe to main-lobe ratio. A higher side-lobe suppression is important to further improve image fidelity. These results suggest that a future combination of both techniques would provide improved signal detection and hence improved image fidelity.

AgCl precipitates in isolated cuticular membranes reduce rates of cuticular transpiration.

PubMed

Schreiber, Lukas; Elshatshat, Salem; Koch, Kerstin; Lin, Jinxing; Santrucek, Jiri

2006-01-01

Counter diffusion of chloride, applied as NaCl at the inner side of isolated cuticles, and silver, applied as AgNO(3) at the outer side, lead to the formation of insoluble AgCl precipitates in isolated cuticles. AgCl precipitates could be visualized by light and scanning electron microscopy. The presence of AgCl precipitates in isolated cuticles was verified by energy dispersive X-ray analysis. It is argued that insoluble AgCl precipitates formed in polar pores of cuticles and as a consequence, cuticular transpiration of 13 out of 15 investigated species was significantly reduced up to three-fold. Water as a small and uncharged but polar molecule penetrates cuticles via two parallel paths: a lipophilic path, formed by lipophilic cutin and wax domains, and a aqueous pathe, formed by polar pores. Thus, permeances P (m s(-1)) of water, which is composed of the two quantities P (Lipid) and P (Pore), decreased, since water transport across polar pores was affected by AgCl precipitates. Cuticles with initially high rates of cuticular transpiration were generally more sensitive towards AgCl precipitates compared to cuticles with initially low rates of transpiration. Results presented here, significantly improves the current model of the structure of the cuticular transpiration barrier, since the pronounced heterogeneity of the cuticular transport barrier, composed of lipophilic as well as polar paths of diffusion, has to be taken into account in future.

Diffusion, subdiffusion, and localization of active colloids in random post lattices

NASA Astrophysics Data System (ADS)

Morin, Alexandre; Lopes Cardozo, David; Chikkadi, Vijayakumar; Bartolo, Denis

2017-10-01

Combining experiments and theory, we address the dynamics of self-propelled particles in crowded environments. We first demonstrate that motile colloids cruising at constant speed through random lattices undergo a smooth transition from diffusive to subdiffusive to localized dynamics upon increasing the obstacle density. We then elucidate the nature of these transitions by performing extensive simulations constructed from a detailed analysis of the colloid-obstacle interactions. We evidence that repulsion at a distance and hard-core interactions both contribute to slowing down the long-time diffusion of the colloids. In contrast, the localization transition stems solely from excluded-volume interactions and occurs at the void-percolation threshold. Within this critical scenario, equivalent to that of the random Lorentz gas, genuine asymptotic subdiffusion is found only at the critical density where the motile particles explore a fractal maze.

Reactions between palladium and gallium arsenide: Bulk versus thin-film studies

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

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

1988-01-01

Reactions between Pd and GaAs have been studied using bulk-diffusion couples of Pd (approx.0.6 mm thick)/GaAs and thin-film Pd (50 and 160 nm)/GaAs samples. The sequence of phase formation at 600 /sup 0/C between bulk Pd and GaAs was established. Initial formation of the solution phase ..mu.. and the ternary phase T does not represent the stable configuration. The stable configuration is GaAs chemically bondepsilonchemically bondlambdachemically bond..gamma..chemically bond..nu..chemically bondPd and is termed the diffusion path between GaAs and Pd. The sequence of phase formation for the bulk-diffusion couples is similar at 500 /sup 0/C. Phase formation for the thin-film Pd/GaAsmore » specimens was studied at 180, 220, 250, 300, 350, 400, 450, 600, and 1000 /sup 0/C for various annealing times. The sequence of phase formation obtained from the thin-film experiments is rationalized readily from the known ternary phase equilibria of Ga--Pd--As and the results from the bulk-diffusion couples of Pd/GaAs. The thin-film results reported in the literature are likewise rationalized. The diffusion path concept provides a useful guide in understanding the phase formation in Pd--GaAs interface or any other M--GaAs interface. This information is important in designing a uniform, stable contact for the metallization of GaAs.« less

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

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

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 the magnetism of impurities on their diffusion in metals: Bulk diffusion of iron, cobalt, and rhodium in iridium single crystals

NASA Astrophysics Data System (ADS)

Klotsman, S. M.; Tatarinova, G. N.

2008-12-01

The coefficients and parameters of the temperature dependences of the coefficients of bulk diffusion of Fe, Co, Rh, and Au atomic probes (APs) in iridium single crystals (mono-Ir) have been determined from the diffusion profiles obtained using secondary-ion mass spectrometry of the diffusion zones. The enthalpies of activation of diffusion of Fe, Co, and Rh APs are considerably lower than the enthalpy of activation of selfdiffusion in mono-Ir. This is caused by the negative contributions of the intraatomic exchange energy and energy of relaxation of the environment of the d transition APs to the enthalpy of interaction of magnetically active APs with the vacancies in the iridium lattice. The interaction energy of partners in such complexes and the relationships between the magnetic moments of d transition APs in complexes with vacancies have been estimated. The Rh APs in complexes with vacancies in iridium possess stable magnetic moments.

Diffusion of Brownian particles in a tilted periodic potential under the influence of an external Ornstein-Uhlenbeck noise

NASA Astrophysics Data System (ADS)

Bai, Zhan-Wu; Zhang, Wei

2018-01-01

The diffusion behaviors of Brownian particles in a tilted periodic potential under the influence of an internal white noise and an external Ornstein-Uhlenbeck noise are investigated through numerical simulation. In contrast to the case when the bias force is smaller or absent, the diffusion coefficient exhibits a nonmonotonic dependence on the correlation time of the external noise when bias force is large. A mechanism different from locked-to-running transition theory is presented for the diffusion enhancement by a bias force in intermediate to large damping. In the underdamped regime and the presence of external noise, the diffusion coefficient is a monotonically decreasing function of low temperature rather than a nonmonotonic function when external noise is absent. The diffusive process undergoes four regimes when bias force approaches but is less than its critical value and noises intensities are small. These behaviors can be attributed to the locked-to-running transition of particles.

A Non-Abelian Geometric Phase for Spin Systems

NASA Astrophysics Data System (ADS)

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

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

PubMed

Takayanagi, Toshiyuki; Nakatomi, Taiki; Yonetani, Yoshiteru

2018-04-20

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

Dynamic Switching of Helical Microgel Ribbons.

PubMed

Zhang, Hang; Mourran, Ahmed; Möller, Martin

2017-03-08

We report on a microscopic poly(N-isopropylacrylamide) hydrogel ribbon, coated by a thin gold layer, that shows helical coiling. Confined swelling and shrinkage of the hydrogel below and above its characteristic volume phase transition leads to a temperature actuated reversal of the sense of the helix. The extent and the shape of the winding are controlled by the dimensions and mechanical properties of the bilayer ribbon. We focus on a cylindrical helix geometry and monitor the morphing under equilibrium and nonequilibrium conditions, that is, when the temperature changes faster than the volume (millisecond range). For slow temperature variations, the water release and uptake follow the equilibrium transition trajectory determined by the time needed for the diffusion of water into and out of the microscopic gel. Much faster variations of the temperature are accomplished by internal heating of embedded gold nanorods by IR-light irradiation. This causes elastic stresses that strongly affect the motions. This method enables well-reproducible deviations from the equilibrium transition path and allows us to control rather precisely the spatiotemporal transformation in a cyclic repetitive process. Actuation and response are sensitive to small variations of temperature and composition of the aqueous sol in which the gel is immersed. The principle as described may be used to detect specific analytes that bind either to the surface of the gold layer or within the gel and can modify the interaction between the water and the gel. The reported nonequilibrium morphing implies that the system dissipates energy and may also be able to perform work as required for a microscopic motor.

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

NCI study offers genetic insights into common lymphoma

Cancer.gov

An NCI study identifies genetic subtypes of diffuse large B-cell lymphoma (DLBCL), helping explain why only some patients with this most common lymphoma respond to treatment, and offering a path toward targeted therapies.

Flow and fracturing of viscoelastic media under diffusion-driven bubble growth: An analogue experiment for eruptive volcanic conduits

NASA Astrophysics Data System (ADS)

Taddeucci, J.; Spieler, O.; Ichihara, M.; Dingwell, D. B.; Scarlato, P.

2006-03-01

To visualize the behavior of erupting magma in volcanic conduits, we performed shock tube experiments on the ductile-brittle response of a viscoelastic medium to diffusion-driven bubble expansion. A sample of shear-thinning magma analogue is saturated by gas Ar under high pressure. On rapid decompression, Ar supersaturation causes bubbles to nucleate, grow, and coalesce in the sample, forcing it to expand, flow, and fracture. Experimental variables include saturation pressure and duration, and shape and lubrication of the flow path. Bubble growth in the experiments controls both flow and fracturing, and is consistent with physical models of magma vesiculation. Two types of fractures are observed: i) sharp fractures along the uppermost rim of the sample, and ii) fractures pervasively diffused throughout the sample. Rim fractures open when shear stress accumulates and strain rate is highest at the margin of the flow (a process already inferred from observations and models to occur in magma). Pervasive fractures originate when wall-friction retards expansion of the sample, causing pressure to build-up in the bubbles. When bubble pressure overcomes wall-friction and the tensile strength of the porous sample, fractures open with a range of morphologies. Both types of fracture open normally to flow direction, and both may heal as the flow proceeds. These experiments also illustrate how the development of pervasive fractures allows exsolving gas to escape from the sample before the generation of a permeable network via other processes, e.g., bubble coalescence. This is an observation that potentially impact the degassing of magma and the transition between explosive and effusive eruptions.

Disorder-induced transition from grain boundary to bulk dominated ionic diffusion in pyrochlores

DOE PAGES

Perriot, Romain; Dholabhai, Pratik P.; Uberuaga, Blas P.

2017-05-04

In this paper, we use molecular dynamics simulations to investigate the role of grain boundaries (GBs) on ionic diffusion in pyrochlores, as a function of the GB type, chemistry of the compound, and level of cation disorder. We observe that the presence of GBs promotes oxygen transport in ordered and low-disordered systems, as the GBs are found to have a higher concentration of mobile carriers with higher mobilities than in the bulk. Thus, in ordered samples, the ionic diffusion is 2D, localized along the grain boundary. When cation disorder is introduced, bulk carriers begin to contribute to the overall diffusion,more » while the GB contribution is only slightly enhanced. In highly disordered samples, the diffusive behavior at the GBs is bulk-like, and the two contributions (bulk vs. GB) can no longer be distinguished. There is thus a transition from 2D/GB dominated oxygen diffusivity to 3D/bulk dominated diffusivity versus disorder in pyrochlores. Finally, these results provide new insights into the possibility of using internal interfaces to enhance ionic conductivity in nanostructured complex oxides.« less

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

A helium-based model for the effects of radiation damage annealing on helium diffusion kinetics in apatite

NASA Astrophysics Data System (ADS)

Willett, Chelsea D.; Fox, Matthew; Shuster, David L.

2017-11-01

Widely used to study surface processes and the development of topography through geologic time, (U-Th)/He thermochronometry in apatite depends on a quantitative description of the kinetics of 4He diffusion across a range of temperatures, timescales, and geologic scenarios. Empirical observations demonstrate that He diffusivity in apatite is not solely a function of temperature, but also depends on damage to the crystal structure from radioactive decay processes. Commonly-used models accounting for the influence of thermal annealing of radiation damage on He diffusivity assume the net effects evolve in proportion to the rate of fission track annealing, although the majority of radiation damage results from α-recoil. While existing models adequately quantify the net effects of damage annealing in many geologic scenarios, experimental work suggests different annealing rates for the two damage types. Here, we introduce an alpha-damage annealing model (ADAM) that is independent of fission track annealing kinetics, and directly quantifies the influence of thermal annealing on He diffusivity in apatite. We present an empirical fit to diffusion kinetics data and incorporate this fit into a model that tracks the competing effects of radiation damage accumulation and annealing on He diffusivity in apatite through geologic time. Using time-temperature paths to illustrate differences between models, we highlight the influence of damage annealing on data interpretation. In certain, but not all, geologic scenarios, the interpretation of low-temperature thermochronometric data can be strongly influenced by which model of radiation damage annealing is assumed. In particular, geologic scenarios involving 1-2 km of sedimentary burial are especially sensitive to the assumed rate of annealing and its influence on He diffusivity. In cases such as basement rocks in Grand Canyon and the Canadian Shield, (U-Th)/He ages predicted from the ADAM can differ by hundreds of Ma from those predicted by other models for a given thermal path involving extended residence between ∼40-80 °C.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Unveiling the chemistry of interstellar CH. Spectroscopy of the 2 THz N = 2 ← 1 ground state line

NASA Astrophysics Data System (ADS)

Wiesemeyer, H.; Güsten, R.; Menten, K. M.; Durán, C. A.; Csengeri, T.; Jacob, A. M.; Simon, R.; Stutzki, J.; Wyrowski, F.

2018-04-01

Context. The methylidyne radical CH is commonly used as a proxy for molecular hydrogen in the cold, neutral phase of the interstellar medium. The optical spectroscopy of CH is limited by interstellar extinction, whereas far-infrared observations provide an integral view through the Galaxy. While the HF ground state absorption, another H2 proxy in diffuse gas, frequently suffers from saturation, CH remains transparent both in spiral-arm crossings and high-mass star forming regions, turning this light hydride into a universal surrogate for H2. However, in slow shocks and in regions dissipating turbulence its abundance is expected to be enhanced by an endothermic production path, and the idea of a "canonical" CH abundance needs to be addressed. Aim. The N = 2 ← 1 ground state transition of CH at λ149 μm has become accessible to high-resolution spectroscopy thanks to the German Receiver for Astronomy at Terahertz Frequencies (GREAT) aboard the Stratospheric Observatory for Infrared Astronomy (SOFIA). Its unsaturated absorption and the absence of emission from the star forming regions makes it an ideal candidate for the determination of column densities with a minimum of assumptions. Here we present an analysis of four sightlines towards distant Galactic star forming regions, whose hot cores emit a strong far-infrared dust continuum serving as background signal. Moreover, if combined with the sub-millimeter line of CH at λ560 μm , environments forming massive stars can be analyzed. For this we present a case study on the "proto-Trapezium" cluster W3 IRS5. Methods: While we confirm the global correlation between the column densities of HF and those of CH, both in arm and interarm regions, clear signposts of an over-abundance of CH are observed towards lower densities. However, a significant correlation between the column densities of CH and HF remains. A characterization of the hot cores in the W3 IRS5 proto-cluster and its envelope demonstrates that the sub-millimeter/far-infrared lines of CH reliably trace not only diffuse but also dense, molecular gas. Results: In diffuse gas, at lower densities a quiescent ion-neutral chemistry alone cannot account for the observed abundance of CH. Unlike the production of HF, for CH+ and CH, vortices forming in turbulent, diffuse gas may be the setting for an enhanced production path. However, CH remains a valuable tracer for molecular gas in environments reaching from diffuse clouds to sites of high-mass star formation. The reduced spectra (Fig. 2) are only and Table 2 is also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/612/A37

Diffusion Monte Carlo approach versus adiabatic computation for local Hamiltonians

NASA Astrophysics Data System (ADS)

Bringewatt, Jacob; Dorland, William; Jordan, Stephen P.; Mink, Alan

2018-02-01

Most research regarding quantum adiabatic optimization has focused on stoquastic Hamiltonians, whose ground states can be expressed with only real non-negative amplitudes and thus for whom destructive interference is not manifest. This raises the question of whether classical Monte Carlo algorithms can efficiently simulate quantum adiabatic optimization with stoquastic Hamiltonians. Recent results have given counterexamples in which path-integral and diffusion Monte Carlo fail to do so. However, most adiabatic optimization algorithms, such as for solving MAX-k -SAT problems, use k -local Hamiltonians, whereas our previous counterexample for diffusion Monte Carlo involved n -body interactions. Here we present a 6-local counterexample which demonstrates that even for these local Hamiltonians there are cases where diffusion Monte Carlo cannot efficiently simulate quantum adiabatic optimization. Furthermore, we perform empirical testing of diffusion Monte Carlo on a standard well-studied class of permutation-symmetric tunneling problems and similarly find large advantages for quantum optimization over diffusion Monte Carlo.

Dislocation-pipe diffusion in nitride superlattices observed in direct atomic resolution.

PubMed

Garbrecht, Magnus; Saha, Bivas; Schroeder, Jeremy L; Hultman, Lars; Sands, Timothy D

2017-04-06

Device failure from diffusion short circuits in microelectronic components occurs via thermally induced migration of atoms along high-diffusivity paths: dislocations, grain boundaries, and free surfaces. Even well-annealed single-grain metallic films contain dislocation densities of about 10 14  m -2 ; hence dislocation-pipe diffusion (DPD) becomes a major contribution at working temperatures. While its theoretical concept was established already in the 1950s and its contribution is commonly measured using indirect tracer, spectroscopy, or electrical methods, no direct observation of DPD at the atomic level has been reported. We present atomically-resolved electron microscopy images of the onset and progression of diffusion along threading dislocations in sequentially annealed nitride metal/semiconductor superlattices, and show that this type of diffusion can be independent of concentration gradients in the system but governed by the reduction of strain fields in the lattice.

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

PubMed

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

2016-01-01

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

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

PubMed

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

2012-08-01

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

Random-walk diffusion and drying of porous materials

NASA Astrophysics Data System (ADS)

Mehrafarin, M.; Faghihi, M.

2001-12-01

Based on random-walk diffusion, a microscopic model for drying is proposed to explain the characteristic features of the drying-rate curve of porous materials. The constant drying-rate period is considered as a normal diffusion process. The transition to the falling-rate regime is attributed to the fractal nature of porous materials which results in crossover to anomalous diffusion.

Compact structure and non-Gaussian dynamics of ring polymer melts.

