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

PubMed

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

2017-10-30

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

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.

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…

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.

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.

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.

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

Nonequilibrium umbrella sampling in spaces of many order parameters

NASA Astrophysics Data System (ADS)

Dickson, Alex; Warmflash, Aryeh; Dinner, Aaron R.

2009-02-01

We recently introduced an umbrella sampling method for obtaining nonequilibrium steady-state probability distributions projected onto an arbitrary number of coordinates that characterize a system (order parameters) [A. Warmflash, P. Bhimalapuram, and A. R. Dinner, J. Chem. Phys. 127, 154112 (2007)]. Here, we show how our algorithm can be combined with the image update procedure from the finite-temperature string method for reversible processes [E. Vanden-Eijnden and M. Venturoli, "Revisiting the finite temperature string method for calculation of reaction tubes and free energies," J. Chem. Phys. (in press)] to enable restricted sampling of a nonequilibrium steady state in the vicinity of a path in a many-dimensional space of order parameters. For the study of transitions between stable states, the adapted algorithm results in improved scaling with the number of order parameters and the ability to progressively refine the regions of enforced sampling. We demonstrate the algorithm by applying it to a two-dimensional model of driven Brownian motion and a coarse-grained (Ising) model for nucleation under shear. It is found that the choice of order parameters can significantly affect the convergence of the simulation; local magnetization variables other than those used previously for sampling transition paths in Ising systems are needed to ensure that the reactive flux is primarily contained within a tube in the space of order parameters. The relation of this method to other algorithms that sample the statistics of path ensembles is discussed.

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…

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

Free energy landscape from path-sampling: application to the structural transition in LJ38

NASA Astrophysics Data System (ADS)

Adjanor, G.; Athènes, M.; Calvo, F.

2006-09-01

We introduce a path-sampling scheme that allows equilibrium state-ensemble averages to be computed by means of a biased distribution of non-equilibrium paths. This non-equilibrium method is applied to the case of the 38-atom Lennard-Jones atomic cluster, which has a double-funnel energy landscape. We calculate the free energy profile along the Q4 bond orientational order parameter. At high or moderate temperature the results obtained using the non-equilibrium approach are consistent with those obtained using conventional equilibrium methods, including parallel tempering and Wang-Landau Monte Carlo simulations. At lower temperatures, the non-equilibrium approach becomes more efficient in exploring the relevant inherent structures. In particular, the free energy agrees with the predictions of the harmonic superposition approximation.

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.

Laboratory earthquakes triggered during the eclogitization of lawsonite bearing blueschist

NASA Astrophysics Data System (ADS)

Incel, S.; Hilairet, N.; Labrousse, L.; John, T.; Deldicque, D.; Ferrand, T. P.; Wang, Y.; Renner, J.; Morales, L. F. G.; Schubnel, A.

2016-12-01

The origin of intermediate-depth seismicity has been debated for decades. A substantial fraction of these events occur within the upper plane of Wadati-Benioff double seismic zones believed to represent subducting oceanic crust. We deformed natural lawsonite-rich blueschist samples under eclogite-facies conditions (1 < P < 3.5 GPa; 583 K < T < 1121 K), using a D-DIA apparatus installed at a synchrotron beam line continuously monitoring stress, strain, phase content, and acoustic emissions (AEs). Two distinct eclogitization paths were followed: i) a cold path (maximum temperatures of 762 to 927 K), during which lawsonite and glaucophane went gradually unstable at higher pressure; ii) a hot path (maximum temperatures of 1073 to 1121 K) during which the complete breakdown of lawsonite at high temperature was triggered, but glaucophane or amphibole in general remained stable. Brittle failure of the sample, accompanied by the radiation of AEs, occurred for the cold path. In-situ XRD and post-mortem microstructural analysis demonstrate that fractures are topologically related to the growth of omphacite. Amorphous material was detected along the fractures by transmission electron microscopy without evidence for free-water. Since the growth of omphacite is associated with grain-size reduction, we interpret the observed mechanical instability as a transformation-induced thermal runaway under stress (or transformational faulting) triggered during the transition from lawsonite-blueschist to lawsonite-eclogite. In contrast, we find no microstructural evidence that the breakdown of lawsonite, and hence the liberation of water leads to the fracturing of the sample along the hot path, although some AEs were detected during an experiment performed at 1.5 GPa. Our experimental results challenge the concept of "dehydration embrittlement", which ascribes the genesis of intermediate-depth earthquakes to the breakdown of hydrous phases in the subducting oceanic plate. Instead our results demonstrate that grain-size reduction (transformational faulting) during the transition from lawsonite-blueschist to lawsonite-eclogite leads to the brittle failure of the samples.

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

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2010-01-01

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

Mechanism of the α -ɛ phase transformation in iron

NASA Astrophysics Data System (ADS)

Dewaele, A.; Denoual, C.; Anzellini, S.; Occelli, F.; Mezouar, M.; Cordier, P.; Merkel, S.; Véron, M.; Rausch, E.

2015-05-01

The α -Fe↔ɛ -Fe pressure-induced transformation under pure hydrostatic static compression has been characterized with in situ x-ray diffraction using α -Fe single crystals as starting samples. The forward transition starts at 14.9 GPa, and the reverse at 12 GPa, with a width of α -ɛ coexistence domain of the order of 2 GPa. The elastic stress in the sample increases in this domain, and partially relaxes after completion of the transformation. Orientation relations between parent α -Fe and child ɛ -Fe have been determined, which definitely validates the Burgers path for the direct transition. On the reverse transition, an unexpected variant selection is observed. X-ray diffraction data, complemented with ex situ microstructural observations, suggest that this selection is caused by defects and stresses accumulated during the direct transition.

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.

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

USGS Publications Warehouse

Otero, Cassi L.

2007-01-01

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

Water evaporation: a transition path sampling study.

PubMed

Varilly, Patrick; Chandler, David

2013-02-07

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

Chirped quantum cascade laser induced rapid passage signatures in an optically thick gas

NASA Astrophysics Data System (ADS)

Northern, J. H.; Ritchie, G. A. D.; Smakman, E. P.; van Helden, J. H.; Walker, R. J.; Duxbury, G.

2011-01-01

We report observations of rapid passage signals induced in samples of N2O and CH4 present in a multipass cell with an optical path length of 5 m. The effect of laser power and chirp rate upon the signals has been studied by utilising two different chirped quantum cascade lasers operating around 8 μm. The rapid passage signals exhibit an increasing delay in the switch from absorption to emission as a function of increased gas pressure (up to 8 Torr of gas). By comparing a selection of transitions in N2O and CH4, we show that, unlike ammonia, this `pressure shift' is independent of the transition dipole moment, spectroscopic branch probed and laser chirp rate. As the transition dipole moment is much larger in nitrous oxide than methane, we believe that this indicates that N2O-N2O collisions are more efficient at removing coherence from the polarised sample than CH4-CH4 collisions. We have also observed this pressure shift in a short path length of 40 cm, although with a much reduced value, indicating that propagation effects are important in this optically thick minimally damped system.

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.

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.

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

PubMed

Nessler, Ian J; Litman, Jacob M; Schnieders, Michael J

2016-11-09

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol -1 . For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol -1 and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol -1 ) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol -1 ). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling.

PubMed

Dzierlenga, Michael W; Antoniou, Dimitri; Schwartz, Steven D

2015-04-02

The mechanisms involved in enzymatic hydride transfer have been studied for years, but questions remain due, in part, to the difficulty of probing the effects of protein motion and hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and human heart lactate dehydrogenase (LDH). Calculation of the work applied to the hydride allowed for observation of the change in barrier height upon inclusion of quantum dynamics. Similar calculations were performed using deuterium as the transferring particle in order to approximate kinetic isotope effects (KIEs). The change in barrier height in YADH is indicative of a zero-point energy (ZPE) contribution and is evidence that catalysis occurs via a protein compression that mediates a near-barrierless hydride transfer. Calculation of the KIE using the difference in barrier height between the hydride and deuteride agreed well with experimental results.

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.

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.

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

PubMed

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

2018-04-10

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

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.

Transition paths in single-molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Cossio, Pilar; Hummer, Gerhard; Szabo, Attila

2018-03-01

In a typical single-molecule force spectroscopy experiment, the ends of the molecule of interest are connected by long polymer linkers to a pair of mesoscopic beads trapped in the focus of two laser beams. At constant force load, the total extension, i.e., the end-to-end distance of the molecule plus linkers, is measured as a function of time. In the simplest systems, the measured extension fluctuates about two values characteristic of folded and unfolded states, with occasional transitions between them. We have recently shown that molecular (un)folding rates can be recovered from such trajectories, with a small linker correction, as long as the characteristic time of the bead fluctuations is shorter than the residence time in the unfolded (folded) state. Here, we show that accurate measurements of the molecular transition path times require an even faster apparatus response. Transition paths, the trajectory segments in which the molecule (un)folds, are properly resolved only if the beads fluctuate more rapidly than the end-to-end distance of the molecule. Therefore, over a wide regime, the measured rates may be meaningful but not the transition path times. Analytic expressions for the measured mean transition path times are obtained for systems diffusing anisotropically on a two-dimensional free energy surface. The transition path times depend on the properties both of the molecule and of the pulling device.