PubMed

Brás, Ana R; Goossen, Sebastian; Krutyeva, Margarita; Radulescu, Aurel; Farago, Bela; Allgaier, Jürgen; Pyckhout-Hintzen, Wim; Wischnewski, Andreas; Richter, Dieter

2014-05-28

We present a neutron scattering analysis of the structure and dynamics of PEO polymer rings with a molecular weight 2.5 times higher than the entanglement mass. The melt structure was found to be more compact than a Gaussian model would suggest. With increasing time the center of mass (c.o.m.) diffusion undergoes a transition from sub-diffusive to diffusive behavior. The transition time agrees well with the decorrelation time predicted by a mode coupling approach. As a novel feature well pronounced non-Gaussian behavior of the c.o.m. diffusion was found that shows surprising analogies to the cage effect known from glassy systems. Finally, the longest wavelength Rouse modes are suppressed possibly as a consequence of an onset of lattice animal features as hypothesized in theoretical approaches.

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

ERIC Educational Resources Information Center

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

2002-01-01

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

The Bulgarian Academic Profession in Transition.

ERIC Educational Resources Information Center

Slantcheva, Snejana

2003-01-01

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

Global diffusive fluxes of methane in marine sediments

NASA Astrophysics Data System (ADS)

Egger, Matthias; Riedinger, Natascha; Mogollón, José M.; Jørgensen, Bo Barker

2018-06-01

Anaerobic oxidation of methane provides a globally important, yet poorly constrained barrier for the vast amounts of methane produced in the subseafloor. Here we provide a global map and budget of the methane flux and degradation in diffusion-controlled marine sediments in relation to the depth of the methane oxidation barrier. Our new budget suggests that 45-61 Tg of methane are oxidized with sulfate annually, with approximately 80% of this oxidation occurring in continental shelf sediments (<200 m water depth). Using anaerobic oxidation as a nearly quantitative sink for methane in steady-state diffusive sediments, we calculate that 3-4% of the global organic carbon flux to the seafloor is converted to methane. We further report a global imbalance of diffusive methane and sulfate fluxes into the sulfate-methane transition with no clear trend with respect to the corresponding depth of the methane oxidation barrier. The observed global mean net flux ratio between sulfate and methane of 1.4:1 indicates that, on average, the methane flux to the sulfate-methane transition accounts for only 70% of the sulfate consumption in the sulfate-methane transition zone of marine sediments.

Exact representation of the asymptotic drift speed and diffusion matrix for a class of velocity-jump processes

NASA Astrophysics Data System (ADS)

Mascia, Corrado

2016-01-01

This paper examines a class of linear hyperbolic systems which generalizes the Goldstein-Kac model to an arbitrary finite number of speeds vi with transition rates μij. Under the basic assumptions that the transition matrix is symmetric and irreducible, and the differences vi -vj generate all the space, the system exhibits a large-time behavior described by a parabolic advection-diffusion equation. The main contribution is to determine explicit formulas for the asymptotic drift speed and diffusion matrix in term of the kinetic parameters vi and μij, establishing a complete connection between microscopic and macroscopic coefficients. It is shown that the drift speed is the arithmetic mean of the velocities vi. The diffusion matrix has a more complicate representation, based on the graph with vertices the velocities vi and arcs weighted by the transition rates μij. The approach is based on an exhaustive analysis of the dispersion relation and on the application of a variant of the Kirchoff's matrix tree Theorem from graph theory.

Thermophysical properties and oxygen transport in (Th x,Pu 1-x)O 2

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

Galvin, C. O. T.; Cooper, M. W. D.; Rushton, M. J. D.

Using Molecular Dynamics, this paper investigates the thermophysical properties and oxygen transport of (Th x,Pu 1–x)O 2 (0 ≤ x ≤ 1) between 300–3500 K. Specifically, the superionic transition is investigated and viewed via the thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure. Oxygen diffusivity and activation enthalpy are also investigated. Below the superionic temperature an increase of oxygen diffusivity for certain compositions of (Th x,Pu 1–x)O 2 compared to the pure end members is predicted. Oxygen defect formation enthalpies are also examined, as they underpin the superionic transition temperature and themore » increase in oxygen diffusivity. The increase in oxygen diffusivity for (Th x,Pu 1–x)O 2 is explained in terms of lower oxygen defect formation enthalpies for (Th x,Pu 1–x)O 2 than PuO 2 and ThO 2, while links are drawn between the superionic transition temperature and oxygen Frenkel disorder.« less

Thermophysical properties and oxygen transport in (Th x,Pu 1-x)O 2

DOE PAGES

Galvin, C. O. T.; Cooper, M. W. D.; Rushton, M. J. D.; ...

2016-10-31

Using Molecular Dynamics, this paper investigates the thermophysical properties and oxygen transport of (Th x,Pu 1–x)O 2 (0 ≤ x ≤ 1) between 300–3500 K. Specifically, the superionic transition is investigated and viewed via the thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure. Oxygen diffusivity and activation enthalpy are also investigated. Below the superionic temperature an increase of oxygen diffusivity for certain compositions of (Th x,Pu 1–x)O 2 compared to the pure end members is predicted. Oxygen defect formation enthalpies are also examined, as they underpin the superionic transition temperature and themore » increase in oxygen diffusivity. The increase in oxygen diffusivity for (Th x,Pu 1–x)O 2 is explained in terms of lower oxygen defect formation enthalpies for (Th x,Pu 1–x)O 2 than PuO 2 and ThO 2, while links are drawn between the superionic transition temperature and oxygen Frenkel disorder.« less

A Hot-electron Direct Detector for Radioastronomy

NASA Technical Reports Server (NTRS)

Karasik, B. S.; McGrath, W. R.; LeDuc, H. G.

2000-01-01

A new approach is proposed to improve the sensitivity of direct-detection bolometers. The idea is to adjust a speed of the thermal relaxation of hot-electrons in a nanometer size normal metal or superconductive transition edge bolometer by controlling the elastic electron mean free path. If the bolometer contacts are made of a superconductor with high critical temperature then the thermal diffusion into the contacts is absent because of the Andreev's reflection and the electron-phonon relaxation is the only mechanism for heat removal. The relaxation rate should behave as 7(exp 4)l at subkelvin temperatures (l is the electron elastic mean free path) and can be reduced by factor of 10 - 100 by decreasing l. Then an antenna- or waveguide-coupled bolometer with a time constant approx. 10(exp -3) to 10(exp -5) S at T approx. = 0.1 - 0.3 K will exhibit photon-noise limited performance in millimeter and subn-millimeter range. The bolometer will have a figure-of-merit NEk square root of tau approx. = 10(exp -22) 10(exp -21) W/Hz at 100 mK which is 10(exp 3) times smaller than that of a state-of-the-art bolometer. This will allow for a tremendous increase in speed which will have a significant impact for observational mapping applications. Alternatively, the bolometer could operate at higher temperature with still superior sensitivity This research was performed by the Center for Space Microelectronics Technology, JPL, California Institute of Technology, under the contract for NASA.

A Tomographic Method for the Reconstruction of Local Probability Density Functions

NASA Technical Reports Server (NTRS)

Sivathanu, Y. R.; Gore, J. P.

1993-01-01

A method of obtaining the probability density function (PDF) of local properties from path integrated measurements is described. The approach uses a discrete probability function (DPF) method to infer the PDF of the local extinction coefficient from measurements of the PDFs of the path integrated transmittance. The local PDFs obtained using the method are compared with those obtained from direct intrusive measurements in propylene/air and ethylene/air diffusion flames. The results of this comparison are good.

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

Causal Diffusion and the Survival of Charge Fluctuations

NASA Astrophysics Data System (ADS)

Abdel-Aziz, Mohamed; Gavin, Sean

2004-10-01

Diffusion may obliterate fluctuation signals of the QCD phase transition in nuclear collisions at SPS and RHIC energies. We propose a hyperbolic diffusion equation to study the dissipation of net charge fluctuations [1]. This equation is needed in a relativistic context, because the classic parabolic diffusion equation violates causality. We find that causality substantially limits the extent to which diffusion can dissipate these fluctuations. [1] M. Abdel-Aziz and S. Gavin, nucl-th/0404058

Transformers: the changing phases of low-dimensional vanadium oxide bronzes.

PubMed

Marley, Peter M; Horrocks, Gregory A; Pelcher, Kate E; Banerjee, Sarbajit

2015-03-28

In this feature article, we explore the electronic and structural phase transformations of ternary vanadium oxides with the composition MxV2O5 where M is an intercalated cation. The periodic arrays of intercalated cations ordered along quasi-1D tunnels or layered between 2D sheets of the V2O5 framework induce partial reduction of the framework vanadium atoms giving rise to charge ordering patterns that are specific to the metal M and stoichiometry x. This periodic charge ordering makes these materials remarkably versatile platforms for studying electron correlation and underpins the manifestation of phenomena such as colossal metal-insulator transitions, quantized charge corrals, and superconductivity. We describe current mechanistic understanding of these emergent phenomena with a particular emphasis on the benefits derived from scaling these materials to nanostructured dimensions wherein precise ordering of cations can be obtained and phase relationships can be derived that are entirely inaccessible in the bulk. In particular, structural transformations induced by intercalation are dramatically accelerated due to the shorter diffusion path lengths at nanometer-sized dimensions, which cause a dramatic reduction of kinetic barriers to phase transformations and facilitate interconversion between the different frameworks. We conclude by summarizing numerous technological applications that have become feasible due to recent advances in controlling the structural chemistry and both electronic and structural phase transitions in these versatile frameworks.

Photopyroelectric Calorimetry Investigations of 8CB Liquid Crystal-Microemulsion System

NASA Astrophysics Data System (ADS)

Paoloni, S.; Zammit, U.; Mercuri, F.

2018-02-01

In this work, the photopyroelectric technique has been used to investigate the phase transitions in a liquid crystal microemulsion by combining the simultaneous high temperature resolution thermal diffusivity measurements and optical polarization microscopy observations. It has been found that, during the conversion from the isotropic phase into the nematic one, the micelles are expelled from the nematic domains and remain confined in islands of isotropic material which survive down to the smectic temperature range. A hysteresis in the thermal diffusivity profiles between heating and cooling run over the isotropic-nematic transition temperature range has been observed which has been ascribed to the different micelles distribution into the sample volume during cooling and heating runs. Finally, the almost bulk-like behavior of the thermal diffusivity over the nematic-smectic phase transition confirms that a significant fraction of the micelles are expelled during the nucleation of the nematic phase.

Microelectrode-assisted low-voltage atmospheric pressure glow discharge in air

NASA Astrophysics Data System (ADS)

Liu, Wenzheng; Zhao, Shuai; Niu, Jiangqi; Chai, Maolin

2017-09-01

During the process of discharge, appropriately changing the paths corresponding to electric field lines and the field strength distribution along these paths, as well as increasing the number of initial electrons, can effectively enhance the uniformity of discharge and inhibit the formation of filamentary discharge. A method is proposed that uses a microelectrode to initiate the macroscopic discharge phenomenon. An asymmetric structure was designed comprising a single electrode of carbon fiber; this electrode structure is of helical-contact type. Benefitting from the special electric field distribution and the microdischarge process, a three-dimensional atmospheric pressure glow discharge was achieved in air, characterized by low discharge voltage, low energy consumption, good diffusion performance, and less ozone generation. The plasma studied is uniform and stable with good diffusion characteristics and low levels of contaminants and hence has potential applications in the field of air purification.

Guiding brine shrimp through mazes by solving reaction diffusion equations

NASA Astrophysics Data System (ADS)

Singal, Krishma; Fenton, Flavio

Excitable systems driven by reaction diffusion equations have been shown to not only find solutions to mazes but to also to find the shortest path between the beginning and the end of the maze. In this talk we describe how we can use the Fitzhugh-Nagumo model, a generic model for excitable media, to solve a maze by varying the basin of attraction of its two fixed points. We demonstrate how two dimensional mazes are solved numerically using a Java Applet and then accelerated to run in real time by using graphic processors (GPUs). An application of this work is shown by guiding phototactic brine shrimp through a maze solved by the algorithm. Once the path is obtained, an Arduino directs the shrimp through the maze using lights from LEDs placed at the floor of the Maze. This method running in real time could be eventually used for guiding robots and cars through traffic.

Backscattering enhancement factor dependence of a Laguerre-Gaussian laser beam propagating on the location path in the atmosphere on optical turbulence intensity

NASA Astrophysics Data System (ADS)

Rytchkov, D. S.

2017-11-01

The paper presents the results of a study of the backscattering enhancement factor (BSE) dependence of vortex LaguerreGaussian beams propagating on monostatic location paths in the atmosphere on optical turbulence intensity. The numeric simulation split-step method of laser beam propagation was used to obtain BSE factor values of a laser beam propagated on monostatic location path in the turbulent atmosphere and reflected from a diffuse target. It is shown that BSE factor of the averaged intensity of a backscattered vortex laser beam of any topological charge is less than BSE factor values of backscattered Gaussian beam in arbitrary turbulent conditions.

Forward- and reverse-bias tunneling effects in n/+/p silicon solar cells

NASA Technical Reports Server (NTRS)

Garlick, G. F. J.; Kachare, A. H.

1980-01-01

Excess currents due to field-assisted tunneling in both forward and reverse bias directions have been observed in n(+)-p silicon solar cells. These currents arise from the effect of conducting paths produced in the depletion layer by n(+) diffusion and cell processing. Forward-bias data indicate a small potential barrier with height of 0.04 eV at the n(+) end of conducting paths. Under reverse bias, excess tunneling currents involve a potential barrier at the p end of the conducting paths, the longer paths being associated with smaller barrier heights and dominating at the lower temperatures. Low-reverse-bias data give energy levels of 0.11 eV for lower temperatures (253-293 K) and 0.35 eV for higher temperatures (293-380 K). A model is suggested to explain the results.

Metallic Thin-Film Bonding and Alloy Generation

NASA Technical Reports Server (NTRS)

Peotter, Brian S. (Inventor); Fryer, Jack Merrill (Inventor); Campbell, Geoff (Inventor); Droppers, Lloyd (Inventor)

2016-01-01

Diffusion bonding a stack of aluminum thin films is particularly challenging due to a stable aluminum oxide coating that rapidly forms on the aluminum thin films when they are exposed to atmosphere and the relatively low meting temperature of aluminum. By plating the individual aluminum thin films with a metal that does not rapidly form a stable oxide coating, the individual aluminum thin films may be readily diffusion bonded together using heat and pressure. The resulting diffusion bonded structure can be an alloy of choice through the use of a carefully selected base and plating metals. The aluminum thin films may also be etched with distinct patterns that form a microfluidic fluid flow path through the stack of aluminum thin films when diffusion bonded together.

Master equations and the theory of stochastic path integrals

NASA Astrophysics Data System (ADS)

Weber, Markus F.; Frey, Erwin

2017-04-01

This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations. We focus on numerical and analytical methods going beyond the low-noise limit and provide a unified framework for the study of master equations. After deriving the forward and backward master equations from the Chapman-Kolmogorov equation, we show how the two master equations can be cast into either of four linear partial differential equations (PDEs). Three of these PDEs are discussed in detail. The first PDE governs the time evolution of a generalized probability generating function whose basis depends on the stochastic process under consideration. Spectral methods, WKB approximations, and a variational approach have been proposed for the analysis of the PDE. The second PDE is novel and is obeyed by a distribution that is marginalized over an initial state. It proves useful for the computation of mean extinction times. The third PDE describes the time evolution of a ‘generating functional’, which generalizes the so-called Poisson representation. Subsequently, the solutions of the PDEs are expressed in terms of two path integrals: a ‘forward’ and a ‘backward’ path integral. Combined with inverse transformations, one obtains two distinct path integral representations of the conditional probability distribution solving the master equations. We exemplify both path integrals in analysing elementary chemical reactions. Moreover, we show how a well-known path integral representation of averaged observables can be recovered from them. Upon expanding the forward and the backward path integrals around stationary paths, we then discuss and extend a recent method for the computation of rare event probabilities. Besides, we also derive path integral representations for processes with continuous state spaces whose forward and backward master equations admit Kramers-Moyal expansions. A truncation of the backward expansion at the level of a diffusion approximation recovers a classic path integral representation of the (backward) Fokker-Planck equation. One can rewrite this path integral in terms of an Onsager-Machlup function and, for purely diffusive Brownian motion, it simplifies to the path integral of Wiener. To make this review accessible to a broad community, we have used the language of probability theory rather than quantum (field) theory and do not assume any knowledge of the latter. The probabilistic structures underpinning various technical concepts, such as coherent states, the Doi-shift, and normal-ordered observables, are thereby made explicit.

Master equations and the theory of stochastic path integrals.

PubMed

Weber, Markus F; Frey, Erwin

2017-04-01

This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations. We focus on numerical and analytical methods going beyond the low-noise limit and provide a unified framework for the study of master equations. After deriving the forward and backward master equations from the Chapman-Kolmogorov equation, we show how the two master equations can be cast into either of four linear partial differential equations (PDEs). Three of these PDEs are discussed in detail. The first PDE governs the time evolution of a generalized probability generating function whose basis depends on the stochastic process under consideration. Spectral methods, WKB approximations, and a variational approach have been proposed for the analysis of the PDE. The second PDE is novel and is obeyed by a distribution that is marginalized over an initial state. It proves useful for the computation of mean extinction times. The third PDE describes the time evolution of a 'generating functional', which generalizes the so-called Poisson representation. Subsequently, the solutions of the PDEs are expressed in terms of two path integrals: a 'forward' and a 'backward' path integral. Combined with inverse transformations, one obtains two distinct path integral representations of the conditional probability distribution solving the master equations. We exemplify both path integrals in analysing elementary chemical reactions. Moreover, we show how a well-known path integral representation of averaged observables can be recovered from them. Upon expanding the forward and the backward path integrals around stationary paths, we then discuss and extend a recent method for the computation of rare event probabilities. Besides, we also derive path integral representations for processes with continuous state spaces whose forward and backward master equations admit Kramers-Moyal expansions. A truncation of the backward expansion at the level of a diffusion approximation recovers a classic path integral representation of the (backward) Fokker-Planck equation. One can rewrite this path integral in terms of an Onsager-Machlup function and, for purely diffusive Brownian motion, it simplifies to the path integral of Wiener. To make this review accessible to a broad community, we have used the language of probability theory rather than quantum (field) theory and do not assume any knowledge of the latter. The probabilistic structures underpinning various technical concepts, such as coherent states, the Doi-shift, and normal-ordered observables, are thereby made explicit.

Direct measurement of the ballistic motion of a freely floating colloid in Newtonian and viscoelastic fluids.

PubMed

Hammond, Andrew P; Corwin, Eric I

2017-10-01

A thermal colloid suspended in a liquid will transition from a short-time ballistic motion to a long-time diffusive motion. However, the transition between ballistic and diffusive motion is highly dependent on the properties and structure of the particular liquid. We directly observe a free floating tracer particle's ballistic motion and its transition to the long-time regime in both a Newtonian fluid and a viscoelastic Maxwell fluid. We examine the motion of the free particle in a Newtonian fluid and demonstrate a high degree of agreement with the accepted Clercx-Schram model for motion in a dense fluid. Measurements of the functional form of the ballistic-to-diffusive transition provide direct measurements of the temperature, viscosity, and tracer radius. We likewise measure the motion in a viscoelastic Maxwell fluid and find a significant disagreement between the theoretical asymptotic behavior and our measured values of the microscopic properties of the fluid. We observe a greatly increased effective mass for a freely moving particle and a decreased plateau modulus.

Bent paths of a positive streamer and a cathode-directed spark leader in diffuse discharges preionized by runaway electrons

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

Zhang, Cheng; Shao, Tao, E-mail: st@mail.iee.ac.cn; Wang, Ruixue

2015-03-15

Diffuse discharges preionized by runaway electrons can produce large-area homogeneous discharges at elevated pressures, which is an intriguing phenomenon in the physics of pulsed discharges. In this paper, runaway-electron-preionized diffuse discharge (REP DD) was obtained in a wide pressure range (0.05–0.25 MPa), and under certain conditions a positive streamer and a cathode-directed spark leader could be observed to propagate at some angles to the applied (background) electric field lines. For a 16-mm gap at an air pressure of 0.08–0.1 MPa, the percentage of pulses in which such propagation is observed is about 5%–50% of their total number, and in the other pulsesmore » such bent paths could not be observed because there is even no streamer or cathode-directed spark leader in diffuse discharges. In our opinion, such propagation of the positive streamer and the cathode-directed spark leader at some angle to the background electric field lines owes to different increase rates of the electron density in different regions of the discharge volume under REP DD conditions. Therefore, during the formation of a REP DD, the increase of the electron density is inhomogeneous and nonsimultaneous, resulting in an electron density gradient at the ionization wave front.« less

Investigation of the oxygen exchange mechanism on Pt|yttria stabilized zirconia at intermediate temperatures: Surface path versus bulk path

PubMed Central

Opitz, Alexander K.; Lutz, Alexander; Kubicek, Markus; Kubel, Frank; Hutter, Herbert; Fleig, Jürgen

2011-01-01

The oxygen exchange kinetics of platinum on yttria-stabilized zirconia (YSZ) was investigated by means of geometrically well-defined Pt microelectrodes. By variation of electrode size and temperature it was possible to separate two temperature regimes with different geometry dependencies of the polarization resistance. At higher temperatures (550–700 °C) an elementary step located close to the three phase boundary (TPB) with an activation energy of ∼1.6 eV was identified as rate limiting. At lower temperatures (300–400 °C) the rate limiting elementary step is related to the electrode area and exhibited a very low activation energy in the order of 0.2 eV. From these observations two parallel pathways for electrochemical oxygen exchange are concluded. The nature of these two elementary steps is discussed in terms of equivalent circuits. Two combinations of parallel rate limiting reaction steps are found to explain the observed geometry dependencies: (i) Diffusion through an impurity phase at the TPB in parallel to diffusion of oxygen through platinum – most likely along Pt grain boundaries – as area-related process. (ii) Co-limitation of oxygen diffusion along the Pt|YSZ interface and charge transfer at the interface with a short decay length of the corresponding transmission line (as TPB-related process) in parallel to oxygen diffusion through platinum. PMID:22210951

Approximate models for the ion-kinetic regime in inertial-confinement-fusion capsule implosions

DOE PAGES

Hoffman, Nelson M.; Zimmerman, George B.; Molvig, Kim; ...

2015-05-19

“Reduced” (i.e., simplified or approximate) ion-kinetic (RIK) models in radiation-hydrodynamic simulations permit a useful description of inertial-confinement-fusion (ICF) implosions where kinetic deviations from hydrodynamic behavior are important. For implosions in or near the kinetic regime (i.e., when ion mean free paths are comparable to the capsule size), simulations using a RIK model give a detailed picture of the time- and space-dependent structure of imploding capsules, allow an assessment of the relative importance of various kinetic processes during the implosion, enable explanations of past and current observations, and permit predictions of the results of future experiments. The RIK simulation method describedmore » here uses moment-based reduced kinetic models for transport of mass, momentum, and energy by long-mean-free-path ions, a model for the decrease of fusion reactivity owing to the associated modification of the ion distribution function, and a model of hydrodynamic turbulent mixing. Transport models are based on local gradient-diffusion approximations for the transport of moments of the ion distribution functions, with coefficients to impose flux limiting or account for transport modification. After calibration against a reference set of ICF implosions spanning the hydrodynamic-to-kinetic transition, the method has useful, quantifiable predictive ability over a broad range of capsule parameter space. Calibrated RIK simulations show that an important contributor to ion species separation in ICF capsule implosions is the preferential flux of longer-mean-free-path species out of the fuel and into the shell, leaving the fuel relatively enriched in species with shorter mean free paths. Also, the transport of ion thermal energy is enhanced in the kinetic regime, causing the fuel region to have a more uniform, lower ion temperature, extending over a larger volume, than implied by clean simulations. Furthermore, we expect that the success of our simple approach will motivate continued theoretical research into the development of first-principles-based, comprehensive, self-consistent, yet useable models of kinetic multispecies ion behavior in ICF plasmas.« less

Modeling fluid diffusion in cerebral white matter with random walks in complex environments

NASA Astrophysics Data System (ADS)

Levy, Amichai; Cwilich, Gabriel; Buldyrev, Sergey V.; Weeden, Van J.

2012-02-01

Recent studies with diffusion MRI have shown new aspects of geometric order in the brain, including complex path coherence within the cerebral cortex, and organization of cerebral white matter and connectivity across multiple scales. The main assumption of these studies is that water molecules diffuse along myelin sheaths of neuron axons in the white matter and thus the anisotropy of their diffusion tensor observed by MRI can provide information about the direction of the axons connecting different parts of the brain. We model the diffusion of particles confined in the space of between the bundles of cylindrical obstacles representing fibrous structures of various orientations. We have investigated the directional properties of the diffusion, by studying the angular distribution of the end point of the random walks as a function of their length, to understand the scale over which the distribution randomizes. We will show evidence of qualitative change in the behavior of the diffusion for different volume fractions of obstacles. Comparisons with three-dimensional MRI images will be illustrated.

Rotation and diffusion of naphthalene on Pt(111)

NASA Astrophysics Data System (ADS)

Kolsbjerg, E. L.; Goubert, G.; McBreen, P. H.; Hammer, B.

2018-03-01

The behavior of naphthalene on Pt(111) surfaces is studied by combining insight from scanning tunneling microscopy (STM) and van der Waals enabled density functional theory. Adsorption, diffusion, and rotation are investigated by a series of variable temperature STM experiments revealing naphthalene ability to rotate on-site with ease with a rotational barrier of 0.69 eV. Diffusion to neighbouring sites is found to be more difficult. The experimental results are in good agreement with the theoretical investigations which confirm that the barrier for diffusion is slightly higher than the one for rotation. The theoretical barriers for rotation and translation are found to be 0.75 and 0.78 eV, respectively. An automatic mapping of the possible diffusion pathways reveals very detailed diffusion paths with many small local minima that would have been practically impossible to find manually. This automated procedure provides detailed insight into the preferred diffusion pathways that are important for our understanding of molecule-substrate interactions.

Spin-Hall effect and emergent antiferromagnetic phase transition in n-Si

NASA Astrophysics Data System (ADS)

Lou, Paul C.; Kumar, Sandeep

2018-04-01

Spin current experiences minimal dephasing and scattering in Si due to small spin-orbit coupling and spin-lattice interactions is the primary source of spin relaxation. We hypothesize that if the specimen dimension is of the same order as the spin diffusion length then spin polarization will lead to non-equilibrium spin accumulation and emergent phase transition. In n-Si, spin diffusion length has been reported up to 6 μm. The spin accumulation in Si will modify the thermal transport behavior of Si, which can be detected with thermal characterization. In this study, we report observation of spin-Hall effect and emergent antiferromagnetic phase transition behavior using magneto-electro-thermal transport characterization. The freestanding Pd (1 nm)/Ni80Fe20 (75 nm)/MgO (1 nm)/n-Si (2 μm) thin film specimen exhibits a magnetic field dependent thermal transport and spin-Hall magnetoresistance behavior attributed to Rashba effect. An emergent phase transition is discovered using self-heating 3ω method, which shows a diverging behavior at 270 K as a function of temperature similar to a second order phase transition. We propose that spin-Hall effect leads to the spin accumulation and resulting emergent antiferromagnetic phase transition. We propose that the length scale for Rashba effect can be equal to the spin diffusion length and two-dimensional electron gas is not essential for it. The emergent antiferromagnetic phase transition is attributed to the site inversion asymmetry in diamond cubic Si lattice.

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

Off-great-circle paths in transequatorial propagation: 1. Discrete and diffuse types

NASA Astrophysics Data System (ADS)

Tsunoda, Roland T.; Maruyama, Takashi; Tsugawa, Takuya; Yokoyama, Tatsuhiro; Ishii, Mamoru; Nguyen, Trang T.; Ogawa, Tadahiko; Nishioka, Michi

2016-11-01

There is mounting evidence that plasma structure in nighttime equatorial F layer evolves from large-scale wave structure (LSWS) in the bottomside F layer. This process cannot be ignored because equatorial plasma bubbles (EPBs) arise from large-amplitude LSWS; and, because intense radiowave scintillations are associated with EPBs, understanding the LSWS-to-EPB process is a crucial step toward reliable Space Weather Forecasting. In this regard, the transequatorial propagation (TEP) experiment appears to be the most useful among available research instruments. After a lapse of 30 years, the TEP experiment has been resurrected; a goal of this research is to understand TEP measurements well enough so that they can be used to diagnose the LSWS-to-EPB process. Toward this end, new results are presented in two companion papers. Herein (P1), off-great-circle (OGC) propagation paths are shown to consist of two types, discrete and diffuse. The new findings include the following: (1) a generalized multireflection model that can explain most of the observed properties; (2) the discrete type is supported by multireflections from an unstructured upwelling, (3) the diffuse type is supported by reflections from plasma structure in EPBs; and (4) the observed east-west (EW) asymmetry can be explained in terms of a distorted upwelling or plasma structure along the west wall of an upwelling. In Paper 2 (P2), a second form of observed EW asymmetry is explained in terms of plasma structure, which is not aligned with the geomagnetic field. The findings strongly confirm a close relationship between upwellings, ESF patches, and OGC paths.

Binding energies and spatial structures of small carrier complexes in monolayer transition-metal dichalcogenides via diffusion Monte Carlo

DOE PAGES

Mayers, Matthew Z.; Berkelbach, Timothy C.; Hybertsen, Mark S.; ...

2015-10-09

Ground-state diffusion Monte Carlo is used to investigate the binding energies and intercarrier radial probability distributions of excitons, trions, and biexcitons in a variety of two-dimensional transition-metal dichalcogenide materials. We compare these results to approximate variational calculations, as well as to analogous Monte Carlo calculations performed with simplified carrier interaction potentials. Our results highlight the successes and failures of approximate approaches as well as the physical features that determine the stability of small carrier complexes in monolayer transition-metal dichalcogenide materials. In conclusion, we discuss points of agreement and disagreement with recent experiments.

Reduction of ion thermal diffusivity associated with the transition of the radial electric field in neutral-beam-heated plasmas in the large helical device.

PubMed

Ida, K; Funaba, H; Kado, S; Narihara, K; Tanaka, K; Takeiri, Y; Nakamura, Y; Ohyabu, N; Yamazaki, K; Yokoyama, M; Murakami, S; Ashikawa, N; deVries, P C; Emoto, M; Goto, M; Idei, H; Ikeda, K; Inagaki, S; Inoue, N; Isobe, M; Itoh, K; Kaneko, O; Kawahata, K; Khlopenkov, K; Komori, A; Kubo, S; Kumazawa, R; Liang, Y; Masuzaki, S; Minami, T; Miyazawa, J; Morisaki, T; Morita, S; Mutoh, T; Muto, S; Nagayama, Y; Nakanishi, H; Nishimura, K; Noda, N; Notake, T; Kobuchi, T; Ohdachi, S; Ohkubo, K; Oka, Y; Osakabe, M; Ozaki, T; Pavlichenko, R O; Peterson, B J; Sagara, A; Saito, K; Sakakibara, S; Sakamoto, R; Sanuki, H; Sasao, H; Sasao, M; Sato, K; Sato, M; Seki, T; Shimozuma, T; Shoji, M; Suzuki, H; Sudo, S; Tamura, N; Toi, K; Tokuzawa, T; Torii, Y; Tsumori, K; Yamamoto, T; Yamada, H; Yamada, I; Yamaguchi, S; Yamamoto, S; Yoshimura, Y; Watanabe, K Y; Watari, T; Hamada, Y; Motojima, O; Fujiwara, M

2001-06-04

Recent large helical device experiments revealed that the transition from ion root to electron root occurred for the first time in neutral-beam-heated discharges, where no nonthermal electrons exist. The measured values of the radial electric field were found to be in qualitative agreement with those estimated by neoclassical theory. A clear reduction of ion thermal diffusivity was observed after the mode transition from ion root to electron root as predicted by neoclassical theory when the neoclassical ion loss is more dominant than the anomalous ion loss.

New generation of universal modeling for centrifugal compressors calculation

NASA Astrophysics Data System (ADS)

Galerkin, Y.; Drozdov, A.

2015-08-01

The Universal Modeling method is in constant use from mid - 1990th. Below is presented the newest 6th version of the Method. The flow path configuration of 3D impellers is presented in details. It is possible to optimize meridian configuration including hub/shroud curvatures, axial length, leading edge position, etc. The new model of vaned diffuser includes flow non-uniformity coefficient based on CFD calculations. The loss model was built from the results of 37 experiments with compressors stages of different flow rates and loading factors. One common set of empirical coefficients in the loss model guarantees the efficiency definition within an accuracy of 0.86% at the design point and 1.22% along the performance curve. The model verification was made. Four multistage compressors performances with vane and vaneless diffusers were calculated. As the model verification was made, four multistage compressors performances with vane and vaneless diffusers were calculated. Two of these compressors have quite unusual flow paths. The modeling results were quite satisfactory in spite of these peculiarities. One sample of the verification calculations is presented in the text. This 6th version of the developed computer program is being already applied successfully in the design practice.

Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

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

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ionmore » diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.« less

Genome-scale modeling of the evolutionary path to C4 photosynthesis

NASA Astrophysics Data System (ADS)

Myers, Christopher R.; Bogart, Eli

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

MEPSA: minimum energy pathway analysis for energy landscapes.

PubMed

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

2015-12-01

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

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

NASA Astrophysics Data System (ADS)

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

1999-11-01

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

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

PubMed

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

2015-12-01

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

Determination of In-situ Porosity and Investigation of Diffusion Processes at the Grimsel Test Site, Switzerland.

NASA Astrophysics Data System (ADS)

Biggin, C.; Ota, K.; Siittari-Kauppi, M.; Moeri, A.

2004-12-01

In the context of a repository for radioactive waste, 'matrix diffusion' is used to describe the process by which solute, flowing in distinct flow paths, penetrates the surrounding rock matrix. Diffusion into the matrix occurs in a connected system of pores or microfractures. Matrix diffusion provides a mechanism for greatly enlarging the area of rock surface in contact with advecting radionuclides, from that of the flow path surfaces (and infills), to a much larger portion of the bulk rock and increases the global pore volume which can retard radionuclides. In terms of a repository safety assessment, demonstration of a significant depth of diffusion-accessible pore space may result in a significant delay in the calculated release of any escaping radionuclides to the environment and a dramatic reduction in the resulting concentration released into the biosphere. For the last decade, Nagra has investigated in situ matrix diffusion at the Grimsel Test Site (GTS) in the Swiss Alps. The in situ investigations offer two distinct advantages to those performed in the lab, namely: 1. Lab-based determination of porosity and diffusivity can lead to an overestimation of matrix diffusion due to stress relief when the rock is sampled (which would overestimate the retardation in the geosphere) 2. Lab-based analysis usually examines small (cm scale) samples and cannot therefore account for any matrix heterogeneity over the hundreds or thousands of metres a typical flow path The in situ investigations described began with the Connected Porosity project, wherein a specially developed acrylic resin was injected into the rock matrix to fill the pore space and determine the depth of connected porosity. The resin was polymerised in situ and the entire rock mass removed by overcoring. The results indicated that lab-based porosity measurements may be two to three times higher than those obtained in situ. While the depth of accessible matrix from a water-conducting feature assumed in repository performance assessments is generally 1 to 10 cm, the results from the GTS in situ experiment suggested depths of several metres could be more appropriate. More recently, the Pore Space Geometry (PSG) experiment at the GTS has used a C-14 doped acrylic resin, combined with state-of-the-art digital beta autoradiography and fluorescence detection to examine a larger area of rock for determination of porosity and the degree of connected pore space. Analysis is currently ongoing and the key findings will be reported in this paper. Starting at the GTS in 2005, the Long-term Diffusion (LTD) project will investigate such processes over spatial and temporal scales more relevant to a repository than traditional lab-based experiments. In the framework of this experiment, long-term (10 to 50 years) in situ diffusion experiments and resin injection experiments are planned to verify current models for matrix diffusion as a radionuclide retardation process. This paper will discuss the findings of the first two experiments and their significance to repository safety assessments before discussing the strategy for the future in relation to the LTD project.