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

PubMed

Hobolth, Asger; Stone, Eric A

2009-09-01

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

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.

Computationally efficient characterization of potential energy surfaces based on fingerprint distances

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

Schaefer, Bastian; Goedecker, Stefan, E-mail: stefan.goedecker@unibas.ch

2016-07-21

An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows us to understand important characteristics like thermodynamic, dynamic, and structural properties. Unfortunately computing the transition states and reaction pathways in addition to the significant energetically low-lying local minima is a computationally demanding task. We here introduce a computationally efficient method that is based on a combination of the minima hopping global optimization method and the insight that uphill barriers tend to increase with increasing structural distances of the educt and product states. This methodmore » allows us to replace the exact connectivity information and transition state energies with alternative and approximate concepts. Without adding any significant additional cost to the minima hopping global optimization approach, this method allows us to generate an approximate network of the minima, their connectivity, and a rough measure for the energy needed for their interconversion. This can be used to obtain a first qualitative idea on important physical and chemical properties by means of a disconnectivity graph analysis. Besides the physical insight obtained by such an analysis, the gained knowledge can be used to make a decision if it is worthwhile or not to invest computational resources for an exact computation of the transition states and the reaction pathways. Furthermore it is demonstrated that the here presented method can be used for finding physically reasonable interconversion pathways that are promising input pathways for methods like transition path sampling or discrete path sampling.« less

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.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

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

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Peter, Emanuel K.

2017-12-01

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation.

PubMed

Peter, Emanuel K

2017-12-07

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

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

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

DOE PAGES

McGibbon, J.; Bretherton, C. S.

2017-03-17

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

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

NASA Astrophysics Data System (ADS)

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

1998-12-01

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

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.

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

DOE PAGES

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

2017-08-01

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

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

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

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

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

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.

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.

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.

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

NASA Astrophysics Data System (ADS)

Wang, Ting; Plecháč, Petr

2017-12-01

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

Sequencing chess

NASA Astrophysics Data System (ADS)

Atashpendar, Arshia; Schilling, Tanja; Voigtmann, Thomas

2016-10-01

We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess pieces into another, we conclude that the state space consists of several pockets between which transitions are rare. Skilled players explore an even smaller subset of positions that populate some of these pockets only very sparsely. These results suggest that the usual measures to estimate both the size of the state space and the size of the tree of legal moves are not unique indicators of the complexity of the game, but that considerations regarding the connectedness of states are equally important.

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

NASA Astrophysics Data System (ADS)

Channell, J. E. T.

2016-12-01

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

Drift-Induced Selection Between Male and Female Heterogamety.

PubMed

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

2017-10-01

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

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

NASA Technical Reports Server (NTRS)

2011-01-01

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

Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations

PubMed Central

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M.

2011-01-01

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, Transition Path Theory (TPT) for constructing folding pathways and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270K and 566K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the Weighted-Histogram-Analysis Method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (Pfold) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding “tubes”, a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways. PMID:21254767

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

PubMed

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M

2011-02-17

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, transition path theory (TPT) for constructing folding pathways, and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270 and 566 K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the weighted-histogram-analysis method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (P(fold)) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding "tubes", a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network, and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways.

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...

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.

The Microstructural Evolution of Quartzite During Gradually Increasing Stress.

NASA Astrophysics Data System (ADS)

Soleymani, Hamid; Kidder, Steven B.; Hirth, Greg

2016-12-01

In settings where rocks are exhumed along shear zones, mylonites are thought to experience a gradual increase in stress and localization as they approach the brittle-ductile transition (Figure 1. left panel). Our aim is to investigate the microstructural characteristics of experimental samples that have experienced such a stress path and make comparisons to natural samples. A common characteristic of recrystallized grains in shear zones is what appears, at least qualitatively, to be a bimodal distribution of grain size (Figure 1. right panel). We hypothesize that such distributions might form as a natural consequence of a gradual stress increase in rocks approaching the brittle-ductile transition. We carried out several general-shear, Griggs rig experiments on Arkansas novaculite ( 10 micron grain size) and Black Hills quartzite synthesized powder (10-20 micron) annealed at 915°C and confining pressure of 1.5 GPa. To simulate exhumation, stress was increased by gradually decreasing the temperature at various constant rates. Experimental design and mechanical data are presented along with a discussion on grain growth and evolution. Initial results show that the technique is able to successfully simulate the exhumation stre­­­­ss path. The experiments also show that novaculite is roughly twice as strong (at similar water concentrations) as Black Hills quartzite powder ( 10-20 microns). We anticipate that detailed, quantitative study of the microstructure and grain statistics of experiments of this type can lead to improved interpretation of the microstructural development of natural samples.

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

PubMed

Gao, Yi Qin

2008-04-07

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

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).

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.

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.

Behavior problems and placement change in a national child welfare sample: a prospective study.

PubMed

Aarons, Gregory A; James, Sigrid; Monn, Amy R; Raghavan, Ramesh; Wells, Rebecca S; Leslie, Laurel K

2010-01-01

There is ongoing debate regarding the impact of youth behavior problems on placement change in child welfare compared to the impact of placement change on behavior problems. Existing studies provide support for both perspectives. The purpose of this study was to prospectively examine the relations of behavior problems and placement change in a nationally representative sample of youths in the National Survey of Child and Adolescent Well-Being. The sample consisted of 500 youths in the child welfare system with out-of-home placements over the course of the National Survey of Child and Adolescent Well-Being study. We used a prospective cross-lag design and path analysis to examine reciprocal effects of behavior problems and placement change, testing an overall model and models examining effects of age and gender. In the overall model, out of a total of eight path coefficients, behavior problems significantly predicted placement changes for three paths and placement change predicted behavior problems for one path. Internalizing and externalizing behavior problems at baseline predicted placement change between baseline and 18 months. Behavior problems at an older age and externalizing behavior at 18 months appear to confer an increased risk of placement change. Of note, among female subjects, placement changes later in the study predicted subsequent internalizing and externalizing behavior problems. In keeping with recommendations from a number of professional bodies, we suggest that initial and ongoing screening for internalizing and externalizing behavior problems be instituted as part of standard practice for youths entering or transitioning in the child welfare system.

Non-Conventional Techniques for the Study of Phase Transitions in NiTi-Based Alloys

NASA Astrophysics Data System (ADS)

Nespoli, Adelaide; Villa, Elena; Passaretti, Francesca; Albertini, Franca; Cabassi, Riccardo; Pasquale, Massimo; Sasso, Carlo Paolo; Coïsson, Marco

2014-07-01

Differential scanning calorimetry and electrical resistance measurements are the two most common techniques for the study of the phase transition path and temperatures of shape memory alloys (SMA) in stress-free condition. Besides, it is well known that internal friction measurements are also useful for this purpose. There are indeed some further techniques which are seldom used for the basic characterization of SMA transition: dilatometric analysis, magnetic measurements, and Seebeck coefficient study. In this work, we discuss the attitude of these techniques for the study of NiTi-based phase transition. Measurements were conducted on several fully annealed Ni50- x Ti50Cu x samples ranging from 3 to 10 at.% in Cu content, fully annealed at 850 °C for 1 h in vacuum and quenched in water at room temperature. Results show that all these techniques are sensitive to phase transition, and they provide significant information about the existence of intermediate phases.

Dependence of Internal Friction on Folding Mechanism

PubMed Central

2016-01-01

An outstanding challenge in protein folding is understanding the origin of “internal friction” in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein. PMID:25721133

Dependence of internal friction on folding mechanism.

PubMed

Zheng, Wenwei; De Sancho, David; Hoppe, Travis; Best, Robert B

2015-03-11

An outstanding challenge in protein folding is understanding the origin of "internal friction" in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

NASA Astrophysics Data System (ADS)

Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik

2016-08-01

Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.

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.

Broadband extreme ultraviolet probing of transient gratings in vanadium dioxide

DOE PAGES

Sistrunk, Emily; Grilj, Jakob; Jeong, Jaewoo; ...

2015-02-11

Nonlinear spectroscopy in the extreme ultraviolet (EUV) and soft x-ray spectral range offers the opportunity for element selective probing of ultrafast dynamics using core-valence transitions (Mukamel et al., Acc. Chem. Res. 42, 553 (2009)). The study demonstrate a step on this path showing core-valence sensitivity in transient grating spectroscopy with EUV probing. We study the optically induced insulator-to-metal transition (IMT) of a VO 2 film with EUV diffraction from the optically excited sample. The VO 2 exhibits a change in the 3p-3d resonance of V accompanied by an acoustic response. Due to the broadband probing we are able to separatemore » the two features.« less

Local Magnetic Measurements of Trapped Flux Through a Permanent Current Path in Graphite

NASA Astrophysics Data System (ADS)

Stiller, Markus; Esquinazi, Pablo D.; Quiquia, José Barzola; Precker, Christian E.