Diffusion of strongly magnetized cosmic ray particles in a turbulent medium

NASA Technical Reports Server (NTRS)

Ptuskin, V. S.

1985-01-01

Cosmic ray (CR) propagation in a turbulent medium is usually considered in the diffusion approximation. Here, the diffusion equation is obtained for strongly magnetized particles in the general form. The influence of a large-scale random magnetic field on CR propagation in interstellar medium is discussed. Cosmic rays are assumed to propagate in a medium with a regular field H and an ensemble of random MHD waves. The energy density of waves on scales smaller than the free path 1 of CR particles is small. The collision integral of the general form which describes interaction between relativistic particles and waves in the quasilinear approximation is used.

Diffusion Dynamics and Creative Destruction in a Simple Classical Model

PubMed Central

2015-01-01

ABSTRACT The article explores the impact of the diffusion of new methods of production on output and employment growth and income distribution within a Classical one‐sector framework. Disequilibrium paths are studied analytically and in terms of simulations. Diffusion by differential growth affects aggregate dynamics through several channels. The analysis reveals the non‐steady nature of economic change and shows that the adaptation pattern depends both on the innovation's factor‐saving bias and on the extent of the bias, which determines the strength of the selection pressure on non‐innovators. The typology of different cases developed shows various aspects of Schumpeter's concept of creative destruction. PMID:27642192

Path optimization with limited sensing ability

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

Kang, Sung Ha, E-mail: kang@math.gatech.edu; Kim, Seong Jun, E-mail: skim396@math.gatech.edu; Zhou, Haomin, E-mail: hmzhou@math.gatech.edu

2015-10-15

We propose a computational strategy to find the optimal path for a mobile sensor with limited coverage to traverse a cluttered region. The goal is to find one of the shortest feasible paths to achieve the complete scan of the environment. We pose the problem in the level set framework, and first consider a related question of placing multiple stationary sensors to obtain the full surveillance of the environment. By connecting the stationary locations using the nearest neighbor strategy, we form the initial guess for the path planning problem of the mobile sensor. Then the path is optimized by reducingmore » its length, via solving a system of ordinary differential equations (ODEs), while maintaining the complete scan of the environment. Furthermore, we use intermittent diffusion, which converts the ODEs into stochastic differential equations (SDEs), to find an optimal path whose length is globally minimal. To improve the computation efficiency, we introduce two techniques, one to remove redundant connecting points to reduce the dimension of the system, and the other to deal with the entangled path so the solution can escape the local traps. Numerical examples are shown to illustrate the effectiveness of the proposed method.« less

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

PubMed

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

2009-05-01

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

Numerical study of air ingress transition to natural circulation in a high temperature helium loop

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

Franken, Daniel; Gould, Daniel; Jain, Prashant K.

Here, the generation-IV high temperature gas cooled reactors (HTGRs) are designed with many passive safety features, one of which is the ability to passively remove heat under a loss of coolant accident (LOCA). However, several common reactor designs do not prevent against a large break in the coolant system and may therefore experience a depressurized LOCA. This would lead to air entering into the reactor system via several potential modes of ingress: diffusion, gravity currents, and natural circulation. At the onset of a LOCA, the initial rate of air ingress is expected to be very slow because it is governedmore » by molecular diffusion. However, after several hours, natural circulation would commence, thus, bringing the air into the reactor system at a much higher rate. As a consequence, air ingress would cause the high temperature graphite matrix to oxidize, leading to its thermal degradation and decreased passive heat (decay) removal capability. Therefore, it is essential to understand the transition of air ingress from molecular diffusion to natural circulation in an HTGR system. This paper presents results from a computational fluid dynamics (CFD) model to study the air ingress transition behavior. These results are validated against an h-shaped high temperature helium loop experiment. Details are provided to quantitatively predict the transition time from molecular diffusion to natural circulation.« less

Numerical study of air ingress transition to natural circulation in a high temperature helium loop

DOE PAGES

Franken, Daniel; Gould, Daniel; Jain, Prashant K.; ...

2017-09-21

Here, the generation-IV high temperature gas cooled reactors (HTGRs) are designed with many passive safety features, one of which is the ability to passively remove heat under a loss of coolant accident (LOCA). However, several common reactor designs do not prevent against a large break in the coolant system and may therefore experience a depressurized LOCA. This would lead to air entering into the reactor system via several potential modes of ingress: diffusion, gravity currents, and natural circulation. At the onset of a LOCA, the initial rate of air ingress is expected to be very slow because it is governedmore » by molecular diffusion. However, after several hours, natural circulation would commence, thus, bringing the air into the reactor system at a much higher rate. As a consequence, air ingress would cause the high temperature graphite matrix to oxidize, leading to its thermal degradation and decreased passive heat (decay) removal capability. Therefore, it is essential to understand the transition of air ingress from molecular diffusion to natural circulation in an HTGR system. This paper presents results from a computational fluid dynamics (CFD) model to study the air ingress transition behavior. These results are validated against an h-shaped high temperature helium loop experiment. Details are provided to quantitatively predict the transition time from molecular diffusion to natural circulation.« less

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Study of compressible flow through a rectangular-to-semiannular transition duct

NASA Technical Reports Server (NTRS)

Foster, Jeffry; Okiishi, Theodore H.; Wendt, Bruce J.; Reichert, Bruce A.

1995-01-01

Detailed flow field measurements are presented for compressible flow through a diffusing rectangular-to-semiannular transition duct. Comparisons are made with published computational results for flow through the duct. Three-dimensional velocity vectors and total pressures were measured at the exit plane of the diffuser model. The inlet flow was also measured. These measurements are made using calibrated five-hole probes. Surface oil flow visualization and surface static pressure data were also taken. The study was conducted with an inlet Mach number of 0.786. The diffuser Reynolds based on the inlet centerline velocity and the exit diameter of the diffuser was 3,200,000. Comparison of the measured data with previously published computational results are made. Data demonstrating the ability of vortex generators to reduce flow separation and circumferential distortion is also presented.

Modelling Solar Energetic Particle Events Using the iPATH Model

NASA Astrophysics Data System (ADS)

Li, G.; Hu, J.; Ao, X.; Zank, G. P.; Verkhoglyadova, O. P.

2016-12-01

Solar Energetic Particles (SEPs) is the No. 1 space weather hazard. Understanding how particles are energized and propagated in these events is of practical concerns to the manned space missions. In particular, both the radial evolution and the longitudinal extent of a gradual solarenergetic particle (SEP) event are central topics for space weather forecasting. In this talk, I discuss the improved Particle Acceleration and Transport in the Heliosphere (iPATH) model. The iPATH model consists of three parts: (1) an updated ZEUS3D V3.5 MHD module that models thebackground solar wind and the initiation of a CME in a 2D domain; (2) an updated shock acceleration module where we investigate particle acceleration at different longitudinal locations along the surface of a CME-driven shock. Accelerated particle spectrum are obtained at the shock under the diffusive shock acceleration mechanism. Shock parameters and particle distributions are recorded and used as inputs for the later part. (3) an updated transport module where we follow the transport of accelerated particles from the shock to any destinations (Earth and/or Mars, e.g.) using a Monte-Carlo method. Both pitch angle scattering due to MHD turbulence and perpendicular diffusion across magnetic field are included. Our iPATH model is therefore intrinsically 2D in nature. The model is capable of generating time intensity profiles and instantaneous particle spectra atvarious locations and can greatly improve our current space weather forecasting capability.

Hydrogeological characterization of flow system in a karstic aquifer, Seymareh dam, Iran

NASA Astrophysics Data System (ADS)

Behrouj Peely, Ahmad; Mohammadi, Zargham; Raeisi, Ezzatollah; Solgi, Khashayar; Mosavi, Mohammad J.; Kamali, Majid

2018-07-01

In order to determine the characteristics of the flow system in a karstic aquifer, an extensive hydrogeological study includes dye tracing test was conducted. The aquifer suited left abutment of Seymareh Dam, in Ravandi Anticline and discharges by more than 50 springs in the southern flank. Flow system in the aquifer is mainly controlled by the reservoir of Seymareh Dam. Time variations of the spring discharge and water table in the observation wells were highly correlated with the reservoir water level. The average groundwater velocity ranges from 0.2 to more than 14 m/h based on the dye tracing test. The probable flow paths were differentiated in two groups including the flow paths in the northern and southern flanks of Ravandi Anticline. Types of groundwater flow in the proposed flow paths are determined as diffuse or conduit flow type considering groundwater velocity and shape of the breakthrough curves. An index is proposed for differentiation of diffuse and conduit flow system based on relationship of groundwater velocity and hydraulic gradient. Dominant geometry of the flow routs (e.g., conduit diameter and fracture aperture) is estimated for the groundwater flow paths toward the springs. Based on velocity variations and variance coefficient of the water table and discharge of springs on map view a major karst conduit was probably developed in the aquifer. This research emphasizes applying of an extensive hydrogeological study for characterization of flow system in the karst aquifer.

Signs and stability in higher-derivative gravity

NASA Astrophysics Data System (ADS)

Narain, Gaurav

2018-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-08-20

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

Path Flow Estimation Using Time Varying Coefficient State Space Model

NASA Astrophysics Data System (ADS)

Jou, Yow-Jen; Lan, Chien-Lun

2009-08-01

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

Distributional behavior of diffusion coefficients obtained by single trajectories in annealed transit time model

NASA Astrophysics Data System (ADS)

Akimoto, Takuma; Yamamoto, Eiji

2016-12-01

Local diffusion coefficients in disordered systems such as spin glass systems and living cells are highly heterogeneous and may change over time. Such a time-dependent and spatially heterogeneous environment results in irreproducibility of single-particle-tracking measurements. Irreproducibility of time-averaged observables has been theoretically studied in the context of weak ergodicity breaking in stochastic processes. Here, we provide rigorous descriptions of equilibrium and non-equilibrium diffusion processes for the annealed transit time model, which is a heterogeneous diffusion model in living cells. We give analytical solutions for the mean square displacement (MSD) and the relative standard deviation of the time-averaged MSD for equilibrium and non-equilibrium situations. We find that the time-averaged MSD grows linearly with time and that the time-averaged diffusion coefficients are intrinsically random (irreproducible) even in the long-time measurements in non-equilibrium situations. Furthermore, the distribution of the time-averaged diffusion coefficients converges to a universal distribution in the sense that it does not depend on initial conditions. Our findings pave the way for a theoretical understanding of distributional behavior of the time-averaged diffusion coefficients in disordered systems.

Bounded diffusion impedance characterization of battery electrodes using fractional modeling

NASA Astrophysics Data System (ADS)

Gabano, Jean-Denis; Poinot, Thierry; Huard, Benoît

2017-06-01

This article deals with the ability of fractional modeling to describe the bounded diffusion behavior encountered in modern thin film and nanoparticles lithium battery electrodes. Indeed, the diffusion impedance of such batteries behaves as a half order integrator characterized by the Warburg impedance at high frequencies and becomes a classical integrator described by a capacitor at low frequencies. The transition between these two behaviors depends on the particles geometry. Three of them will be considered in this paper: planar, cylindrical and spherical ones. The fractional representation proposed is a gray box model able to perfectly fit the low and high frequency diffusive impedance behaviors while optimizing the frequency response transition. Identification results are provided using frequential simulation data considering the three electrochemical diffusion models based on the particles geometry. Furthermore, knowing this geometry allows to estimate the diffusion ionic resistance and time constant using the relationships linking these physical parameters to the structural fractional model parameters. Finally, other simulations using Randles impedance models including the charge transfer impedance and the external resistance demonstrate the interest of fractional modeling in order to identify properly not only the charge transfer impedance but also the diffusion physical parameters whatever the particles geometry.

SHIR competitive information diffusion model for online social media

NASA Astrophysics Data System (ADS)

Liu, Yun; Diao, Su-Meng; Zhu, Yi-Xiang; Liu, Qing

2016-11-01

In online social media, opinion divergences and differentiations generally exist as a result of individuals' extensive participation and personalization. In this paper, a Susceptible-Hesitated-Infected-Removed (SHIR) model is proposed to study the dynamics of competitive dual information diffusion. The proposed model extends the classical SIR model by adding hesitators as a neutralized state of dual information competition. It is both hesitators and stable spreaders that facilitate information dissemination. Researching on the impacts of diffusion parameters, it is found that the final density of stiflers increases monotonically as infection rate increases and removal rate decreases. And the advantage information with larger stable transition rate takes control of whole influence of dual information. The density of disadvantage information spreaders slightly grows with the increase of its stable transition rate, while whole spreaders of dual information and the relaxation time remain almost unchanged. Moreover, simulations imply that the final result of competition is closely related to the ratio of stable transition rates of dual information. If the stable transition rates of dual information are nearly the same, a slightly reduction of the smaller one brings out a significant disadvantage in its propagation coverage. Additionally, the relationship of the ratio of final stiflers versus the ratio of stable transition rates presents power characteristic.

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

PubMed Central

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

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

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

NASA Astrophysics Data System (ADS)

David Froning, H.; Meholic, Gregory V.

2010-01-01

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

Maximum Path Information and Fokker Planck Equation

NASA Astrophysics Data System (ADS)

Li, Wei; Wang A., Q.; LeMehaute, A.

2008-04-01

We present a rigorous method to derive the nonlinear Fokker-Planck (FP) equation of anomalous diffusion directly from a generalization of the principle of least action of Maupertuis proposed by Wang [Chaos, Solitons & Fractals 23 (2005) 1253] for smooth or quasi-smooth irregular dynamics evolving in Markovian process. The FP equation obtained may take two different but equivalent forms. It was also found that the diffusion constant may depend on both q (the index of Tsallis entropy [J. Stat. Phys. 52 (1988) 479] and the time t.

A hyperbolastic type-I diffusion process: Parameter estimation by means of the firefly algorithm.

PubMed

Barrera, Antonio; Román-Román, Patricia; Torres-Ruiz, Francisco

2018-01-01

A stochastic diffusion process, whose mean function is a hyperbolastic curve of type I, is presented. The main characteristics of the process are studied and the problem of maximum likelihood estimation for the parameters of the process is considered. To this end, the firefly metaheuristic optimization algorithm is applied after bounding the parametric space by a stagewise procedure. Some examples based on simulated sample paths and real data illustrate this development. Copyright © 2017 Elsevier B.V. All rights reserved.

Conical diffuser for fuel cells

NASA Technical Reports Server (NTRS)

Craft, D. W.

1976-01-01

Diffuser is inserted into inlet manifold, producing smooth transition of flow from pipe diameter to manifold diameter. Expected pressure gradient and resulting cell-to-cell temperature gradient are reduced. Outlet manifold has nozzle insert that reduces exit losses.

The Senior Year: Culminating Experiences and Transitions

ERIC Educational Resources Information Center

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

2012-01-01

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

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

ERIC Educational Resources Information Center

Lane, Joel A.

2016-01-01

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

Youth Transition to Employment in Vietnam: A Vulnerable Path

ERIC Educational Resources Information Center

Tran, Thi Tuyet

2018-01-01

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

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

ERIC Educational Resources Information Center

Doede, Robert

2011-01-01

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

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

ERIC Educational Resources Information Center

Wang, Yan; Ye, Feifei; Pilarzyk, Tom

2014-01-01

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

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

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2008-01-01

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

A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection.

PubMed

Song, Yun S; Steinrücken, Matthias

2012-03-01

The transition density function of the Wright-Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright-Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation-selection balance.

Red Fluorescent Line Emission from Hydrogen Molecules in Diffuse Molecular Clouds

NASA Technical Reports Server (NTRS)

Neufeld, David A.; Spaans, Marco

1996-01-01

We have modeled the fluorescent pumping of electronic and vibrational emissions of molecular hydrogen (H2) within diffuse molecular clouds that are illuminated by ultraviolet continuum radiation. Fluorescent line intensities are predicted for transitions at ultraviolet, infrared, and red visible wavelengths as functions of the gas density, the visual extinction through the cloud, and the intensity of the incident UV continuum radiation. The observed intensity in each fluorescent transition is roughly proportional to the integrated rate of H2 photodissociation along the line of sight. Although the most luminous fluorescent emissions detectable from ground-based observatories lie at near-infrared wavelengths, we argue that the lower sky brightness at visible wavelengths makes the red fluorescent transitions a particularly sensitive probe. Fabry-Perot spectrographs of the type that have been designed to observe very faint diffuse Ha emissions are soon expected to yield sensitivities that will be adequate to detect H2 vibrational emissions from molecular clouds that are exposed to ultraviolet radiation no stronger than the mean radiation field within the Galaxy. Observations of red H2 fluorescent emission together with cospatial 21 cm H I observations could serve as a valuable probe of the gas density in diffuse molecular clouds.

Ultrafast Spectral Diffusion of the First Subband Exciton in Single-Wall Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Schilling, Daniel; Hertel, Tobias

2013-03-01

The width of optical transitions in semiconductors is determined by homogeneous and inhomogeneous contributions. Here, we report on the determination of homogeneous linewidths for the first exciton subband transition and the dynamics of spectral diffusion in single-wall carbon nanotubes (SWNTs) using one- and two-dimensional time resolved spectral hole burning spectroscopy. Our investigation of highly purified semiconducting (6,5)-SWNTs suggests that room temperature homogeneous linewidths are on the order of 4 meV and are rapidly broadened by an ultrafast sub-ps spectral diffusion process. These findings are supported by our off-resonant excitation experiments where we observe sub-ps population transfer reflecting the thermal distribution of energy levels around the first subband exciton transition. The results of temperature-dependent spectral hole burning experiments between 17 K and 293 K suggest that homogeneous linewidths are due to exciton interaction with low energy optical phonons, most likely of the radial breathing mode type. In contrast, we find that inhomogeneous broadening is determined by an electronic degree of freedom such as ultrafast intra-tube exciton diffusion which is characteristic and unique for excitons in these one-dimensional semiconductors.

A Simple Method for Finding Explicit Analytic Transition Densities of Diffusion Processes with General Diploid Selection

PubMed Central

Song, Yun S.; Steinrücken, Matthias

2012-01-01

The transition density function of the Wright–Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright–Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation–selection balance. PMID:22209899

Kinetics of self-interstitial migration in bcc and fcc transition metals

NASA Astrophysics Data System (ADS)

Bukkuru, S.; Bhardwaj, U.; Srinivasa Rao, K.; Rao, A. D. P.; Warrier, M.; Valsakumar, M. C.

2018-03-01

Radiation damage is a multi-scale phenomenon. A thorough understanding of diffusivities and the migration energies of defects is a pre-requisite to quantify the after-effects of irradiation. We investigate the thermally activated mobility of self-interstitial atom (SIA) in bcc transition metals Fe, Mo, Nb and fcc transition metals Ag, Cu, Ni, Pt using molecular dynamics (MD) simulations. The self-interstitial diffusion involves various mechanisms such as interstitialcy, dumbbell or crowdion mechanisms. Max-Space Clustering (MSC) method has been employed to identify the interstitial and its configuration over a wide range of temperature. The self-interstitial diffusion is Arrhenius like, however, there is a slight deviation at high temperatures. The migration energies, pre-exponential factors of diffusion and jump-correlation factors, obtained from these simulations can be used as inputs to Monte Carlo simulations of defect transport. The jump-correlation factor shows the degree of preference of rectilinear or rotational jumps. We obtain the average jump-correlation factor of 1.4 for bcc metals and 0.44 for fcc metals. It indicates that rectilinear jumps are preferred in bcc metals and rotational jumps are preferred in fcc metals.

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

PubMed

Banerjee, Rahul; Cukier, Robert I

2014-03-20

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

Influence of doping on thermal diffusivity of single crystals used in photonics: measurements based on thermal wave methods.

PubMed

Bodzenta, Jerzy; Kaźmierczak-Bałata, Anna; Wokulska, Krystyna B; Kucytowski, Jacek; Łukasiewicz, Tadeusz; Hofman, Władysław

2009-03-01

Three crystals used in solid-state lasers, namely, yttrium aluminum garnet (YAG), yttrium orthovanadate (YVO(4)), and gadolinium calcium oxoborate (GdCOB), were investigated to determine the influence of dopants on their thermal diffusivity. The thermal diffusivity was measured by thermal wave method with a signal detection based on mirage effect. The YAG crystals were doped with Yb or V, the YVO(4) with Nd or Ca and Tm, and the GdCOB crystals contained Nd or Yb. In all cases, the doping caused a decrease in thermal diffusivity. The analysis of complementary measurements of ultrasound velocity changes caused by dopants leads to the conclusion that impurities create phonon scattering centers. This additional scattering reduces the phonon mean free path and accordingly results in the decrease of the thermal diffusivity of the crystal. The influence of doping on lattice parameters was investigated, additionally.

Geometric diffusion of quantum trajectories

PubMed Central

Yang, Fan; Liu, Ren-Bao

2015-01-01

A quantum object can acquire a geometric phase (such as Berry phases and Aharonov–Bohm phases) when evolving along a path in a parameter space with non-trivial gauge structures. Inherent to quantum evolutions of wavepackets, quantum diffusion occurs along quantum trajectories. Here we show that quantum diffusion can also be geometric as characterized by the imaginary part of a geometric phase. The geometric quantum diffusion results from interference between different instantaneous eigenstate pathways which have different geometric phases during the adiabatic evolution. As a specific example, we study the quantum trajectories of optically excited electron-hole pairs in time-reversal symmetric insulators, driven by an elliptically polarized terahertz field. The imaginary geometric phase manifests itself as elliptical polarization in the terahertz sideband generation. The geometric quantum diffusion adds a new dimension to geometric phases and may have applications in many fields of physics, e.g., transport in topological insulators and novel electro-optical effects. PMID:26178745

Diffusion-Cooled Tantalum Hot-Electron Bolometer Mixers

NASA Technical Reports Server (NTRS)

Skalare, Anders; McGrath, William; Bumble, Bruce; LeDuc, Henry

2004-01-01

A batch of experimental diffusion-cooled hot-electron bolometers (HEBs), suitable for use as mixers having input frequencies in the terahertz range and output frequencies up to about a gigahertz, exploit the superconducting/normal-conducting transition in a thin strip of tantalum. The design and operation of these HEB mixers are based on mostly the same principles as those of a prior HEB mixer that exploited the superconducting/normal- conducting transition in a thin strip of niobium and that was described elsewhere.

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

Treesearch

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

2012-01-01

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

The one-dimensional asymmetric persistent random walk

NASA Astrophysics Data System (ADS)

Rossetto, Vincent

2018-04-01

Persistent random walks are intermediate transport processes between a uniform rectilinear motion and a Brownian motion. They are formed by successive steps of random finite lengths and directions travelled at a fixed speed. The isotropic and symmetric 1D persistent random walk is governed by the telegrapher’s equation, also called the hyperbolic heat conduction equation. These equations have been designed to resolve the paradox of the infinite speed in the heat and diffusion equations. The finiteness of both the speed and the correlation length leads to several classes of random walks: Persistent random walk in one dimension can display anomalies that cannot arise for Brownian motion such as anisotropy and asymmetries. In this work we focus on the case where the mean free path is anisotropic, the only anomaly leading to a physics that is different from the telegrapher’s case. We derive exact expression of its Green’s function, for its scattering statistics and distribution of first-passage time at the origin. The phenomenology of the latter shows a transition for quantities like the escape probability and the residence time.

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

PubMed

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

2016-12-14

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Cubature on Wiener Space: Pathwise Convergence

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

Bayer, Christian, E-mail: christian.bayer@wias-berlin.de; Friz, Peter K., E-mail: friz@math.tu-berlin.de

2013-04-15

Cubature on Wiener space (Lyons and Victoir in Proc. R. Soc. Lond. A 460(2041):169-198, 2004) provides a powerful alternative to Monte Carlo simulation for the integration of certain functionals on Wiener space. More specifically, and in the language of mathematical finance, cubature allows for fast computation of European option prices in generic diffusion models.We give a random walk interpretation of cubature and similar (e.g. the Ninomiya-Victoir) weak approximation schemes. By using rough path analysis, we are able to establish weak convergence for general path-dependent option prices.

Dynamical Generation of the Transition Zone in the Earth's Mantle

NASA Astrophysics Data System (ADS)

Hansen, U.; Stemmer, K.

2005-12-01

The internal structure of the Earth is made up by a series of layers, though it is unclear how many layers exist and if there are layers invisible to remote sensing techniques. The transition zone is likely to be a boundary layer separating the convective systems in the lower and upper mantle. It seems likely that currently there is some mass exchange across this boundary, rather than the two systems beeing strictly separated.a Double-diffusive convection(d.d.c) is a vital mechanism which can generate layered structure and may thus be an important mmical machinery behind the formation of the transition zone. Double-diffusive convection determines the dynamics of systems whose density is influenced by at least two components with different molecular diffusivities.In the mantle, composition and temperature play the role of those two components. By means of numerical experiments we demonstrate that under mantle relevant conditions d.d.c typically leads to the formation of a transition zone. The calculations encompass two- and three dimensional Cartesian geometries as well as fully 3D spherical domains. We have further included strongly temperature dependent viscosity and find that this leads to even more pronounced layering. In most cases a layered flow pattern emerges, where two layers with a transition zone in between resembles a quasistationary state. Thus, the transition zone can be the result of a self organization process of the convective flow in the mantle. The presence of a phase transition further helps to stabilize the boundary against overturning, even on a time scale on the order of the age of the Earth.

Scaling of Turbulence and Transport with ρ* in LAPD

NASA Astrophysics Data System (ADS)

Guice, Daniel; Carter, Troy; Rossi, Giovanni

2014-10-01

The plasma column size of the Large Plasma Device (LAPD) is varied in order to investigate the variation of turbulence and transport with ρ* =ρs / a . The data set includes plasmas produced by the standard BaO plasma source (straight field plasma radius a 30 cm) as well as the new higher density, higher temperature LaB6 plasma source (straight field plasma radius a 10 cm). The size of the plasma column is scaled in order to observe a Bohm to Gyro-Bohm diffusion transition. The main plasma column magnetic field is held fixed while the field in the cathode region is changed in order to map the cathode to different plasma column scales in the main chamber. Past experiments in the LAPD have shown a change in the observed diffusion but no transition to Gyro-Bohm diffusion. Results will be presented from an ongoing campaign to push the LAPD into the Gyro-Bohm diffusion regime.

Non-translational Molecular Diffusive Motion on Two Different Time Scales in Alkane Nanoparticles

NASA Astrophysics Data System (ADS)

Wang, S.-K.; Bai, M.; Taub, H.; Mamontov, E.; Herwig, K. W.; Hansen, F. Y.; Copley, J. R. D.; Jenkins, T.; Tyagi, M.; Volkmann, U. G.

2009-03-01

Using quasielastic neutron scattering, we have investigated molecular diffusive motion in n-C32H66 nanoparticles whose structure and phase transitions have been studied previously.^2 The spectra reveal non-translational (dispersionless) diffusive motion occurring simultaneously on time scales of ˜1 ns and ˜40 ps. The onset of the faster motion occurs in the crystalline phase at least 15 K below the melting point and is tentatively identified with rotation about the long molecular axis. Similarly, we suggest that the slower motion involves molecular conformational changes whose onset appears to coincide with the abrupt transition to the bulk rotator phase about 3 K below melting. These two types of diffusive motion bear a strong resemblance to those observed previously in C24 monolayers adsorbed on a graphite surface.^3 ^2M. Bai et al., Europhys. Lett. 79, 26003 (2007). ^3F. Y. Hansen et al., Phys. Rev. Lett. 92, 046103 (2004)].

Diffuse X-ray scattering near a two-dimensional solid–liquid phase transition at the n-hexane–water interface

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

Tikhonov, A. M.

According to experimental data on X-ray scattering and reflectometry with synchrotron radiation, a twodimensional crystallization phase transition in a monolayer of melissic acid at the n-hexane–water interface with a decrease in the temperature occurs after a wetting transition.

On extreme points of the diffusion polytope

DOE PAGES

Hay, M. J.; Schiff, J.; Fisch, N. J.

2017-01-04

Here, we consider a class of diffusion problems defined on simple graphs in which the populations at any two vertices may be averaged if they are connected by an edge. The diffusion polytope is the convex hull of the set of population vectors attainable using finite sequences of these operations. A number of physical problems have linear programming solutions taking the diffusion polytope as the feasible region, e.g. the free energy that can be removed from plasma using waves, so there is a need to describe and enumerate its extreme points. We also review known results for the case ofmore » the complete graph Kn, and study a variety of problems for the path graph Pn and the cyclic graph Cn. Finall, we describe the different kinds of extreme points that arise, and identify the diffusion polytope in a number of simple cases. In the case of increasing initial populations on Pn the diffusion polytope is topologically an n-dimensional hypercube.« less

Diffusion of helium, hydrogen and deuterium in diamond: Experiment, theory and geochemical applications

NASA Astrophysics Data System (ADS)

Cherniak, D. J.; Watson, E. B.; Meunier, V.; Kharche, N.

2018-07-01

Diffusivities of helium, deuterium and hydrogen have been characterized in diamond. Polished CVD diamond was implanted with either 3He, 2H, or 1H. Implanted samples were sealed under vacuum in silica glass capsules, and annealed in 1-atm furnaces. 3He, 2H and 1H distributions were measured with Nuclear Reaction Analysis. We obtain these Arrhenius relations: DHe = 4.00 × 10-15 exp(-138 ± 14 kJ mol-1/RT) m2 s-1. D2H = 1.02 × 10-4 exp(-262 ± 17 kJ mol-1/RT) m2 s-1. D1H = 2.60 × 10-4 exp(-267 ± 15 kJ mol-1/RT) m2 s-1. Diffusivities of 1H and 2H agree within experimental uncertainties, indicating little diffusive mass fractionation of hydrogen in diamond. To complement the experimental measurements, we performed calculations using a first-principles quantum mechanical description of diffusion in diamond within the Density Functional Theory (DFT). Differences in 1H and 2H diffusivities from calculations are found to be ∼4.5%, reflected in differences in the pre-exponential factor. This small difference in diffusivities, despite the large relative mass difference between these isotopes, is due to the fact that the atomistic process involved in the transition along the diffusion pathway is dictated by local changes to the diamond structures rather than to vibrations involving 1H/2H. This finding is consistent with the experimental results given experimental uncertainties. In contrast, calculations for helium diffusion in diamond indicate a difference of 15% between diffusivities of 3He and 4He. Calculations of diffusion distances for hydrogen using our data yield a distance of 50 μm in diamond in 300,000 years at 500 °C and ∼30 min at 1400 °C. Diffusion distances for He in diamond are shorter than for H at all temperatures above ∼350 °C, but differences increase dramatically with temperature because of the higher activation energy for H diffusion. For example, a 50 μm diffusion distance for He would be attained in ∼40 Myr at 500 °C and 400 yr at 1400 °C. For comparison, a 50 μm diffusion distance for N in diamond would require nearly 1 billion years at 1400 °C. The experimental data indicate that diamonds equilibrate with ambient H and He in the mantle on timescales brief relative to most geological processes and events. However, He diffusion in diamond is slower than in any other mineral measured to date, including other kimberlite-hosted minerals. Under some circumstances, diamond may provide information about mantle He not recoverable from other minerals. One possibility is diamonds entrained in kimberlites. Since the ascent of kimberlite from the mantle to near-surface is very rapid, entrained diamonds may retain most or all of the H and He acquired in mantle environments. Calculations using reasonable ascent rates and T-t paths indicate that He diffusive loss from kimberlite-hosted diamonds is negligible for grains of 1.0-0.2 mm radius, with fractional losses <0.15% for all ascent rates considered. If the host kimberlite magma is effectively quenched in the near-surface (or is erupted), diamonds should contain a faithful record of [He] and He isotopes from the mantle source region. Preservation of H in kimberlite-hosted diamonds is less clear-cut, with model outcomes depending critically upon rates of ascent and cooling.

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

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

Sinitsyn, Nikolai A.

2015-04-23

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

Calorimetric and Neutron Scattering Studies on Glass Transitions and Ionic Diffusions in Imidazolium-based Ionic Liquids

NASA Astrophysics Data System (ADS)

Yamamuro, O.; Kofu, M.

2017-05-01

Glass transition is one of the central research issues of ionic liquids (ILs). In particular, the most typical ILs, imidazolium-basedones (ImILs) are readily supercooled and exhibit glass transitions below room temperature. We have measured the heat capacities of several ImILs, encoded as CnmimX (n: alkyl carbon number, n = 2-8, X: anion, X = Cl, I, FeCl4, TFSI) using an adiabatic calorimeter. We found that most of ImILs exhibit glass transitions with large Cp jumps in a temperature range between 170 K and 230 K. The large Cp jumps reflect that these ILs are fragile liquids that exhibit large structural change depending on temperature near the glass transition temperature T g. It is also revealed that T g does not depend much on n but on the anion radius. We have investigated the dynamics of CnmimX (n = 2-8, X = Cl, NO3, PF6, TF, FSI, TFSI) by means of a quasielastic neutron scattering (QENS) technique. It was clarified that the ionic diffusion is directly associated with the viscosity and glass transition. The activation energy ΔE a of the ionic diffusion increases with decreasing anion size but remains almost unchanged with n as found for T g. These systematic change of T g and ΔE a can be explained well by taking account the nano-domain structure which is the most characteristic feature of ImILs.

Materials Science Laboratory - Columnar-to-Equiaxed Transition in Solidification Processing and Microstructure Formation in Casting of Technical Alloys under Diffusive and Magnetically Controlled Convective Conditions

NASA Technical Reports Server (NTRS)

Gandin, Charles-Andre; Ratke, Lorenz

2008-01-01

The Materials Science Laboratory - Columnar-to-Equiaxed Transition in Solidification Processing and Microstructure Formation in Casting of Technical Alloys under Diffusive and Magnetically Controlled Convective Conditions (MSL-CETSOL and MICAST) are two investigations which supports research into metallurgical solidification, semiconductor crystal growth (Bridgman and zone melting), and measurement of thermo-physical properties of materials. This is a cooperative investigation with the European Space Agency (ESA) and National Aeronautics and Space Administration (NASA) for accommodation and operation aboard the International Space Station (ISS). Research Summary: Materials Science Laboratory - Columnar-to-Equiaxed Transition in Solidification Processing (CETSOL) and Microstructure Formation in Casting of Technical Alloys under Diffusive and Magnetically Controlled Convective Conditions (MICAST) are two complementary investigations which will examine different growth patterns and evolution of microstructures during crystallization of metallic alloys in microgravity. The aim of these experiments is to deepen the quantitative understanding of the physical principles that govern solidification processes in cast alloys by directional solidification.

Spring operated accelerator and constant force spring mechanism therefor

NASA Technical Reports Server (NTRS)

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

1977-01-01

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

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

DTIC Science & Technology

1982-04-01

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

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

PubMed Central

Bhatt, Divesh; Zuckerman, Daniel M.

2010-01-01

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

Self-similar space-time evolution of an initial density discontinuity

NASA Astrophysics Data System (ADS)

Rekaa, V. L.; Pécseli, H. L.; Trulsen, J. K.