2018-04-01

Temperature- and field-dependent measurements of the electrical resistance of different natural graphite samples suggest the existence of superconductivity at room temperature in some regions of the samples. To verify whether dissipationless electrical currents are responsible for the trapped magnetic flux inferred from electrical resistance measurements, we localized them using magnetic force microscopy on a natural graphite sample in remanent state after applying a magnetic field. The obtained evidence indicates that at room temperature a permanent current flows at the border of the trapped flux region. The current path vanishes at the same transition temperature T_c≈ 370 K as the one obtained from electrical resistance measurements on the same sample. This sudden decrease in the phase is different from what is expected for a ferromagnetic material. Time-dependent measurements of the signal show the typical behavior of flux creep of a permanent current flowing in a superconductor. The overall results support the existence of room-temperature superconductivity at certain regions in the graphite structure and indicate that magnetic force microscopy is suitable to localize them. Magnetic coupling is excluded as origin of the observed phase signal.

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

Identification of transitional disks in Chamaeleon with Herschel

NASA Astrophysics Data System (ADS)

Ribas, Á.; Merín, B.; Bouy, H.; Alves de Oliveira, C.; Ardila, D. R.; Puga, E.; Kóspál, Á.; Spezzi, L.; Cox, N. L. J.; Prusti, T.; Pilbratt, G. L.; André, Ph.; Matrà, L.; Vavrek, R.

2013-04-01

Context. Transitional disks are circumstellar disks with inner holes that in some cases are produced by planets and/or substellar companions in these systems. For this reason, these disks are extremely important for the study of planetary system formation. Aims: The Herschel Space Observatory provides an unique opportunity for studying the outer regions of protoplanetary disks. In this work we update previous knowledge on the transitional disks in the Chamaeleon I and II regions with data from the Herschel Gould Belt Survey. Methods: We propose a new method for transitional disk classification based on the WISE 12 μm - PACS 70 μm color, together with inspection of the Herschel images. We applied this method to the population of Class II sources in the Chamaeleon region and studied the spectral energy distributions of the transitional disks in the sample. We also built the median spectral energy distribution of Class II objects in these regions for comparison with transitional disks. Results: The proposed method allows a clear separation of the known transitional disks from the Class II sources. We find six transitional disks, all previously known, and identify five objects previously thought to be transitional as possibly non-transitional. We find higher fluxes at the PACS wavelengths in the sample of transitional disks than those of Class II objects. Conclusions: We show the Herschel 70 μm band to be a robust and efficient tool for transitional disk identification. The sensitivity and spatial resolution of Herschel reveals a significant contamination level among the previously identified transitional disk candidates for the two regions, which calls for a revision of previous samples of transitional disks in other regions. The systematic excess found at the PACS bands could be either a result of the mechanism that produces the transitional phase, or an indication of different evolutionary paths for transitional disks and Class II sources. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.Appendix A is available in electronic form at http://www.aanda.org

Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.

PubMed

Chen, Changjun; Huang, Yanzhao; Xiao, Yi

2013-01-01

Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of freedom in the molecule to environment temperature, like dihedrals in generalized coordinates or nonhydrogen atoms in Cartesian coordinate. After applying to ALA dipeptide model, we find that this modified molecular dynamics greatly enhances the sampling behavior in the conformational space and provides more information about the state-to-state transition, while conventional molecular dynamics fails to do so. Moreover, from the results of 16 independent 100 ns simulations by the new method, it shows that trpzip2 has one-half chances to reach the naive state in all the trajectories, which is greatly higher than conventional molecular dynamics. Such an improvement would provide a potential way for searching the conformational space or predicting the most stable states of peptides and proteins.

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

PubMed

Varga, Matthew J; Schwartz, Steven D

2016-04-12

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

Defining conditions of garnet growth across the central and southern Menderes Massif, western Turkey

NASA Astrophysics Data System (ADS)

Etzel, T. M.; Catlos, E. J.; Kelly, E. D.; Cemen, I.; Ozerdem, C.; Atakturk, K. R.

2017-12-01

Here we apply thermodynamic modeling using Theriak-Domino to garnet-bearing rocks from the central and southern portions of the Menderes Massif to gain insight into the dynamics of western Turkey as the region experienced a transition from collisional to extensional tectonics. To this end, we report new pressure-temperature (P-T) paths from garnet-bearing rocks collected along the Alasehir detachment fault, a prominent exhumation structure in the central portion of the Menderes Massif in western Turkey, constituting the southern margin of the Alasehir Graben. These paths are compared to those from the Selimiye shear zone in the Southern (Cine) Massif. Two Alasehir garnets collected from the same outcrop record two P-T paths: 1) a prograde path beginning at 565oC and 6.4 kbar increasing to 592 oC and 7.5 kbar; and 2) near isobaric growth initiating at 531oC and 7.1 kbar and terminating at 571oC and 7.3 kbar. High-resolution P-T paths could not be modeled for the majority of Alasehir samples due to diffusional modification of garnet. However, conditions were estimated by garnet isopleth thermobarometry at the point of highest spessartine content for each crystal. Calculated P-T values for this subset of samples range between 566-651oC and 6.2-6.8 kbar. Despite this broad range, these P-T conditions are consistent with what is observed in the modeled paths. Th-Pb ages of matrix monazite range from 35.8±3.0 to 20.6±2.4 Ma, suggesting metamorphism in the central Menderes Massif occurred over a 15 m.y. period. Selimiye shear zone rocks show distinct N-shaped P-T paths, suggesting garnets in the central and southern portion of the Menderes Massif record distinctly different tectonic histories.

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…

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

PubMed

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

2006-02-01

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

Self- and Air-Broadened Line Shapes in the 2v3 P and R Branches of 12CH4

NASA Technical Reports Server (NTRS)

Devi, V. Malathy; Benner, D. Chris; Sung, Keeyoon; Crawford, Timothy J.; Yu, Shanshan; Brown, Linda R.; Smith, Mary Ann H.; Mantz, Arlan W.; Boudon, Vincent; Ismail, Syed

2015-01-01

In this paper we report line shape parameters of 12CH4 for several hundred 2V(sub 3) transitions in the spectral regions 5891-5996 cm( exp -1) (P branch) and 6015-6115 cm(exp -1) (R branch). Air- and self-broadening coefficients were measured as a function of temperature; line mixing via off-diagonal relaxation matrix element coefficients was also obtained for 47 transition pairs. In total, nearly 1517 positions and intensities were retrieved, but many transitions were too weak for the line shape study. For this analysis, we used 25 high-resolution (0.0056 and 0.0067 cm(ex[ -1) and high signal-to-noise (S/N) spectra of high-purity 12CH4 and the same high-purity 12CH4 broadened by dry air recorded at different sample temperatures between 130 K and 295 K with the Bruker IFS 125HR Fourier transform spectrometer at JPL. Three different absorption cells were used (1) a White cell set to a path length of 13.09 m for room temperature data, (2) a single-pass 0.2038 m long coolable cell (for self-broadening) and (3) a multipass cell with 20.941 m total path coolable Herriott cell (for air-broadening). In total there were 13 spectra with pure 12CH4 (0.27-599 Torr) and 12 air-broadened spectra with total sample pressures of 80-805 Torr and volume mixing ratios (VMR) of methane between 0.18 and 1.0. An interactive multispectrum nonlinear least-squares technique was employed to fit the individual P10-P1 and R0-R10 manifolds in all the spectra simultaneously. Results obtained from the present analysis are compared to other recent measurements.

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

2169 steel waveform experiments.

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

Furnish, Michael David; Alexander, C. Scott; Reinhart, William Dodd

2012-11-01

In support of LLNL efforts to develop multiscale models of a variety of materials, we have performed a set of eight gas gun impact experiments on 2169 steel (21% Cr, 6% Ni, 9% Mn, balance predominantly Fe). These experiments provided carefully controlled shock, reshock and release velocimetry data, with initial shock stresses ranging from 10 to 50 GPa (particle velocities from 0.25 to 1.05 km/s). Both windowed and free-surface measurements were included in this experiment set to increase the utility of the data set, as were samples ranging in thickness from 1 to 5 mm. Target physical phenomena included themore » elastic/plastic transition (Hugoniot elastic limit), the Hugoniot, any phase transition phenomena, and the release path (windowed and free-surface). The Hugoniot was found to be nearly linear, with no indications of the Fe phase transition. Releases were non-hysteretic, and relatively consistent between 3- and 5-mmthick samples (the 3 mm samples giving slightly lower wavespeeds on release). Reshock tests with explosively welded impactors produced clean results; those with glue bonds showed transient releases prior to the arrival of the reshock, reducing their usefulness for deriving strength information. The free-surface samples, which were steps on a single piece of steel, showed lower wavespeeds for thin (1 mm) samples than for thicker (2 or 4 mm) samples. A configuration used for the last three shots allows release information to be determined from these free surface samples. The sample strength appears to increase with stress from ~1 GPa to ~ 3 GPa over this range, consistent with other recent work but about 40% above the Steinberg model.« less

Variational Identification of Markovian Transition States

NASA Astrophysics Data System (ADS)

Martini, Linda; Kells, Adam; Covino, Roberto; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

2017-07-01

We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5 , and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting) transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

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

NASA Astrophysics Data System (ADS)

Smolka, Bogdan; Cyganek, Boguslaw

2015-02-01

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

Methodology for Augmenting Existing Paths with Additional Parallel Transects

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

Wilson, John E.