2013-07-01

The space-time evolution of an initial step-like plasma density variation is studied. We give particular attention to formulate the problem in a way that opens for the possibility of realizing the conditions experimentally. After a short transient time interval of the order of the electron plasma period, the solution is self-similar as illustrated by a video where the space-time evolution is reduced to be a function of the ratio x/t. Solutions of this form are usually found for problems without characteristic length and time scales, in our case the quasi-neutral limit. By introducing ion collisions with neutrals into the numerical analysis, we introduce a length scale, the collisional mean free path. We study the breakdown of the self-similarity of the solution as the mean free path is made shorter than the system length. Analytical results are presented for charge exchange collisions, demonstrating a short time collisionless evolution with an ensuing long time diffusive relaxation of the initial perturbation. For large times, we find a diffusion equation as the limiting analytical form for a charge-exchange collisional plasma, with a diffusion coefficient defined as the square of the ion sound speed divided by the (constant) ion collision frequency. The ion-neutral collision frequency acts as a parameter that allows a collisionless result to be obtained in one limit, while the solution of a diffusion equation is recovered in the opposite limit of large collision frequencies.

Non-Local Diffusion of Energetic Electrons during Solar Flares

NASA Astrophysics Data System (ADS)

Bian, N. H.; Emslie, G.; Kontar, E.

2017-12-01

The transport of the energy contained in suprathermal electrons in solar flares plays a key role in our understanding of many aspects of flare physics, from the spatial distributions of hard X-ray emission and energy deposition in the ambient atmosphere to global energetics. Historically the transport of these particles has been largely treated through a deterministic approach, in which first-order secular energy loss to electrons in the ambient target is treated as the dominant effect, with second-order diffusive terms (in both energy and angle) generally being either treated as a small correction or even neglected. Here, we critically analyze this approach, and we show that spatial diffusion through pitch-angle scattering necessarily plays a very significant role in the transport of electrons. We further show that a satisfactory treatment of the diffusion process requires consideration of non-local effects, so that the electron flux depends not just on the local gradient of the electron distribution function but on the value of this gradient within an extended region encompassing a significant fraction of a mean free path. Our analysis applies generally to pitch-angle scattering by a variety of mechanisms, from Coulomb collisions to turbulent scattering. We further show that the spatial transport of electrons along the magnetic field of a flaring loop can be modeled as a Continuous Time Random Walk with velocity-dependent probability distribution functions of jump sizes and occurrences, both of which can be expressed in terms of the scattering mean free path.

A Reactive-Transport Model Describing Methanogen Growth and Methane Production in Diffuse Flow Vents at Axial Seamount

NASA Astrophysics Data System (ADS)

Algar, C. K.

2015-12-01

Hydrogenotrophic methanogenesis is an important mode of metabolism in deep-sea hydrothermal vents. Diffuse vent fluids often show a depletion in hydrogen with a corresponding increase in methane relative to pure-mixing of end member fluid and seawater, and genomic surveys show an enrichment in genetic sequences associated with known methanogens. However, because we cannot directly sample the subseafloor habitat where these organisms are living, constraining the size and activity of these populations remains a challenge and limits our ability to quantify the role they play in vent biogeochemistry. Reactive-transport modeling may provide a useful tool for approaching this problem. Here we present a reactive-transport model describing methane production along the flow-path of hydrothermal fluid from its high temperature end-member to diffuse venting at the seafloor. The model is set up to reflect conditions at several diffuse vents in the Axial Seamount. The model describes the growth of the two dominant thermophilic methanogens, Methanothermococcus and Methanocaldococcus, observed at Axial seamount. Monod and Arrhenius constants for Methanothermococcus thermolithotrophicus and Methanocaldococcus jannaschii were obtained for the model using chemostat and bottle experiments at varying temperatures. The model is used to investigate the influence of different mixing regimes on the subseafloor populations of these methanogens. By varying the model flow path length and subseafloor cell concentrations, and fitting to observed hydrogen and methane concentrations in the venting fluid, the subseafloor biomass, fluid residence time, and methane production rate can be constrained.

Gas diffusion in and out of super-hydrophobic surface in transitional and turbulent boundary layers

NASA Astrophysics Data System (ADS)

Ling, Hangjian; Fu, Matthew; Hultmark, Marcus; Katz, Joseph

2017-11-01

The rate of gas diffusion in and out of a super-hydrophobic surface (SHS) located in boundary layers is investigated at varying Reynolds numbers and ambient pressures. The hierarchical SHS consists of nano-textured, 100 μm wide spanwise grooves. The boundary layers over the SHS under the Cassie-Baxter and Wenzel states as well as a smooth wall at same conditions are characterized by particle image velocimetry. The Reynolds number based on momentum thickness of the smooth wall, ReΘ0, ranges from 518 to 2088, covering transitional and turbulent boundary layer regimes. The mass diffusion rate is estimated by using microscopy to measure the time-evolution of plastron shape and volume. The data is used for calculating the Sherwood number based on smooth wall momentum thickness, ShΘ0. As expected, the diffusion rate increases linearly with the under- or super-saturation level, i.e., ShΘ0 is independent of ambient pressure. For the turbulent boundary layers, the data collapses onto ShΘ0 = 0.47ReΘ00.77 . For the transitional boundary layer, ShΘ0 is lower than the turbulent power law. When ShΘ0 is plotted against the friction Reynolds number (Reτ0) , both the transitional and turbulent boundary layer data collapse onto a single power law, ShΘ0 = 0.34Reτ00.913 . Results scaled based on Wenzel state momentum thickness show very similar trends. Sponsored by ONR.

Heavy-tailed fractional Pearson diffusions.

PubMed

Leonenko, N N; Papić, I; Sikorskii, A; Šuvak, N

2017-11-01

We define heavy-tailed fractional reciprocal gamma and Fisher-Snedecor diffusions by a non-Markovian time change in the corresponding Pearson diffusions. Pearson diffusions are governed by the backward Kolmogorov equations with space-varying polynomial coefficients and are widely used in applications. The corresponding fractional reciprocal gamma and Fisher-Snedecor diffusions are governed by the fractional backward Kolmogorov equations and have heavy-tailed marginal distributions in the steady state. We derive the explicit expressions for the transition densities of the fractional reciprocal gamma and Fisher-Snedecor diffusions and strong solutions of the associated Cauchy problems for the fractional backward Kolmogorov equation.

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

ERIC Educational Resources Information Center

Florio, Carol; And Others

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

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

ERIC Educational Resources Information Center

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

2011-01-01

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

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

Treesearch

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

2012-01-01

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

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

ERIC Educational Resources Information Center

Bottoms, Gene; Young, Marna

2008-01-01

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

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

DTIC Science & Technology

2015-05-08

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

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

ERIC Educational Resources Information Center

Hoddinott, John; Lethbridge, Lynn; Phipps, Shelley

2002-01-01

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

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

PubMed Central

2015-01-01

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

Theory of Disk-to-Vesicle Transformation

NASA Astrophysics Data System (ADS)

Li, Jianfeng; Shi, An-Chang

2009-03-01

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

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

PubMed

Sesé, Luis M; Bailey, Lorna E

2007-04-28

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

Diffusion of Cd and Te adatoms on CdTe(111) surfaces: A computational study using density functional theory

NASA Astrophysics Data System (ADS)

Naderi, Ebadollah; Nanavati, Sachin; Majumder, Chiranjib; Ghaisas, S. V.

2015-01-01

CdTe is one of the most promising semiconductor for thin-film based solar cells. Here we report a computational study of Cd and Te adatom diffusion on the CdTe (111) A-type (Cd terminated) and B-type (Te terminated) surfaces and their migration paths. The atomic and electronic structure calculations are performed under the DFT formalism and climbing Nudge Elastic Band (cNEB) method has been applied to evaluate the potential barrier of the Te and Cd diffusion. In general the minimum energy site on the surface is labeled as Aa site. In case of Te and Cd on B-type surface, the sub-surface site (a site just below the top surface) is very close in energy to the A site. This is responsible for the subsurface accumulation of adatoms and therefore, expected to influence the defect formation during growth. The diffusion process of adatoms is considered from Aa (occupied) to Aa (empty) site at the nearest distance. We have explored three possible migration paths for the adatom diffusion. The adatom surface interaction is highly dependent on the type of the surface. Typically, Te interaction with both type (5.2 eV for A-type and 3.8 eV for B-type) is stronger than Cd interactions(2.4 eV for B-type and 0.39 eV for A-type). Cd interaction with the A-type surface is very weak. The distinct behavior of the A-type and B-type surfaces perceived in our study explain the need of maintaining the A-type surface during growth for smooth and stoichiometric growth.

Review on first-principles study of defect properties of CdTe as a solar cell absorber

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

Yang, Ji-Hui; Yin, Wan-Jian; Park, Ji-Sang

2016-07-15

CdTe is one of the leading materials for high-efficiency, low-cost, and thin-film solar cells. In this work, we review the recent first-principles study of defect properties of CdTe and present that: (1) When only intrinsic defects are present, p-type doping in CdTe is weak and the hole density is low due to the relatively deep acceptor levels of Cd vacancy. (2) When only intrinsic defects present, the dominant non-radiative recombination center in p-type CdTe is Te-2+/Cd, which limits the carrier lifetime to be around 200 ns. (3) Extrinsic p-type doping in CdTe by replacing Te with group V elements generallymore » will be limited by the formation of AX centers. This could be overcome through a non-equilibrium cooling process and the hole density can achieve 10^17 cm-3. However, the long-term stability will be a challenging issue. (4) Extrinsic p-type doping by replacing Cd with alkaline group I elements is limited by alkaline interstitials and a non-equilibrium cooling process can efficiently enhance the hole density to the order of 10^17 cm-3. (5) Cu and Cl treatments are discussed. In bulk CdTe, Cu can enhance p-type doping, but Cl is found to be unsuitable for this. Both Cu and Cl show segregation at grain boundaries, especially at those with Te-Te wrong bonds. (6) External impurities are usually incorporated by diffusion. Therefore, the diffusion processes in CdTe are investigated. We find that cation interstitial (Nai, Cui) diffusion follows relatively simple diffusion paths, but anion diffusion (Cli, Pi) follows more complicated paths due to the degenerated defect wavefunctions.« less

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

NASA Astrophysics Data System (ADS)

Seyler, Sean L.

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

An Extended Trajectory Mechanics Approach for Calculating the Path of a Pressure Transient: Derivation and Illustration

NASA Astrophysics Data System (ADS)

Vasco, D. W.

2018-04-01

Following an approach used in quantum dynamics, an exponential representation of the hydraulic head transforms the diffusion equation governing pressure propagation into an equivalent set of ordinary differential equations. Using a reservoir simulator to determine one set of dependent variables leaves a reduced set of equations for the path of a pressure transient. Unlike the current approach for computing the path of a transient, based on a high-frequency asymptotic solution, the trajectories resulting from this new formulation are valid for arbitrary spatial variations in aquifer properties. For a medium containing interfaces and layers with sharp boundaries, the trajectory mechanics approach produces paths that are compatible with travel time fields produced by a numerical simulator, while the asymptotic solution produces paths that bend too strongly into high permeability regions. The breakdown of the conventional asymptotic solution, due to the presence of sharp boundaries, has implications for model parameter sensitivity calculations and the solution of the inverse problem. For example, near an abrupt boundary, trajectories based on the asymptotic approach deviate significantly from regions of high sensitivity observed in numerical computations. In contrast, paths based on the new trajectory mechanics approach coincide with regions of maximum sensitivity to permeability changes.

Girsanov reweighting for path ensembles and Markov state models

NASA Astrophysics Data System (ADS)

Donati, L.; Hartmann, C.; Keller, B. G.

2017-06-01

The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor "on the fly" during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics.

Diffusion pseudotime robustly reconstructs lineage branching.

PubMed

Haghverdi, Laleh; Büttner, Maren; Wolf, F Alexander; Buettner, Florian; Theis, Fabian J

2016-10-01

The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.

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

NASA Astrophysics Data System (ADS)

Wróbel, Joanna; Kulawik, Adam

2016-06-01

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

Translational diffusion of cumene and 3-methylpentane on free surfaces and pore walls studied by time-of-flight secondary ion mass spectrometry

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

Souda, Ryutaro

2010-12-07

Mobility of molecules in confined geometry has been studied extensively, but the origins of finite size effects on reduction of the glass transition temperature, T{sub g}, are controversial especially for supported thin films. We investigate uptake of probe molecules in vapor-deposited thin films of cumene, 3-methylpentane, and heavy water using secondary ion mass spectrometry and discuss roles of individual molecular motion during structural relaxation and glass-liquid transition. The surface mobility is found to be enhanced for low-density glasses in the sub-T{sub g} region because of the diffusion of molecules on pore walls, resulting in densification of a film via poremore » collapse. Even for high-density glasses without pores, self-diffusion commences prior to the film morphology change at T{sub g}, which is thought to be related to decoupling between translational diffusivity and viscosity. The diffusivity of deeply supercooled liquid tends to be enhanced when it is confined in pores of amorphous solid water. The diffusivity of molecules is further enhanced at temperatures higher than 1.2-1.3 T{sub g} irrespective of the confinement.« less

Theoretical and experimental investigation of near-infrared light propagation in a model of the adult head.

PubMed

Okada, E; Firbank, M; Schweiger, M; Arridge, S R; Cope, M; Delpy, D T

1997-01-01

Near-infrared light propagation in various models of the adult head is analyzed by both time-of-flight measurements and mathematical prediction. The models consist of three- or four-layered slabs, the latter incorporating a clear cerebrospinal fluid (CSF) layer. The most sophisticated model also incorporates slots that imitate sulci on the brain surface. For each model, the experimentally measured mean optical path length as a function of source-detector spacing agrees well with predictions from either a Monte Carlo model or a finite-element method based on diffusion theory or a hybrid radiosity-diffusion theory. Light propagation in the adult head is shown to be highly affected by the presence of the clear CSF layer, and both the optical path length and the spatial sensitivity profile of the models with a CSF layer are quite different from those without the CSF layer. However, the geometry of the sulci and the boundary between the gray and the white matter have little effect on the detected light distribution.

Microscale cavitation as a mechanism for nucleating earthquakes at the base of the seismogenic zone.

PubMed

Verberne, Berend A; Chen, Jianye; Niemeijer, André R; de Bresser, Johannes H P; Pennock, Gillian M; Drury, Martyn R; Spiers, Christopher J

2017-11-21

Major earthquakes frequently nucleate near the base of the seismogenic zone, close to the brittle-ductile transition. Fault zone rupture at greater depths is inhibited by ductile flow of rock. However, the microphysical mechanisms responsible for the transition from ductile flow to seismogenic brittle/frictional behaviour at shallower depths remain unclear. Here we show that the flow-to-friction transition in experimentally simulated calcite faults is characterized by a transition from dislocation and diffusion creep to dilatant deformation, involving incompletely accommodated grain boundary sliding. With increasing shear rate or decreasing temperature, dislocation and diffusion creep become too slow to accommodate the imposed shear strain rate, leading to intergranular cavitation, weakening, strain localization, and a switch from stable flow to runaway fault rupture. The observed shear instability, triggered by the onset of microscale cavitation, provides a key mechanism for bringing about the brittle-ductile transition and for nucleating earthquakes at the base of the seismogenic zone.

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

NASA Astrophysics Data System (ADS)

D'Cruz, Noella L.

2012-05-01

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

Temporal dynamics of catchment transit times from stable isotope data

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

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

NASA Astrophysics Data System (ADS)

Ertaş, Mehmet; Keskin, Mustafa

2015-03-01

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

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

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

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

Markov State Models of gene regulatory networks.

PubMed

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

2017-02-06

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

Lensless digital holography with diffuse illumination through a pseudo-random phase mask.

PubMed

Bernet, Stefan; Harm, Walter; Jesacher, Alexander; Ritsch-Marte, Monika

2011-12-05

Microscopic imaging with a setup consisting of a pseudo-random phase mask, and an open CMOS camera, without an imaging objective, is demonstrated. The pseudo random phase mask acts as a diffuser for an incoming laser beam, scattering a speckle pattern to a CMOS chip, which is recorded once as a reference. A sample which is afterwards inserted somewhere in the optical beam path changes the speckle pattern. A single (non-iterative) image processing step, comparing the modified speckle pattern with the previously recorded one, generates a sharp image of the sample. After a first calibration the method works in real-time and allows quantitative imaging of complex (amplitude and phase) samples in an extended three-dimensional volume. Since no lenses are used, the method is free from lens abberations. Compared to standard inline holography the diffuse sample illumination improves the axial sectioning capability by increasing the effective numerical aperture in the illumination path, and it suppresses the undesired so-called twin images. For demonstration, a high resolution spatial light modulator (SLM) is programmed to act as the pseudo-random phase mask. We show experimental results, imaging microscopic biological samples, e.g. insects, within an extended volume at a distance of 15 cm with a transverse and longitudinal resolution of about 60 μm and 400 μm, respectively.

Diffusive sampling of methylene chloride with solid phase microextraction.

PubMed

Chen, Cheng-Yao; Hsiech, Chunming; Lin, Jia-Ming

2006-12-29

This study examined the characteristics of a solid phase microextraction (SPME) assembly as a passive sampler to determine the short-term exposure level (STEL) of methylene chloride. Two types of SPME fibers and six sampling-related factors were chosen and nested in an L(18) Taguchi's orthogonal array. Samples were thermally desorpted and analyzed by gas chromatograph equipped with an electron capture detector (GC/ECD). The use of 85-mum Carboxen/polydimethylsiloxane (Car/PDMS) fibers resulted in greater adsorbed mass, which was highly correlated with the product of concentration and sampling time (r>0.99, p<0.0001), than 85-microm polyacrylate fibers. The sampling rate (SR) of the 85-microm Carboxen/polydimethylsiloxane fibers was not significantly affected by variations in relative humidity (0-80%) and coexistent toluene (none to 100 ppm). Variance of sampling rate was predominantly attributed to the diffusive path length (86.4%) and sampling time (5.7%). With diffusive paths of 3, 10 and 15 mm, the sampling rates of 85-microm Carboxen/polydimethylsiloxane fibers for methylene chloride were 1.4 x 10(-2), 7.7 x 10(-3) and 5.1 x1 0(-3)mL min(-1), respectively. The measured sampling rates were greater than the theoretical values, and decreased with increment of sampling time until they came to constant.