2013-09-30

Visual Sample Plan (VSP) is sample planning software that is used, among other purposes, to plan transect sampling paths to detect areas that were potentially used for munition training. This module was developed for application on a large site where existing roads and trails were to be used as primary sampling paths. Gap areas between these primary paths needed to found and covered with parallel transect paths. These gap areas represent areas on the site that are more than a specified distance from a primary path. These added parallel paths needed to optionally be connected together into a single path—themore » shortest path possible. The paths also needed to optionally be attached to existing primary paths, again with the shortest possible path. Finally, the process must be repeatable and predictable so that the same inputs (primary paths, specified distance, and path options) will result in the same set of new paths every time. This methodology was developed to meet those specifications.« less

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

PubMed

Tiwari, Ambuj; Ensing, Bernd

2016-12-22

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

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.

PROBING THE ROLE OF CARBON IN ULTRAVIOLET EXTINCTION ALONG GALACTIC SIGHT LINES

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

Parvathi, V. S.; Babu, B. R. S.; Sofia, U. J.

2012-11-20

We report previously undetermined interstellar gas and dust-phase carbon abundances along 15 Galactic sight lines based on archival data of the strong 1334.5323 A transition observed with the Space Telescope Imaging Spectrograph. These are combined with previously reported carbon measurements along six sight lines to produce a complete sample of interstellar C II measurements determined with the 1334 A transition. Our data set includes a variety of Galactic disk environments characterized by different extinctions and samples paths ranging over three orders of magnitude in average density of hydrogen ((n(H))). Our data support the idea that dust, specifically carbon-based grains, aremore » processed in the neutral interstellar medium. We, however, do not find that the abundance of carbon in dust or the grain-size distribution is related to the strength of the 2175 A bump. This is surprising, given that many current models have polycyclic aromatic hydrocarbons as the bump-producing dust.« less

Using Approximate Bayesian Computation to Probe Multiple Transiting Planet Systems

NASA Astrophysics Data System (ADS)

Morehead, Robert C.

2015-08-01

The large number of multiple transiting planet systems (MTPS) uncovered with Kepler suggest a population of well-aligned planetary systems. Previously, the distribution of transit duration ratios in MTPSs has been used to place constraints on the distributions of mutual orbital inclinations and orbital eccentricities in these systems. However, degeneracies with the underlying number of planets in these systems pose added challenges and make explicit likelihood functions intractable. Approximate Bayesian computation (ABC) offers an intriguing path forward. In its simplest form, ABC proposes from a prior on the population parameters to produce synthetic datasets via a physically-motivated model. Samples are accepted or rejected based on how close they come to reproducing the actual observed dataset to some tolerance. The accepted samples then form a robust and useful approximation of the true posterior distribution of the underlying population parameters. We will demonstrate the utility of ABC in exoplanet populations by presenting new constraints on the mutual inclination and eccentricity distributions in the Kepler MTPSs. We will also introduce Simple-ABC, a new open-source Python package designed for ease of use and rapid specification of general models, suitable for use in a wide variety of applications in both exoplanet science and astrophysics as a whole.

Employees on the rebound: Extending the careers literature to include boomerang employment.

PubMed

Swider, Brian W; Liu, Joseph T; Harris, T Brad; Gardner, Richard G

2017-06-01

As employee careers have evolved from linear trajectories confined within 1 organization to more dynamic and boundaryless paths, organizations and individuals alike have increasingly considered reestablishing prior employment relationships. These "boomerang employees" follow career paths that feature 2 or more temporally separated tenures in particular organizations ("boomerang organizations"). Yet, research to date is mute on how or to what extent differences across boomerang employees' career experiences, and the learning and knowledge developed at and away from boomerang organizations, meaningfully impact their performance following their return. Addressing this omission, we extend a careers-based learning perspective to construct a theoretical framework of a parsimonious, yet generalizable, set of factors that influence boomerang employee return performance. Results based on a sample of boomerang employees and employers in the same industry (professional basketball) indicate that intra- and extraorganizational knowledge construction and disruptions, as well as transition events, are significantly predictive of boomerangs' return performance. Comparisons with 2 matched samples of nonboomerang employees likewise suggest distinctive patterns in the performance of boomerang employees. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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.

Enzymatic reaction paths as determined by transition path sampling

NASA Astrophysics Data System (ADS)

Masterson, Jean Emily

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

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.

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

Power dissipation in the mixed metal-insulator state of self-heated VO2 single crystals and the effect of sliding domains

NASA Astrophysics Data System (ADS)

Fisher, B.; Patlagan, L.

2018-06-01

The mixed metal-insulator state in VO2 sets on within the current-controlled negative differential resistivity regime of I-V loops traced at ambient temperature. In this state, the stability of I(V) and/or spontaneous switching between initial and final steady states are governed by the load resistance RL in series with the sample. With increasing current (decreasing voltage), the power P = IV reaches a maximum (Pmax) and drops to a minimum (Pmin) along a path that depends on RL. For low enough RL, the ratio Pmax/Pmin may exceed by far the contrast in thermal emissivity from films of VO2 over the metal-insulator transition as reported in Kats et al. [Phys. Rev. X 3, 041004 (2013)]. The minimum is followed by a range of currents where the power increases with current. The return path overlaps the original path and continues towards backward switching. For a few samples, there is evidence from optical microscopy that the portion of the P(I) loop between Pmin and backward switching coincides with the range of currents where semiconducting domains slide within a metallic background. Damage induced in crystals by repeated I-V cycling suppresses domain sliding and flattens P(I) in the respective range of currents. This is consistent with the current dependent excess power dissipation being induced by the sliding domains.

Are U-channels measurements appropriate for reversal or excursion records ?

NASA Astrophysics Data System (ADS)

Philippe, E. G. H.; Valet, J. P.

2017-12-01

Sampling of sediment cores by U-channel plastic tubes is a very successful technique that allows to perform measurements of the magnetic remanence and demagnetization of long sections of sediment. This approach made possible the acquisition of detailed records of paleosecular variation, geomagnetic polarity and relative paleointensity over the past million years and yielded significant advances in our knowledge of the geomagnetic field changes. The major pitfall is that the resolution of the signal which is imposed by the deposition rate of the sediment is also attenuated by the response curve of the magnetic sensors used for measurements. This is not so critical to document the dipole field changes, but may have a significant impact to recover fast field changes typical of the non-dipole field that prevail during reversals and excursions. We have investigated possible consequences by comparing 150 successive individual directions of 1 cm side successive single samples with the measurement of the 1.5m equivalent U-channel obtained by placing the same samples adjacent to each other. We compared different transition lengths and generated transitional directions that produce records with similar characteristics as those derived from volcanic records of reversals with a magnetization intensity dropping to 5% of the full polarity value during the transition. The results show that even with transitional intervals as long as 30 cm and therefore associated with deposition rates as high as 10 cm/ka the U-channels considerably smooth all variations with significant consequences on the VGP paths that become more constrained in longitude. Despite little similarity with the global structure of the transition, the U-channels fail to reproduce the complexity of the transitional period. The transitional VGPs never duplicate the variations of the non-dipole field even within several centimeters and generate artificial clusters or periods of apparent fast changes. We are currently testing whether deconvolution techniques can recover the original directions.

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.

Energy landscapes and properties of biomolecules.

PubMed

Wales, David J

2005-11-09

Thermodynamic and dynamic properties of biomolecules can be calculated using a coarse-grained approach based upon sampling stationary points of the underlying potential energy surface. The superposition approximation provides an overall partition function as a sum of contributions from the local minima, and hence functions such as internal energy, entropy, free energy and the heat capacity. To obtain rates we must also sample transition states that link the local minima, and the discrete path sampling method provides a systematic means to achieve this goal. A coarse-grained picture is also helpful in locating the global minimum using the basin-hopping approach. Here we can exploit a fictitious dynamics between the basins of attraction of local minima, since the objective is to find the lowest minimum, rather than to reproduce the thermodynamics or dynamics.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Reliable Transition State Searches Integrated with the Growing String Method.

PubMed

Zimmerman, Paul

2013-07-09

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

Architectures of Kepler Planet Systems with Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Morehead, Robert C.; Ford, Eric B.

2015-12-01

The distribution of period normalized transit duration ratios among Kepler’s multiple transiting planet systems constrains the distributions of mutual orbital inclinations and orbital eccentricities. However, degeneracies in these parameters tied to the underlying number of planets in these systems complicate their interpretation. To untangle the true architecture of planet systems, the mutual inclination, eccentricity, and underlying planet number distributions must be considered simultaneously. The complexities of target selection, transit probability, detection biases, vetting, and follow-up observations make it impractical to write an explicit likelihood function. Approximate Bayesian computation (ABC) offers an intriguing path forward. In its simplest form, ABC generates a sample of trial population parameters from a prior distribution to produce synthetic datasets via a physically-motivated forward model. Samples are then accepted or rejected based on how close they come to reproducing the actual observed dataset to some tolerance. The accepted samples form a robust and useful approximation of the true posterior distribution of the underlying population parameters. We build on the considerable progress from the field of statistics to develop sequential algorithms for performing ABC in an efficient and flexible manner. We demonstrate the utility of ABC in exoplanet populations and present new constraints on the distributions of mutual orbital inclinations, eccentricities, and the relative number of short-period planets per star. We conclude with a discussion of the implications for other planet occurrence rate calculations, such as eta-Earth.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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.

Dual-wavelength pump-probe microscopy analysis of melanin composition

NASA Astrophysics Data System (ADS)

Thompson, Andrew; Robles, Francisco E.; Wilson, Jesse W.; Deb, Sanghamitra; Calderbank, Robert; Warren, Warren S.

2016-11-01

Pump-probe microscopy is an emerging technique that provides detailed chemical information of absorbers with sub-micrometer spatial resolution. Recent work has shown that the pump-probe signals from melanin in human skin cancers correlate well with clinical concern, but it has been difficult to infer the molecular origins of these differences. Here we develop a mathematical framework to describe the pump-probe dynamics of melanin in human pigmented tissue samples, which treats the ensemble of individual chromophores that make up melanin as Gaussian absorbers with bandwidth related via Frenkel excitons. Thus, observed signals result from an interplay between the spectral bandwidths of the individual underlying chromophores and spectral proximity of the pump and probe wavelengths. The model is tested using a dual-wavelength pump-probe approach and a novel signal processing method based on gnomonic projections. Results show signals can be described by a single linear transition path with different rates of progress for different individual pump-probe wavelength pairs. Moreover, the combined dual-wavelength data shows a nonlinear transition that supports our mathematical framework and the excitonic model to describe the optical properties of melanin. The novel gnomonic projection analysis can also be an attractive generic tool for analyzing mixing paths in biomolecular and analytical chemistry.

Dual-wavelength pump-probe microscopy analysis of melanin composition

PubMed Central

Thompson, Andrew; Robles, Francisco E.; Wilson, Jesse W.; Deb, Sanghamitra; Calderbank, Robert; Warren, Warren S.

2016-01-01

Pump-probe microscopy is an emerging technique that provides detailed chemical information of absorbers with sub-micrometer spatial resolution. Recent work has shown that the pump-probe signals from melanin in human skin cancers correlate well with clinical concern, but it has been difficult to infer the molecular origins of these differences. Here we develop a mathematical framework to describe the pump-probe dynamics of melanin in human pigmented tissue samples, which treats the ensemble of individual chromophores that make up melanin as Gaussian absorbers with bandwidth related via Frenkel excitons. Thus, observed signals result from an interplay between the spectral bandwidths of the individual underlying chromophores and spectral proximity of the pump and probe wavelengths. The model is tested using a dual-wavelength pump-probe approach and a novel signal processing method based on gnomonic projections. Results show signals can be described by a single linear transition path with different rates of progress for different individual pump-probe wavelength pairs. Moreover, the combined dual-wavelength data shows a nonlinear transition that supports our mathematical framework and the excitonic model to describe the optical properties of melanin. The novel gnomonic projection analysis can also be an attractive generic tool for analyzing mixing paths in biomolecular and analytical chemistry. PMID:27833147

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

PubMed

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

2005-08-01

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

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.

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.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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.

Electrophoretic sample insertion. [device for uniformly distributing samples in flow path

NASA Technical Reports Server (NTRS)

Mccreight, L. R. (Inventor)

1974-01-01

Two conductive screens located in the flow path of an electrophoresis sample separation apparatus are charged electrically. The sample is introduced between the screens, and the charge is sufficient to disperse and hold the samples across the screens. When the charge is terminated, the samples are uniformly distributed in the flow path. Additionally, a first separation by charged properties has been accomplished.

Stationary properties of maximum-entropy random walks.

PubMed

Dixit, Purushottam D

2015-10-01

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

Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated.

PubMed

Ivanov, Sergei D; Grant, Ian M; Marx, Dominik

2015-09-28

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

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

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.

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...

Computational smart polymer design based on elastin protein mutability.

PubMed

Tarakanova, Anna; Huang, Wenwen; Weiss, Anthony S; Kaplan, David L; Buehler, Markus J

2017-05-01

Soluble elastin-like peptides (ELPs) can be engineered into a range of physical forms, from hydrogels and scaffolds to fibers and artificial tissues, finding numerous applications in medicine and engineering as "smart polymers". Elastin-like peptides are attractive candidates as a platform for novel biomaterial design because they exhibit a highly tunable response spectrum, with reversible phase transition capabilities. Here, we report the design of the first virtual library of elastin-like protein models using methods for enhanced sampling to study the effect of peptide chemistry, chain length, and salt concentration on the structural transitions of ELPs, exposing associated molecular mechanisms. We describe the behavior of the local molecular structure under increasing temperatures and the effect of peptide interactions with nearest hydration shell water molecules on peptide mobility and propensity to exhibit structural transitions. Shifts in the magnitude of structural transitions at the single-molecule scale are explained from the perspective of peptide-ion-water interactions in a library of four unique elastin-like peptide systems. Predictions of structural transitions are subsequently validated in experiment. This library is a valuable resource for recombinant protein design and synthesis as it elucidates mechanisms at the single-molecule level, paving a feedback path between simulation and experiment for smart material designs, with applications in biomedicine and diagnostic devices. Copyright © 2017. Published by Elsevier Ltd.

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

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.

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.

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.

Frictional behaviour of sandstone: A sample-size dependent triaxial investigation

NASA Astrophysics Data System (ADS)

Roshan, Hamid; Masoumi, Hossein; Regenauer-Lieb, Klaus

2017-01-01

Frictional behaviour of rocks from the initial stage of loading to final shear displacement along the formed shear plane has been widely investigated in the past. However the effect of sample size on such frictional behaviour has not attracted much attention. This is mainly related to the limitations in rock testing facilities as well as the complex mechanisms involved in sample-size dependent frictional behaviour of rocks. In this study, a suite of advanced triaxial experiments was performed on Gosford sandstone samples at different sizes and confining pressures. The post-peak response of the rock along the formed shear plane has been captured for the analysis with particular interest in sample-size dependency. Several important phenomena have been observed from the results of this study: a) the rate of transition from brittleness to ductility in rock is sample-size dependent where the relatively smaller samples showed faster transition toward ductility at any confining pressure; b) the sample size influences the angle of formed shear band and c) the friction coefficient of the formed shear plane is sample-size dependent where the relatively smaller sample exhibits lower friction coefficient compared to larger samples. We interpret our results in terms of a thermodynamics approach in which the frictional properties for finite deformation are viewed as encompassing a multitude of ephemeral slipping surfaces prior to the formation of the through going fracture. The final fracture itself is seen as a result of the self-organisation of a sufficiently large ensemble of micro-slip surfaces and therefore consistent in terms of the theory of thermodynamics. This assumption vindicates the use of classical rock mechanics experiments to constrain failure of pressure sensitive rocks and the future imaging of these micro-slips opens an exciting path for research in rock failure mechanisms.

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.

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.

Lagrangian evolution of the marine boundary layer from the Cloud System Evolution in the Trades (CSET) campaign

NASA Astrophysics Data System (ADS)

Mohrmann, J.; Ghate, V. P.; McCoy, I. L.; Bretherton, C. S.; Wood, R.; Minnis, P.; Palikonda, R.

2017-12-01

The Cloud System Evolution in the Trades (CSET) field campaign took place July/August 2015 to study the evolution of clouds, precipitation, and aerosols in the stratocumulus-to-cumulus (Sc-Cu) transition region of the northeast Pacific marine boundary layer (MBL). Aircraft observations sampled across a wide range of cloud and aerosol conditions. The sampling strategy, where MBL airmasses were sampled with the NSF/NCAR Gulfstream-V (HIAPER) and resampled then at their advected location two days later, resulted in a dataset of 14 paired flights suitable for Lagrangian analysis. This analysis shows that Lagrangian coherence of long-lived species (namely CO and O3) across 48 hours are high, but that of subcloud aerosol, MBL depth, and cloud properties is limited. Geostationary satellite retrievals are compared against aircraft observations; these are combined with reanalysis data and HYSPLIT trajectories to document the Lagrangian evolution of cloud fraction, cloud droplet number concentration, liquid water path, estimated inversion strength (EIS), and MBL depth, which are used to expand upon and validate the aircraft-based analysis. Many of the trajectories sampled by the aircraft show a clear Sc-Cu transition. Although satellite cloud fraction and EIS were found to be strongly spatiotemporally correlated, changes in MBL cloud fraction along trajectories did not correlate with any measure of EIS forcing.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.

PubMed

Kamberaj, Hiqmet

2018-05-01

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method. Copyright © 2018 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Influence of Hydrological Flow Paths on Rates and Forms of Nitrogen Losses from Mediterranean Watersheds

NASA Astrophysics Data System (ADS)

Lohse, K. A.; Sanderman, J.; Amundson, R. G.