Improved diffusing wave spectroscopy based on the automatized determination of the optical transport and absorption mean free path

NASA Astrophysics Data System (ADS)

Zhang, Chi; Reufer, Mathias; Gaudino, Danila; Scheffold, Frank

2017-11-01

Diffusing wave spectroscopy (DWS) can be employed as an optical rheology tool with numerous applications for studying the structure, dynamics and linear viscoelastic properties of complex fluids, foams, glasses and gels. To carry out DWS measurements, one first needs to quantify the static optical properties of the sample under investigation, i.e. the transport mean free path l * and the absorption length l a. In the absence of absorption this can be done by comparing the diffuse optical transmission to a calibration sample whose l * is known. Performing this comparison however is cumbersome, time consuming, and prone to mistakes by the operator. Moreover, already weak absorption can lead to significant errors. In this paper, we demonstrate the implementation of an automatized approach, based on which the DWS measurement procedure can be simplified significantly. By comparison with a comprehensive set of calibration measurements we cover the entire parameter space relating measured count rates ( CR t , CR b ) to ( l *, l a). Based on this approach we can determine l * and la of an unknown sample accurately thus making the additional measurement of a calibration sample obsolete. We illustrate the use of this approach by monitoring the coarsening of a commercially available shaving foam with DWS.

(99)Tc(VII) Retardation, Reduction, and Redox Rate Scaling in Naturally Reduced Sediments.

PubMed

Liu, Yuanyuan; Liu, Chongxuan; Kukkadapu, Ravi K; McKinley, James P; Zachara, John; Plymale, Andrew E; Miller, Micah D; Varga, Tamas; Resch, Charles T

2015-11-17

An experimental and modeling study was conducted to investigate pertechnetate (Tc(VII)O4(-)) retardation, reduction, and rate scaling in three sediments from Ringold formation at U.S. Department of Energy's Hanford site, where (99)Tc is a major contaminant in groundwater. Tc(VII) was reduced in all the sediments in both batch reactors and diffusion columns, with a faster rate in a sediment containing a higher concentration of HCl-extractable Fe(II). Tc(VII) migration in the diffusion columns was reductively retarded with retardation degrees correlated with Tc(VII) reduction rates. The reduction rates were faster in the diffusion columns than those in the batch reactors, apparently influenced by the spatial distribution of redox-reactive minerals along transport paths that supplied Tc(VII). X-ray computed tomography and autoradiography were performed to identify the spatial locations of Tc(VII) reduction and transport paths in the sediments, and results generally confirmed the newly found behavior of reaction rate changes from batch to column. The results from this study implied that Tc(VII) migration can be reductively retarded at Hanford site with a retardation degree dependent on reactive Fe(II) content and its distribution in sediments. This study also demonstrated that an effective reaction rate may be faster in transport systems than that in well-mixed reactors.

Vertical mass transfer in open channel flow

USGS Publications Warehouse

Jobson, Harvey E.

1968-01-01

The vertical mass transfer coefficient and particle fall velocity were determined in an open channel shear flow. Three dispersants, dye, fine sand and medium sand, were used with each of three flow conditions. The dispersant was injected as a continuous line source across the channel and downstream concentration profiles were measured. From these profiles along with the measured velocity distribution both the vertical mass transfer coefficient and the local particle fall velocity were determined.The effects of secondary currents on the vertical mixing process were discussed. Data was taken and analyzed in such a way as to largely eliminate the effects of these currents on the measured values. A procedure was developed by which the local value of the fall velocity of sand sized particles could be determined in an open channel flow. The fall velocity of the particles in the turbulent flow was always greater than their fall velocity in quiescent water. Reynolds analogy between the transfer of momentum and marked fluid particles was further substantiated. The turbulent Schmidt number was shown to be approximately 1.03 for an open channel flow with a rough boundary. Eulerian turbulence measurements were not sufficient to predict the vertical transfer coefficient. Vertical mixing of sediment is due to three semi-independent processes. These processes are: secondary currents, diffusion due to tangential velocity fluctuations and diffusion due to the curvature of the fluid particle path lines. The diffusion coefficient due to tangential velocity fluctuations is approximately proportional to the transfer coefficient of marked fluid particles. The proportionality constant is less than or equal to 1.0 and decreases with increasing particle size. The diffusion coefficient due to the curvature of the fluid particle path lines is not related to the diffusion coefficient for marked fluid particles and increases with particle size, at least for sediment particles in the sand size range. The total sediment transfer coefficient is equal to the sum of the coefficient due to tangential velocity fluctuations and the coefficient due to the curvature of the fluid particle path lines. A numerical solution to the conservation of mass equation is given. The effects of the transfer coefficient, fall velocity and bed conditions on the predicted concentration profiles are illustrated.

Size quantization in high-temperature superconducting cuprates and a link to Einstein's diffusion law

NASA Astrophysics Data System (ADS)

Roeser, H. P.; Bohr, A.; Haslam, D. T.; López, J. S.; Stepper, M.; Nikoghosyan, A. S.

2012-07-01

Optimum doping of high-temperature superconductors (HTSC) defines a superconducting unit volume for each HTSC. For a single-mode HTSC, e.g., a cuprate with one CuO2 plane, the volume is given by Vsc=cx2, where c is the unit cell height and x the doping distance. The experimental resistivity at Tc is connected to the structure by ρ(exp)≈c×h/(2e2). Combining this result with the classical definition of resistivity leads to an equation similar to Einstein's diffusion law x2/(2τ)=h/(2Meff)=D, where τ is the relaxation time, Meff=2me and D the diffusion constant. It has also been shown that the mean free path d=x. The Einstein-Smoluchowski diffusion relation D=μkBTc provides a connection to Tc.

High-Temperature Thermal Diffusivity Measurements of Silicate Glasses

NASA Astrophysics Data System (ADS)

Pertermann, M.; Hofmeister, A. M.; Whittington, A. G.; Spera, F. J.; Zayac, J.

2005-12-01

Transport of heat in geologically relevant materials is of great interest because of its key role in heat transport, magmatism and volcanic activity on Earth. To better understand the thermal properties of magmatic materials at high temperatures, we measured the thermal diffusivity of four synthetic end-member silicate glasses with the following compositions: albite (NaAlSi3O8), orthoclase (KAlSi3O8), anorthite (CaAl2Si2O8), and diopside (CaMgSi2O6). Thermal diffusivity measurements were conducted with the laser-flash technique and data were acquired from room temperature to a maximum temperature near 1100°C, depending on the glass transition temperature. The presence of sub-mm sized bubbles in one of the orthoclase samples had no discernable effect on measured diffusivities. At room temperature, the three feldspar-type glasses have thermal diffusivity (D) values of 0.58-0.61 mm2/s, whereas the diopside glass has 0.52 mm2/s. With increasing temperature, D decreases by 5-10% (relative) for all samples and becomes virtually constant at intermediate temperatures. At higher temperatures, the anorthite and diopside glasses exhibit significant drops in thermal diffusivity over a 50-100°C interval, correlating with previously published heat capacity changes near the glass transition for these compositions. For anorthite, D (in mm2/s) decreases from 0.48 at 750-860°C to 0.36 at 975-1075°C; for diopside, D changes from 0.42 at 630-750°C to 0.30 at 850-910°C, corresponding to relative drops of 24 and 29%, respectively. Albite and orthoclase glasses do not exhibit this change and also lack significant changes in heat capacity near the glass transition. Instead, D is constant at 400-800°C for albite, and for orthoclase values go through a minimum at 500-600°C before increasing slightly towards 1100°C but it never exceeds the room temperature D. Our data on thermal diffusivity correlate closely with other thermophysical properties. Thus, at least in case of simple compositions, measurement of thermal diffusivity of glasses above the glass transition may closely approximate the behavior of magmatic liquids. For the orthoclase composition, our new data show that the thermal diffusivity of glass in the range of 20-1100°C is clearly lower than that of orthoclase single crystals (Hoefer and Schilling, 2002, Phys Chem Minerals, 29, 571-584).

Kinetics of nitric oxide and oxygen gases on porous Y-stabilized ZrO2-based sensors.

PubMed

Killa, Sajin; Cui, Ling; Murray, Erica P; Mainardi, Daniela S

2013-08-16

Using impedance spectroscopy the electrical response of sensors with various porous Y-stabilized ZrO2 (YSZ) microstructures was measured for gas concentrations containing 0-100 ppm NO with 10.5%O2 at temperatures ranging from 600-700 °C. The impedance response increased substantially as the sensor porosity increased from 46%-50%. Activation energies calculated based on data from the impedance measurements increased in magnitude (97.4-104.9 kJ/mol for 100 ppm NO) with respect to increasing YSZ porosity. Analysis of the oxygen partial pressure dependence of the sensors suggested that dissociative adsorption was the dominant rate limiting. The PWC/DNP theory level was used to investigate the gas-phase energy barrier of the 2NO+O2 → 2NO2 reaction on a 56-atom YSZ/Au model cluster using Density Functional Theory and Linear Synchronous Transit/Quadratic Synchronous Transit calculations. The reaction path shows oxygen surface reactions that begin with NO association with adsorbed O2 on a Zr surface site, followed by O2 dissociative adsorption, atomic oxygen diffusion, and further NO2 formation. The free energy barrier was calculated to be 181.7 kJ/mol at PWC/DNP. A qualitative comparison with the extrapolated data at 62% ± 2% porosity representing the YSZ model cluster indicates that the calculated barriers are in reasonable agreement with experiments, especially when the RPBE functional is used.

Phonon Scattering and Confinement in Crystalline Films

NASA Astrophysics Data System (ADS)

Parrish, Kevin D.

The operating temperature of energy conversion and electronic devices affects their efficiency and efficacy. In many devices, however, the reference values of the thermal properties of the materials used are no longer applicable due to processing techniques performed. This leads to challenges in thermal management and thermal engineering that demand accurate predictive tools and high fidelity measurements. The thermal conductivity of strained, nanostructured, and ultra-thin dielectrics are predicted computationally using solutions to the Boltzmann transport equation. Experimental measurements of thermal diffusivity are performed using transient grating spectroscopy. The thermal conductivities of argon, modeled using the Lennard-Jones potential, and silicon, modeled using density functional theory, are predicted under compressive and tensile strain from lattice dynamics calculations. The thermal conductivity of silicon is found to be invariant with compression, a result that is in disagreement with previous computational efforts. This difference is attributed to the more accurate force constants calculated from density functional theory. The invariance is found to be a result of competing effects of increased phonon group velocities and decreased phonon lifetimes, demonstrating how the anharmonic contribution of the atomic potential can scale differently than the harmonic contribution. Using three Monte Carlo techniques, the phonon-boundary scattering and the subsequent thermal conductivity reduction are predicted for nanoporous silicon thin films. The Monte Carlo techniques used are free path sampling, isotropic ray-tracing, and a new technique, modal ray-tracing. The thermal conductivity predictions from all three techniques are observed to be comparable to previous experimental measurements on nanoporous silicon films. The phonon mean free paths predicted from isotropic ray-tracing, however, are unphysical as compared to those predicted by free path sampling. Removing the isotropic assumption, leading to the formulation of modal ray-tracing, corrects the mean free path distribution. The effect of phonon line-of-sight is investigated in nanoporous silicon films using free path sampling. When the line-of-sight is cut off there is a distinct change in thermal conductivity versus porosity. By analyzing the free paths of an obstructed phonon mode, it is concluded that the trend change is due to a hard upper limit on the free paths that can exist due to the nanopore geometry in the material. The transient grating technique is an optical contact-less laser based experiment for measuring the in-plane thermal diffusivity of thin films and membranes. The theory of operation and physical setup of a transient grating experiment is detailed. The procedure for extracting the thermal diffusivity from the raw experimental signal is improved upon by removing arbitrary user choice in the fitting parameters used and constructing a parameterless error minimizing procedure. The thermal conductivity of ultra-thin argon films modeled with the Lennard-Jones potential is calculated from both the Monte Carlo free path sampling technique and from explicit reduced dimensionality lattice dynamics calculations. In these ultra-thin films, the phonon properties are altered in more than a perturbative manner, referred to as the confinement regime. The free path sampling technique, which is a perturbative method, is compared to a reduced dimensionality lattice dynamics calculation where the entire film thickness is taken as the unit cell. Divergence in thermal conductivity magnitude and trend is found at few unit cell thick argon films. Although the phonon group velocities and lifetimes are affected, it is found that alterations to the phonon density of states are the primary cause of the deviation in thermal conductivity in the confinement regime.

Populational equilibrium through exosome-mediated Wnt signaling in tumor progression of diffuse large B-cell lymphoma.

PubMed

Koch, Raphael; Demant, Martin; Aung, Thiha; Diering, Nina; Cicholas, Anna; Chapuy, Bjoern; Wenzel, Dirk; Lahmann, Marlen; Güntsch, Annemarie; Kiecke, Christina; Becker, Sabrina; Hupfeld, Timo; Venkataramani, Vivek; Ziepert, Marita; Opitz, Lennart; Klapper, Wolfram; Trümper, Lorenz; Wulf, Gerald G

2014-04-03

Tumors are composed of phenotypically heterogeneous cell populations. The nongenomic mechanisms underlying transitions and interactions between cell populations are largely unknown. Here, we show that diffuse large B-cell lymphomas possess a self-organized infrastructure comprising side population (SP) and non-SP cells, where transitions between clonogenic states are modulated by exosome-mediated Wnt signaling. DNA methylation modulated SP-non-SP transitions and was correlated with the reciprocal expressions of Wnt signaling pathway agonist Wnt3a in SP cells and the antagonist secreted frizzled-related protein 4 in non-SP cells. Lymphoma SP cells exhibited autonomous clonogenicity and exported Wnt3a via exosomes to neighboring cells, thus modulating population equilibrium in the tumor.

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

PubMed

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

2017-10-21

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

New route for hollow materials

NASA Astrophysics Data System (ADS)

Rivaldo-Gómez, C. M.; Ferreira, F. F.; Landi, G. T.; Souza, J. A.

2016-08-01

Hollow micro/nano structures form an important family of functional materials. We have used the thermal oxidation process combined with the passage of electric current during a structural phase transition to disclose a colossal mass diffusion transfer of Ti ions. This combination points to a new route for fabrication of hollow materials. A structural phase transition at high temperature prepares the stage by giving mobility to Ti ions and releasing vacancies to the system. The electric current then drives an inward delocalization of vacancies, condensing into voids, and finally turning into a big hollow. This strong physical phenomenon leading to a colossal mass transfer through ionic diffusion is suggested to be driven by a combination of phase transition and electrical current followed by chemical reaction. We show this phenomenon for Ti leading to TiO2 microtube formation, but we believe that it can be used to other metals undergoing structural phase transition at high temperatures.

Regression-based model of skin diffuse reflectance for skin color analysis

NASA Astrophysics Data System (ADS)

Tsumura, Norimichi; Kawazoe, Daisuke; Nakaguchi, Toshiya; Ojima, Nobutoshi; Miyake, Yoichi

2008-11-01

A simple regression-based model of skin diffuse reflectance is developed based on reflectance samples calculated by Monte Carlo simulation of light transport in a two-layered skin model. This reflectance model includes the values of spectral reflectance in the visible spectra for Japanese women. The modified Lambert Beer law holds in the proposed model with a modified mean free path length in non-linear density space. The averaged RMS and maximum errors of the proposed model were 1.1 and 3.1%, respectively, in the above range.

Gas turbine engine with radial diffuser and shortened mid section

DOEpatents

Charron, Richard C.; Montgomery, Matthew D.

2015-09-08

An industrial gas turbine engine (10), including: a can annular combustion assembly (80), having a plurality of discrete flow ducts configured to receive combustion gas from respective combustors (82) and deliver the combustion gas along a straight flow path at a speed and orientation appropriate for delivery directly onto the first row (56) of turbine blades (62); and a compressor diffuser (32) having a redirecting surface (130, 140) configured to receive an axial flow of compressed air and redirect the axial flow of compressed air radially outward.

Radon detection in conical diffusion chambers: Monte Carlo calculations and experiment

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

Rickards, J.; Golzarri, J. I.; Espinosa, G., E-mail: espinosa@fisica.unam.mx

2015-07-23

The operation of radon detection diffusion chambers of truncated conical shape was studied using Monte Carlo calculations. The efficiency was studied for alpha particles generated randomly in the volume of the chamber, and progeny generated randomly on the interior surface, which reach track detectors placed in different positions within the chamber. Incidence angular distributions, incidence energy spectra and path length distributions are calculated. Cases studied include different positions of the detector within the chamber, varying atmospheric pressure, and introducing a cutoff incidence angle and energy.

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

NASA Astrophysics Data System (ADS)

Channell, J. E. T.

2017-06-01

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

Mobility of Supercooled liquid Toluene, Ethylbenzene, and Benzene near their Glass Transition Temperatures Investigated using Inert Gas Permeation

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

May, Robert A.; Smith, R. Scott; Kay, Bruce D.

We investigate the mobility of supercooled liquid toluene, ethylbenzene, and benzene near their respective glass transition temperatures (Tg). The permeation rate of Ar, Kr, and Xe through the supercooled liquid created when initially amorphous overlayers heated above their glass transition temperature is used to determine the diffusivity. Amorphous benzene crystallizes at temperatures well below its Tg and as a result the inert gas underlayer remains trapped until the onset of benzene desorption. In contrast, for toluene and ethylbenzene the onset of inert gas permeation is observed at temperatues near Tg. The inert gas desorption peak temperature as a function ofmore » the heating rate and overlayer thickness is used to quantify the diffusivity of supercooled liquid toluene and ethylbenzene from 115 K to 135 K. In this temperature range, diffusivities are found to vary across five orders of magnitude (~10-14 to 10-9 cm2/s). These data are compared to viscosity measurements and used to determine the low temperature fractional Stokes-Einstein exponent. Efforts to determine the diffusivity of a mixture of benzene and ethylbenzene are detailed, and the effect of mixing these materials on benzene crystallization is explored using infrared spectroscopy.« less

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.