2005-12-01

Patterns of precipitation and runoff in California are changing and likely to influence the structure and functioning of watersheds. Studies have demonstrated that hydrologic flushing during seasonal transitions in Mediterranean ecosystems can exert a strong control on nitrogen (N) export, yet few studies have examined the influence of different hydrological flow paths on rates and forms of nitrogen (N) losses. Here we illuminate the influence of variations in precipitation and hydrological pathways on the rate and form of N export along a toposequence of a well-characterized Mediterranean catchment in northern California. As a part of a larger study examining particulate and dissolved carbon loss, we analyzed seasonal patterns of dissolved organic nitrogen (DON), nitrate and ammonium concentrations in rainfall, throughfall, matrix and preferential flow, and stream samples over the course of one water year. We also analyzed seasonal soil N dynamics along this toposequence. During the transition to the winter rain season, but prior to any soil water displacement to the stream, DON and nitrate moved through near-surface soils as preferential flow. Once hillslope soils became saturated, saturated subsurface flow flushed nitrate from the hollow resulting in high stream nitrate/DON concentrations. Between storms, stream nitrate/DON concentrations were lower and appeared to reflect deep subsurface water flow chemistry. During the transition to the wet season, rates of soil nitrate production were high in the hollow relative to the hillslope soils. In the spring, these rates systematically declined as soil moisture decreased. Results from our study suggest seasonal fluctuations in soil moisture control soil N cycling and seasonal changes in the hydrological connection between hillslope soils and streams control the seasonal production and export of hydrologic N.

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.

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…

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

PubMed

Einsiedl, Florian; Radke, Michael; Maloszewski, Piotr

2010-09-20

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

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.

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.

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

New assignments in the 2 μm transparency window of the 12CH4 Octad band system

NASA Astrophysics Data System (ADS)

Daumont, L.; Nikitin, A. V.; Thomas, X.; Régalia, L.; Von der Heyden, P.; Tyuterev, Vl. G.; Rey, M.; Boudon, V.; Wenger, Ch.; Loëte, M.; Brown, L. R.

2013-02-01

This paper reports new assignments of rovibrational transitions of 12CH4 bands in the range 4600-4887 cm-1 which is usually referred to as a part of the 2 μm methane transparency window. Several experimental data sources for methane line positions and intensities were combined for this analysis. Three long path Fourier transform spectra newly recorded in Reims with 1603 m absorption path length and pressures of 1, 7 and 34 hPa for samples of natural abundance CH4 provided new measurements of 12CH4 lines. Older spectra for 13CH4 (90% purity) from JPL with 73 m absorption path length were used to identify the corresponding lines. Most of the lines in this region belong to the Octad system of 12CH4. The new spectra allowed us to assign 1014 new line positions and to measure 1095 line intensities in the cold bands of the Octad. These new line positions and intensities were added to the global fit of Hamiltonian and dipole moment parameters of the Ground State, Dyad, Pentad and Octad systems. This leads to a noticeable improvement of the theoretical description in this methane transparency window and a better global prediction of the methane spectrum.

Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

PubMed Central

Wu, Dongsheng; Fajer, Mikolai I.; Cao, Liaoran; Cheng, Xiaolin; Yang, Wei

2016-01-01

Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this mini presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model.

PubMed

Plotnikov, Nikolay V

2014-08-12

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force.

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model

PubMed Central

2015-01-01

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force. PMID:25136268

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

Note: A pure-sampling quantum Monte Carlo algorithm with independent Metropolis.

PubMed

Vrbik, Jan; Ospadov, Egor; Rothstein, Stuart M

2016-07-14

Recently, Ospadov and Rothstein published a pure-sampling quantum Monte Carlo algorithm (PSQMC) that features an auxiliary Path Z that connects the midpoints of the current and proposed Paths X and Y, respectively. When sufficiently long, Path Z provides statistical independence of Paths X and Y. Under those conditions, the Metropolis decision used in PSQMC is done without any approximation, i.e., not requiring microscopic reversibility and without having to introduce any G(x → x'; τ) factors into its decision function. This is a unique feature that contrasts with all competing reptation algorithms in the literature. An example illustrates that dependence of Paths X and Y has adverse consequences for pure sampling.

Note: A pure-sampling quantum Monte Carlo algorithm with independent Metropolis

NASA Astrophysics Data System (ADS)

Vrbik, Jan; Ospadov, Egor; Rothstein, Stuart M.

2016-07-01

Recently, Ospadov and Rothstein published a pure-sampling quantum Monte Carlo algorithm (PSQMC) that features an auxiliary Path Z that connects the midpoints of the current and proposed Paths X and Y, respectively. When sufficiently long, Path Z provides statistical independence of Paths X and Y. Under those conditions, the Metropolis decision used in PSQMC is done without any approximation, i.e., not requiring microscopic reversibility and without having to introduce any G(x → x'; τ) factors into its decision function. This is a unique feature that contrasts with all competing reptation algorithms in the literature. An example illustrates that dependence of Paths X and Y has adverse consequences for pure sampling.

Newcomer adjustment during organizational socialization: a meta-analytic review of antecedents, outcomes, and methods.

PubMed

Bauer, Talya N; Bodner, Todd; Erdogan, Berrin; Truxillo, Donald M; Tucker, Jennifer S

2007-05-01

The authors tested a model of antecedents and outcomes of newcomer adjustment using 70 unique samples of newcomers with meta-analytic and path modeling techniques. Specifically, they proposed and tested a model in which adjustment (role clarity, self-efficacy, and social acceptance) mediated the effects of organizational socialization tactics and information seeking on socialization outcomes (job satisfaction, organizational commitment, job performance, intentions to remain, and turnover). The results generally supported this model. In addition, the authors examined the moderating effects of methodology on these relationships by coding for 3 methodological issues: data collection type (longitudinal vs. cross-sectional), sample characteristics (school-to-work vs. work-to-work transitions), and measurement of the antecedents (facet vs. composite measurement). Discussion focuses on the implications of the findings and suggestions for future research. 2007 APA, all rights reserved

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

PubMed

Aralis, Hilary; Brookmeyer, Ron

2017-01-01

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

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.

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

PubMed

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

2009-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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.

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.

Hierarchical Motion Planning for Autonomous Aerial and Terrestrial Vehicles

NASA Astrophysics Data System (ADS)

Cowlagi, Raghvendra V.

Autonomous mobile robots---both aerial and terrestrial vehicles---have gained immense importance due to the broad spectrum of their potential military and civilian applications. One of the indispensable requirements for the autonomy of a mobile vehicle is the vehicle's capability of planning and executing its motion, that is, finding appropriate control inputs for the vehicle such that the resulting vehicle motion satisfies the requirements of the vehicular task. The motion planning and control problem is inherently complex because it involves two disparate sub-problems: (1) satisfaction of the vehicular task requirements, which requires tools from combinatorics and/or formal methods, and (2) design of the vehicle control laws, which requires tools from dynamical systems and control theory. Accordingly, this problem is usually decomposed and solved over two levels of hierarchy. The higher level, called the geometric path planning level, finds a geometric path that satisfies the vehicular task requirements, e.g., obstacle avoidance. The lower level, called the trajectory planning level, involves sufficient smoothening of this geometric path followed by a suitable time parametrization to obtain a reference trajectory for the vehicle. Although simple and efficient, such hierarchical decomposition suffers a serious drawback: the geometric path planner has no information of the kinematical and dynamical constraints of the vehicle. Consequently, the geometric planner may produce paths that the trajectory planner cannot transform into a feasible reference trajectory. Two main ideas appear in the literature to remedy this problem: (a) randomized sampling-based planning, which eliminates the geometric planner altogether by planning in the vehicle state space, and (b) geometric planning supported by feedback control laws. The former class of methods suffer from a lack of optimality of the resultant trajectory, while the latter class of methods makes a restrictive assumption concerning the vehicle kinematical model. We propose a hierarchical motion planning framework based on a novel mode of interaction between these two levels of planning. This interaction rests on the solution of a special shortest-path problem on graphs, namely, one using costs defined on multiple edge transitions in the path instead of the usual single edge transition costs. These costs are provided by a local trajectory generation algorithm, which we implement using model predictive control and the concept of effective target sets for simplifying the non-convex constraints involved in the problem. The proposed motion planner ensures "consistency" between the two levels of planning, i.e., a guarantee that the higher level geometric path is always associated with a kinematically and dynamically feasible trajectory. The main contributions of this thesis are: 1. A motion planning framework based on history-dependent costs (H-costs) in cell decomposition graphs for incorporating vehicle dynamical constraints: this framework offers distinct advantages in comparison with the competing approaches of discretization of the state space, of randomized sampling-based motion planning, and of local feedback-based, decoupled hierarchical motion planning, 2. An efficient and flexible algorithm for finding optimal H-cost paths, 3. A precise and general formulation of a local trajectory problem (the tile motion planning problem) that allows independent development of the discrete planner and the trajectory planner, while maintaining "compatibility" between the two planners, 4. A local trajectory generation algorithm using mpc, and the application of the concept of effective target sets for a significant simplification of the local trajectory generation problem, 5. The geometric analysis of curvature-bounded traversal of rectangular channels, leading to less conservative results in comparison with a result reported in the literature, and also to the efficient construction of effective target sets for the solution of the tile motion planning problem, 6. A wavelet-based multi-resolution path planning scheme, and a proof of completeness of the proposed scheme: such proofs are altogether absent from other works on multi-resolution path planning, 7. A technique for extracting all information about cells---namely, the locations, the sizes, and the associated image intensities---directly from the set of significant detail coefficients considered for path planning at a given iteration, and 8. The extension of the multi-resolution path planning scheme to include vehicle dynamical constraints using the aforementioned history-dependent costs approach. The future work includes an implementation of the proposed framework involving a discrete planner that solves classical planning problems more general than the single-query path planning problem considered thus far, and involving trajectory generation schemes for realistic vehicle dynamical models such as the bicycle model.

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.

Improved graphite furnace atomizer

DOEpatents

Siemer, D.D.

1983-05-18

A graphite furnace atomizer for use in graphite furnace atomic absorption spectroscopy is described wherein the heating elements are affixed near the optical path and away from the point of sample deposition, so that when the sample is volatilized the spectroscopic temperature at the optical path is at least that of the volatilization temperature, whereby analyteconcomitant complex formation is advantageously reduced. The atomizer may be elongated along its axis to increase the distance between the optical path and the sample deposition point. Also, the atomizer may be elongated along the axis of the optical path, whereby its analytical sensitivity is greatly increased.

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…

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…

Can an inadequate cervical cytology sample in ThinPrep be converted to a satisfactory sample by processing it with a SurePath preparation?

PubMed

Sørbye, Sveinung Wergeland; Pedersen, Mette Kristin; Ekeberg, Bente; Williams, Merete E Johansen; Sauer, Torill; Chen, Ying

2017-01-01

The Norwegian Cervical Cancer Screening Program recommends screening every 3 years for women between 25 and 69 years of age. There is a large difference in the percentage of unsatisfactory samples between laboratories that use different brands of liquid-based cytology. We wished to examine if inadequate ThinPrep samples could be satisfactory by processing them with the SurePath protocol. A total of 187 inadequate ThinPrep specimens from the Department of Clinical Pathology at University Hospital of North Norway were sent to Akershus University Hospital for conversion to SurePath medium. Ninety-one (48.7%) were processed through the automated "gynecologic" application for cervix cytology samples, and 96 (51.3%) were processed with the "nongynecological" automatic program. Out of 187 samples that had been unsatisfactory by ThinPrep, 93 (49.7%) were satisfactory after being converted to SurePath. The rate of satisfactory cytology was 36.6% and 62.5% for samples run through the "gynecology" program and "nongynecology" program, respectively. Of the 93 samples that became satisfactory after conversion from ThinPrep to SurePath, 80 (86.0%) were screened as normal while 13 samples (14.0%) were given an abnormal diagnosis, which included 5 atypical squamous cells of undetermined significance, 5 low-grade squamous intraepithelial lesion, 2 atypical glandular cells not otherwise specified, and 1 atypical squamous cells cannot exclude high-grade squamous intraepithelial lesion. A total of 2.1% (4/187) of the women got a diagnosis of cervical intraepithelial neoplasia 2 or higher at a later follow-up. Converting cytology samples from ThinPrep to SurePath processing can reduce the number of unsatisfactory samples. The samples should be run through the "nongynecology" program to ensure an adequate number of cells.

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

PubMed

Velez-Vega, Camilo; Gilson, Michael K

2012-03-13

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

Quality Characteristics of Ground Water in the Ozark Aquifer of Northwestern Arkansas, Southeastern Kansas, Southwestern Missouri, and Northeastern Oklahoma, 2006-07

USGS Publications Warehouse

Pope, L.M.; Mehl, H.E.; Coiner, R.L.

2009-01-01

Because of water quantity and quality concerns within the Ozark aquifer, the State of Kansas in 2004 issued a moratorium on most new appropriations from the aquifer until results were made available from a cooperative study between the U.S. Geological Survey and the Kansas Water Office. The purposes of the study were to develop a regional ground-water flow model and a water-quality assessment of the Ozark aquifer in northwestern Arkansas, southeastern Kansas, southwestern Missouri, and northeastern Oklahoma (study area). In 2006 and 2007, water-quality samples were collected from 40 water-supply wells completed in the Ozark aquifer and spatially distributed throughout the study area. Samples were analyzed for physical properties, dissolved solids and major ions, nutrients, trace elements, and selected isotopes. This report presents the results of the water-quality assessment part of the cooperative study. Water-quality characteristics were evaluated relative to U.S. Environmental Protection Agency drinking-water standards. Secondary Drinking-Water Regulations were exceeded for dissolved solids (11 wells), sulfate and chloride (2 wells each), fluoride (3 wells), iron (4 wells), and manganese (2 wells). Maximum Contaminant Levels were exceeded for turbidity (3 wells) and fluoride (1 well). The Maximum Contaminant Level Goal for lead (0 milligrams per liter) was exceeded in water from 12 wells. Analyses of isotopes in water from wells along two 60-mile long ground-water flow paths indicated that water in the Ozark aquifer was at least 60 years old but the upper age limit is uncertain. The source of recharge water for the wells along the flow paths appeared to be of meteoric origin because of isotopic similarity to the established Global Meteoric Water Line and a global precipitation relation. Additionally, analysis of hydrogen-3 (3H) and carbon-14 (14C) indicated that there was possible leakage of younger ground water into the lower part of the Ozark aquifer. This may be caused by cracks or fissures in the confining unit that separates the upper and lower parts of the aquifer, poorly constructed or abandoned wells, or historic mining activities. Analyses of major ions in water from wells along the flow paths indicated a transition from freshwater in the east to saline water in the west. Generally, ground water along flow paths evolved from a calcium magnesium bicarbonate type to a sodium calcium bicarbonate or a sodium calcium chloride bicarbonate type as water moved from recharge areas in Missouri into Kansas. Much of this evolution occurred within the last 20 to 25 miles of the flow paths along a water-quality transition zone near the Kansas-Missouri State line and west. The water quality of the Kansas part of the Ozark aquifer is degraded compared to the Missouri part. Geophysical and well-bore flow information and depth-dependent water-quality samples were collected from a large-capacity (1,900-2,300 gallons per minute) municipal-supply well to evaluate vertical ground-water flow accretion and variability in water-quality characteristics at different levels. Although the 1,050-foot deep supply well had 500 feet of borehole open to the Ozark aquifer, 77 percent of ground-water flow entering the borehole came from two 20-foot thick rock layers above the 1,000-foot level. For the most part, water-quality characteristics changed little from the deepest sample to the well-head sample, and upwelling of saline water from deeper geologic formations below the well was not evident. However, more saline water may be present below the bottom of the well.

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

PubMed

Banerjee, Rahul; Cukier, Robert I

2014-03-20

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

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

Treesearch

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

2012-01-01

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

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.

Core self-evaluations and work engagement: Testing a perception, action, and development path.

PubMed

Tims, Maria; Akkermans, Jos

2017-01-01

Core self-evaluations (CSE) have predictive value for important work outcomes such as job satisfaction and job performance. However, little is known about the mechanisms that may explain these relationships. The purpose of the present study is to contribute to CSE theory by proposing and subsequently providing a first test of theoretically relevant mediating paths through which CSE may be related to work engagement. Based on approach/avoidance motivation and Job Demands-Resources theory, we examined a perception (via job characteristics), action (via job crafting), and development path (via career competencies). Two independent samples were obtained from employees working in Germany and The Netherlands (N = 303 and N = 404, respectively). When taking all mediators into account, results showed that the perception path represented by autonomy and social support played a minor role in the relationship between CSE and work engagement. Specifically, autonomy did not function as a mediator in both samples while social support played a marginally significant role in the CSE-work engagement relationship in sample 1 and received full support in sample 2. The action path exemplified by job crafting mediated the relationship between CSE and work engagement in both samples. Finally, the development path operationalized with career competencies mediated the relationship between CSE and work engagement in sample 1. The study presents evidence for an action and development path over and above the often tested perception path to explain how CSE is related to work engagement. This is one of the first studies to propose and show that CSE not only influences perceptions but also triggers employee actions and developmental strategies that relate to work engagement.