Self-diffusion on iridium (100). A structure investigation by field-ion microscopy

NASA Astrophysics Data System (ADS)

Friedl, A.; Schütz, O.; Müller, K.

1992-04-01

An iridium atom was thermally activated for diffusion on the (100) terrace of an Ir tip. The residence sites of the atom between diffusion cycles were recorded by means of a computer-controlled video system which generates a map of all occupied sites. For a field evaporated tip at low temperature this map is a c(2 × 2) grid indicating that only every other fourfold hollow in every other row of an undistor ted (100) surface can be occupied by a diffusing atom. This extraordinary behaviour was already reported by Chen and Tsong [Phys. Rev. Lett. 64 (1990) 3147]. The authors base their interpretation on an exchange diffusion mechanism. As an alternative explanation we propose a local adsorbate induced (2 × 2) reconstruction of the substrate. After heating the same terrace to temperatures above 500 K the residence map of the Ir atom indicates a (1 × 1) structure which, however, contains residues of a c(2 × 2) diffusion pattern: while the diffusion still takes place mainly on a c(2 × 2) sublattice, the diffusion path changes occasionally from one sublattice to the other. This can also be understood by local adsorbate induced distortions.

Innovation-diffusion: a geographical study of the transition of family limitation practice in Taiwan.

PubMed

Ting, T Y

1984-09-01

This paper uses map analysis to study the transition of family limitation practice in Taiwan between 1961-80. The innovation-diffusion perspective emphasizes that birth control, particularly contraception, is a recent innovation and is essentially new in human culture. The innovation-diffusion theory assumes that the decline of fertility began in a setting where there was no, or at most very limited, previous practice of birth control. The theory emphasizes the importance of the spread of information. It also assumes that innovation starts in metropolitan centers, diffuses to other urban places with some delay, and penetrates to rural areas still later. Innovation behavior also diffuses from 1 area to another which is culturally and linguistically similar. Although there was some urban to rural diffusion from the Taiwan family planning program, the government supported program provided services more evenly between urban and rural areas, thus somewhat limiting the diffusion effect from the program. For the diffusion of family practice in Taiwan, it is expected that the availability of of information about and means of family limitation practice may effect the rate of the increase of small m values -- an index of family limitation -- in an area. The case study of Pingtung county shows that the demand-side diffusion from urban to rural areas was important in the earlier decade of the transition of family plimitation practice, but distance from urban center was less important as practice became more uniform through diffusion. Ethnicity, whether or not the township was dominated by Hakka or Fukienese, also seems to have played an important role in determining the pace at which the local residents adopted family practice limitation. Hakka townships seem to have adopted family limitation practice more slowly than Fukienese townships about the same distance from the urban center. The map analysis of Pingtung county provides descriptive evidence to support the diffusion of family limitation from urban centers to distant areas, while ethnic variables like Hakka population tend to delay the adoption of family limitation practice. In general, the urban center had higher m values than the surrounding rural areas in Pingtung county and for areas other than the urban center the the level of m values is a negative function of the distance to the urban center.

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

ERIC Educational Resources Information Center

Lester, Leanne; Waters, Stacey; Cross, Donna

2013-01-01

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

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

ERIC Educational Resources Information Center

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

2010-01-01

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

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

PubMed

Tsuzuki, Manabu

2015-03-30

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

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

NASA Astrophysics Data System (ADS)

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

2011-07-01

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

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

PubMed

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

2014-05-06

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

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

PubMed Central

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

2014-01-01

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

Traveling salesman problem with a center.

PubMed

Lipowski, Adam; Lipowska, Dorota

2005-06-01

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

Transitioning DARPA Technology

DTIC Science & Technology

2001-05-01

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

Doi-Peliti path integral methods for stochastic systems with partial exclusion

NASA Astrophysics Data System (ADS)

Greenman, Chris D.

2018-09-01

Doi-Peliti methods are developed for stochastic models with finite maximum occupation numbers per site. We provide a generalized framework for the different Fock spaces reported in the literature. Paragrassmannian techniques are then utilized to construct path integral formulations of factorial moments. We show that for many models of interest, a Magnus expansion is required to construct a suitable action, meaning actions containing a finite number of terms are not always feasible. However, for such systems, perturbative techniques are still viable, and for some examples, including carrying capacity population dynamics, and diffusion with partial exclusion, the expansions are exactly summable.

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

NASA Astrophysics Data System (ADS)

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

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

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

DOE PAGES

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

2014-11-07

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

Phase Stability and Transformations in Vanadium Oxide Nanocrystals

NASA Astrophysics Data System (ADS)

Bergerud, Amy Jo

Vanadium oxides are both fascinating and complex, due in part to the many compounds and phases that can be stabilized as well as the phase transformations which occur between them. The metal to insulator transitions (MITs) that take place in vanadium oxides are particularly interesting for both fundamental and applied study as they can be induced by a variety of stimuli ( i.e., temperature, pressure, doping) and utilized in many applications (i.e., smart windows, sensors, phase change memory). Nanocrystals also tend to demonstrate interesting phase behavior, due in part to the enhanced influence of surface energy on material thermodynamics. Vanadium oxide nanocrystals are thus expected to demonstrate very interesting properties in regard to phase stability and phase transformations, although synthesizing vanadium oxides in nanocrystal form remains a challenge. Vanadium sesquioxide (V2O3) is an example of a material that undergoes a MIT. For decades, the low temperature monoclinic phase and high temperature corundum phase were the only known crystal structures of V2O3. However, in 2011, a new metastable polymorph of V2O3 was reported with a cubic, bixbyite crystal structure. In Chapter 2, a colloidal route to bixbyite V2O 3 nanocrystals is presented. In addition to being one of the first reported observations of the bixbyite phase in V2O3, it is also one of the first successful colloidal syntheses of any of the vanadium oxides. The nanocrystals possess a flower-like morphology, the size and shape of which are dependent on synthesis time and temperature, respectively. An aminolysis reaction mechanism is determined from Fourier transform infrared spectroscopy data and the bixbyite crystal structure is confirmed by Rietveld refinement of X-ray diffraction (XRD) data. Phase stability is assessed in both air and inert environments, confirming the metastable nature of the material. Upon heating in an inert atmosphere above 700°C, the nanocrystals irreversibly transform to the bulk stable corundum phase of V2O3 with concurrent particle coarsening. This, in combination with the enhanced stability of the nanocrystals over bulk, suggests that the bixbyite phase may be stabilized due to surface energy effects, a well-known phenomenon in nanocrystal research. In Chapter 3, the reversible incorporation of oxygen in bixbyite V 2O3 is reported, which can be controlled by varying temperature and oxygen partial pressure. Based on XRD and thermogravimetric analysis, it is found that oxygen occupies interstitial sites in the bixbyite lattice. Two oxygen atoms per unit cell can be incorporated rapidly and with minimal changes to the structure while the addition of three or more oxygen atoms destabilizes the structure, resulting in a phase change that can be reversed upon oxygen removal. Density functional theory (DFT) supports the reversible occupation of interstitial sites in bixbyite by oxygen and the 1.1 eV barrier to oxygen diffusion predicted by DFT matches the activation energy of the oxidation process derived from observations by in situ XRD. The observed rapid oxidation kinetics are thus facilitated by short diffusion paths through the bixbyite nanocrystals. Due to the exceptionally low temperatures of oxidation and reduction, this material, made from earth-abundant atoms, is proposed for use in oxygen storage applications, where oxygen is reversibly stored and released. Further oxidation of bixbyite V2O3 under controlled oxygen partial pressure can lead to the formation of nanocrystalline vanadium dioxide (VO2), a material that is studied for its MIT that occurs at 68 C in the bulk. This transformation is accompanied by a change in crystal structure, from monoclinic to rutile phase, and a change in optical properties, from infrared transparent to infrared blocking. Because of this, VO2 is promising for thermochromic smart window applications, where optical properties vary with temperature. Recently, alternative stimuli have been utilized to trigger MITs in VO2, including electrochemical gating. Rather than inducing the expected monoclinic to rutile phase transition as originally proposed, electrochemical gating of the insulating phase was recently shown to induce oxygen vacancy formation in VO2, thereby inducing metallization, while the characteristic V-V dimerization of the monoclinic phase was retained. In Chapter 4, the preparation and electrochemical reduction of VO2 nanocrystal films is presented. The nanocrystalline morphology allows for the study of transformations under conditions that enhance the gating effect by creating a large VO2-electrolyte interfacial area and by reducing the path length for diffusion. The resulting transitions are observed optically, from insulator to metal to insulator and back, with in situ visible-near infrared spectroelectrochemistry and correlated with structural changes monitored by Raman and X-ray absorption spectroscopies. The never-before-seen transition to an insulating phase under progressive electrochemical reduction is attributed to an oxygen defect induced phase transition to a new phase. This is likely enabled by the nanocrystalline nature of the sample, which may enhance the kinetics of oxygen diffusion, support a higher degree of lattice expansion-induced strain, or simply alter the thermodynamics of the system.

Interactogeneous: Disease Gene Prioritization Using Heterogeneous Networks and Full Topology Scores

PubMed Central

Gonçalves, Joana P.; Francisco, Alexandre P.; Moreau, Yves; Madeira, Sara C.

2012-01-01

Disease gene prioritization aims to suggest potential implications of genes in disease susceptibility. Often accomplished in a guilt-by-association scheme, promising candidates are sorted according to their relatedness to known disease genes. Network-based methods have been successfully exploiting this concept by capturing the interaction of genes or proteins into a score. Nonetheless, most current approaches yield at least some of the following limitations: (1) networks comprise only curated physical interactions leading to poor genome coverage and density, and bias toward a particular source; (2) scores focus on adjacencies (direct links) or the most direct paths (shortest paths) within a constrained neighborhood around the disease genes, ignoring potentially informative indirect paths; (3) global clustering is widely applied to partition the network in an unsupervised manner, attributing little importance to prior knowledge; (4) confidence weights and their contribution to edge differentiation and ranking reliability are often disregarded. We hypothesize that network-based prioritization related to local clustering on graphs and considering full topology of weighted gene association networks integrating heterogeneous sources should overcome the above challenges. We term such a strategy Interactogeneous. We conducted cross-validation tests to assess the impact of network sources, alternative path inclusion and confidence weights on the prioritization of putative genes for 29 diseases. Heat diffusion ranking proved the best prioritization method overall, increasing the gap to neighborhood and shortest paths scores mostly on single source networks. Heterogeneous associations consistently delivered superior performance over single source data across the majority of methods. Results on the contribution of confidence weights were inconclusive. Finally, the best Interactogeneous strategy, heat diffusion ranking and associations from the STRING database, was used to prioritize genes for Parkinson’s disease. This method effectively recovered known genes and uncovered interesting candidates which could be linked to pathogenic mechanisms of the disease. PMID:23185389

Size Dependent Pore Formation in Germanium Nanowires Undergoing Reversible Delithiation Observed by In Situ TEM

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

Lu, Xiaotang; He, Yang; Mao, Scott X.

Germanium (Ge) nanowires coated with an amorphous silicon (Si) shell undergoing lithiation and delithiation were studied using in situ transmission electron microscopy (TEM). Delithiation creates pores in nanowires with diameters larger than ~25 nm, but not in smaller diameter nanowires. The formation of pores in Ge nanowires undergoing delithiation has been observed before in in situ TEM experiments, but there has been no indication that a critical diameter exists below which pores do not form. Pore formation occurs as a result of fast lithium diffusion compared to vacancy migration. We propose that a short diffusion path for vacancies to themore » nanowire surface plays a role in limiting pore formation even when lithium diffusion is fast.« less

Compatibility of buffered uranium carbides with tungsten.

NASA Technical Reports Server (NTRS)

Phillips, W. M.

1971-01-01

Results of compatibility tests between tungsten and hyperstoichiometric uranium carbide alloys run at 1800 C for 1000 and 2500 hours. These tests compared tungsten-buffered uranium carbide with tungsten-buffered uranium-zirconium carbide. The zirconium carbide addition appeared to widen the homogeneity range of the uranium carbide, making additional carbon available for reaction. Reaction layers could be formed by either of two diffusion paths, one producing UWC2, while the second resulted in the formation of W2C. UWC2 acts as a diffusion barrier for carbon and slows the growth of the reaction layer with time, while carbon diffusion is relatively rapid in W2C, allowing equilibrium to be reached in less than 2500 hours at a temperature of 1800 C.

Exciton Transport Simulations in Phenyl Cored Thiophene Dendrimers

NASA Astrophysics Data System (ADS)

Kim, Kwiseon; Erkan Kose, Muhammet; Graf, Peter; Kopidakis, Nikos; Rumbles, Garry; Shaheen, Sean E.

2009-03-01

Phenyl cored 3-arm and 4-arm thiophene dendrimers are promising materials for use in photovoltaic devices. It is important to understand the energy transfer mechanisms in these molecules to guide the synthesis of novel dendrimers with improved efficiency. A method is developed to estimate the exciton diffusion lengths for the dendrimers and similar chromophores in amorphous films. The approach exploits Fermi's Golden Rule to estimate the energy transfer rates for an ensemble of bimolecular complexes in random orientations. Using Poisson's equation to evaluate Coulomb integrals led to efficient calculation of excitonic couplings between the transition densities. Monte-Carlo simulations revealed the dynamics of energy transport in the dendrimers. Experimental exciton diffusion lengths of the dendrimers range 10 ˜ 20 nm, increasing with the size of the dendrimer. Simulated diffusion lengths correlate well with experiments. The chemical structure of the chromophore, the shape of the transition densities and the exciton lifetime are found to be the most important factors that determine the exciton diffusion length in amorphous films.

Transverse single-file diffusion and enhanced longitudinal diffusion near a subcritical bifurcation

NASA Astrophysics Data System (ADS)

Dessup, Tommy; Coste, Christophe; Saint Jean, Michel

2018-05-01

A quasi-one-dimensional system of repelling particles undergoes a configurational phase transition when the transverse confining potential decreases. Below a threshold, it becomes energetically favorable for the system to adopt one of two staggered raw patterns, symmetric with respect to the system axis. This transition is a subcritical pitchfork bifurcation for short range interactions. As a consequence, the homogeneous zigzag pattern is unstable in a finite zigzag amplitude range [hC 1,hC 2] . We exhibit strong qualitative effects of the subcriticality on the thermal motions of the particles. When the zigzag amplitude is close enough to the limits hC 1 and hC 2, a transverse vibrational soft mode occurs which induces a strongly subdiffusive behavior of the transverse fluctuations, similar to single-file diffusion. On the contrary, the longitudinal fluctuations are enhanced, with a diffusion coefficient which is more than doubled. Conversely, a simple measurement of the thermal fluctuations allows a precise determination of the bifurcation thresholds.

Angular distribution of diffuse reflectance from incoherent multiple scattering in turbid media.

PubMed

Gao, M; Huang, X; Yang, P; Kattawar, G W

2013-08-20

The angular distribution of diffuse reflection is elucidated with greater understanding by studying a homogeneous turbid medium. We modeled the medium as an infinite slab and studied the reflection dependence on the following three parameters: the incident direction, optical depth, and asymmetry factor. The diffuse reflection is produced by incoherent multiple scattering and is solved through radiative transfer theory. At large optical depths, the angular distribution of the diffuse reflection with small incident angles is similar to that of a Lambertian surface, but, with incident angles larger than 60°, the angular distributions have a prominent reflection peak around the specular reflection angle. These reflection peaks are found originating from the scattering within one transport mean free path in the top layer of the medium. The maximum reflection angles for different incident angles are analyzed and can characterize the structure of angular distributions for different asymmetry factors and optical depths. The properties of the angular distribution can be applied to more complex systems for a better understanding of diffuse reflection.

Atomistic modeling of water diffusion in hydrolytic biomaterials.

PubMed

Gautieri, Alfonso; Mezzanzanica, Andrea; Motta, Alberto; Redealli, Alberto; Vesentini, Simone

2012-04-01

One of the most promising applications of hydrolytically degrading biomaterials is their use as drug release carriers. These uses, however, require that the degradation and diffusion of drug are reliably predicted, which is complex to achieve through present experimental methods. Atomistic modeling can help in the knowledge-based design of degrading biomaterials with tuned drug delivery properties, giving insights on the small molecules diffusivity at intermediate states of the degradation process. We present here an atomistic-based approach to investigate the diffusion of water (through which hydrolytic degradation occurs) in degrading bulk models of poly(lactic acid) or PLA. We determine the water diffusion coefficient for different swelling states of the polymeric matrix (from almost dry to pure water) and for different degrees of degradation. We show that water diffusivity is highly influenced by the swelling degree, while little or not influenced by the degradation state. This approach, giving water diffusivity for different states of the matrix, can be combined with diffusion-reaction analytical methods in order to predict the degradation path on longer time scales. Furthermore, atomistic approach can be used to investigate diffusion of other relevant small molecules, eventually leading to the a priori knowledge of degradable biomaterials transport properties, helping the design of the drug delivery systems.

Thermodynamic precursors, liquid-liquid transitions, dynamic and topological anomalies in densified liquid germania

NASA Astrophysics Data System (ADS)

Pacaud, F.; Micoulaut, M.

2015-08-01

The thermodynamic, dynamic, structural, and rigidity properties of densified liquid germania (GeO2) have been investigated using classical molecular dynamics simulation. We construct from a thermodynamic framework an analytical equation of state for the liquid allowing the possible detection of thermodynamic precursors (extrema of the derivatives of the free energy), which usually indicate the possibility of a liquid-liquid transition. It is found that for the present germania system, such precursors and the possible underlying liquid-liquid transition are hidden by the slowing down of the dynamics with decreasing temperature. In this respect, germania behaves quite differently when compared to parent tetrahedral systems such as silica or water. We then detect a diffusivity anomaly (a maximum of diffusion with changing density/volume) that is strongly correlated with changes in coordinated species, and the softening of bond-bending (BB) topological constraints that decrease the liquid rigidity and enhance transport. The diffusivity anomaly is finally substantiated from a Rosenfeld-type scaling law linked to the pair correlation entropy, and to structural relaxation.