Core self-evaluations and work engagement: Testing a perception, action, and development path

PubMed Central

Akkermans, Jos

2017-01-01

Core self-evaluations (CSE) have predictive value for important work outcomes such as job satisfaction and job performance. However, little is known about the mechanisms that may explain these relationships. The purpose of the present study is to contribute to CSE theory by proposing and subsequently providing a first test of theoretically relevant mediating paths through which CSE may be related to work engagement. Based on approach/avoidance motivation and Job Demands-Resources theory, we examined a perception (via job characteristics), action (via job crafting), and development path (via career competencies). Two independent samples were obtained from employees working in Germany and The Netherlands (N = 303 and N = 404, respectively). When taking all mediators into account, results showed that the perception path represented by autonomy and social support played a minor role in the relationship between CSE and work engagement. Specifically, autonomy did not function as a mediator in both samples while social support played a marginally significant role in the CSE–work engagement relationship in sample 1 and received full support in sample 2. The action path exemplified by job crafting mediated the relationship between CSE and work engagement in both samples. Finally, the development path operationalized with career competencies mediated the relationship between CSE and work engagement in sample 1. The study presents evidence for an action and development path over and above the often tested perception path to explain how CSE is related to work engagement. This is one of the first studies to propose and show that CSE not only influences perceptions but also triggers employee actions and developmental strategies that relate to work engagement. PMID:28787464

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

NASA Astrophysics Data System (ADS)

Vanden-Eijnden, Eric; Venturoli, Maddalena

2009-05-01

An improved and simplified version of the finite temperature string (FTS) method [W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005)] is proposed. Like the original approach, the new method is a scheme to calculate the principal curves associated with the Boltzmann-Gibbs probability distribution of the system, i.e., the curves which are such that their intersection with the hyperplanes perpendicular to themselves coincides with the expected position of the system in these planes (where perpendicular is understood with respect to the appropriate metric). Unlike more standard paths such as the minimum energy path or the minimum free energy path, the location of the principal curve depends on global features of the energy or the free energy landscapes and thereby may remain appropriate in situations where the landscape is rough on the thermal energy scale and/or entropic effects related to the width of the reaction channels matter. Instead of using constrained sampling in hyperplanes as in the original FTS, the new method calculates the principal curve via sampling in the Voronoi tessellation whose generating points are the discretization points along this curve. As shown here, this modification results in greater algorithmic simplicity. As a by-product, it also gives the free energy associated with the Voronoi tessellation. The new method can be applied both in the original Cartesian space of the system or in a set of collective variables. We illustrate FTS on test-case examples and apply it to the study of conformational transitions of the nitrogen regulatory protein C receiver domain using an elastic network model and to the isomerization of solvated alanine dipeptide.

Methane Line Intensities: Near and Far IR

NASA Astrophysics Data System (ADS)

Brown, Linda R.; Devi, V. Malathy; Wishnow, Edward H.; Sung, Keeyoon; Crawford, Timothy J.; Mantz, Arlan W.; Smith, Mary Ann H.; Predoi-Cross, Adriana; Benner, D. Chris

2014-11-01

Accurate knowledge of line intensities is crucial input for radiance calculations to interpret atmospheric observations of planets and moons. We have therefore undertaken extensive laboratory studies to measure the methane spectrum line-by-line in order to improve theoretical quantum mechanical modeling for molecular spectroscopy databases (e. g. HITRAN and GEISA) used by planetary astronomers. Preliminary results will be presented for selected ro-vibrational transitions in both the near-IR (1.66 and 2.2 - 2.4 microns) and the far-IR (80 - 120 microns) regions. For this, we have recorded high-resolution spectra (instrumental resolving power: 1,300,000 (NIR) and 10,000 (FIR)) with the Bruker 125HR Fourier transform spectrometer at JPL using isotopically-enriched 12CH4 and 13CH4, as well as normal methane samples. For the NIR wavelengths, three different absorption cells have been employed to achieve sample temperatures ranging from 78 K to 299 K: 1) a White cell set to a path length of 13.09 m for room temperature data, 2) a single-pass 0.2038 m cold cell and 3) a new coolable Herriott cell with a fixed 20.941 m optical path and configured for the first time to a FT-IR spectrometer. For the Far-IR, another coolable absorption chamber set to a 52 m optical path has been used. These new experiments and intensity measurements will be presented and discussed.Part of the research described in this paper was performed at the Jet Propulsion Laboratory, California Institute of Technology, the University of California, Berkeley, Connecticut College, and NASA Langley under contracts and grants with the National Aeronautics and Space Administration. A. Predoi-Cross and her research group have been supported by the National Science and Engineering Research Council of Canada.

Proton transfer pathways, energy landscape, and kinetics in creatine-water systems.

PubMed

Ivchenko, Olga; Whittleston, Chris S; Carr, Joanne M; Imhof, Petra; Goerke, Steffen; Bachert, Peter; Wales, David J

2014-02-27

We study the exchange processes of the metabolite creatine, which is present in both tumorous and normal tissues and has NH2 and NH groups that can transfer protons to water. Creatine produces chemical exchange saturation transfer (CEST) contrast in magnetic resonance imaging (MRI). The proton transfer pathway from zwitterionic creatine to water is examined using a kinetic transition network constructed from the discrete path sampling approach and an approximate quantum-chemical energy function, employing the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. The resulting potential energy surface is visualized by constructing disconnectivity graphs. The energy landscape consists of two distinct regions corresponding to the zwitterionic creatine structures and deprotonated creatine. The activation energy that characterizes the proton transfer from the creatine NH2 group to water was determined from an Arrhenius fit of rate constants as a function of temperature, obtained from harmonic transition state theory. The result is in reasonable agreement with values obtained in water exchange spectroscopy (WEX) experiments.

Mechanisms of passive ion permeation through lipid bilayers

PubMed Central

Tepper, Harald L.; Voth, Gregory A.

2008-01-01

Multi-State Empirical Valence Bond and classical Molecular Dynamics simulations were used to explore mechanisms for passive ion leakage through a dimyristoyl phosphatidylcholine (DMPC) lipid bilayer. In accordance with a previous study on proton leakage, it was found that the permeation mechanism must be a highly concerted one, in which ion, solvent and membrane coordinates are coupled. The presence of the ion itself significantly alters the response of those coordinates, suggesting that simulations of transmembrane water structures without explicit inclusion of the ionic solute are insufficient for elucidating transition mechanisms. The properties of H+, Na+, OH-, and bare water molecules in the membrane interior were compared, both by biased sampling techniques and by constructing complete and unbiased transition paths. It was found that the anomalous difference in leakage rates between protons and other cations can be largely explained by charge delocalization effects, rather than the usual kinetic picture (Grotthuss hopping of the proton). Permeability differences between anions and cations through PC bilayers are correlated with suppression of favorable membrane breathing modes by cations. PMID:17048962

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.

Pre-entry Characteristics, Perceived Social Support, Adjustment and Academic Achievement in First-Year Spanish University Students: A Path Model.

PubMed

Rodríguez, María Soledad; Tinajero, Carolina; Páramo, María Fernanda

2017-11-17

Transition to university is a multifactorial process to which scarce consideration has been given in Spain, despite this being one of the countries with the highest rates of academic failure and attrition within the European Union. The present study proposes an empirical model for predicting Spanish students' academic achievement at university by considering pre-entry characteristics, perceived social support and adaptation to university, in a sample of 300 traditional first-year university students. The findings of the path analysis showed that pre-university achievement and academic and personal-emotional adjustment were direct predictors of academic achievement. Furthermore, gender, parents' education and family support were indirect predictors of academic achievement, mediated by pre-university grades and adjustment to university. The current findings supporting evidence that academic achievement in first-year Spanish students is the cumulative effect of pre-entry characteristics and process variables, key factors that should be taken into account in designing intervention strategies involving families and that establish stronger links between research findings and university policies.

Conversion of Nuclear Waste to Molten Glass: Cold-Cap Reactions in Crucible Tests

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

Xu, Kai; Hrma, Pavel; Rice, Jarrett A.

2016-05-23

The feed-to-glass conversion, which comprises complex chemical reactions and phase transitions, occurs in the cold-cap zone during nuclear waste vitrification. Knowledge of the chemistry and physics of feed-to-glass conversion will help us control the conversion path by changing the melter feed makeup to maximize the glass production rate. To investigate the conversion process, we analyzed heat-treated samples of a simulated high-level waste feed using X-ray diffraction, electron probe microanalysis – wavelength dispersive X-ray spectroscopy, leaching tests, and residual anion analysis. Feed dehydration, gas evolution, and borate phase formation occurred at temperatures below 700 °C before the emerging glass-forming melt wasmore » completely connected. Above 800 °C, intermediate aluminosilicate phases and quartz particles were gradually dissolving in the continuous borosilicate melt, which expanded into transient foam. Knowledge of the chemistry and physics of feed-to-glass conversion will help us control the conversion path by changing the melter feed makeup to maximize the glass production rate.« less

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

Ivanov, Sergei D., E-mail: sergei.ivanov@unirostock.de; Grant, Ian M.; Marx, Dominik

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently andmore » thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.« less

Effects of a mutation on the folding mechanism of a beta-hairpin.

PubMed

Juraszek, Jarek; Bolhuis, Peter G

2009-12-17

The folding mechanism of a protein is determined by its primary sequence. Yet, how the mechanism is changed by a mutation is still poorly understood, even for basic secondary structures such as beta-hairpins. We perform an extensive simulation study of the effects of mutating the GB1 beta-hairpin into Trpzip4 (Y5W, F12W, V14W) on the folding mechanism. While Trpzip4 has a much more stable native state due to very strong hydrophobic interactions of the side chains, its folding rate does not differ significantly from the wild type beta-hairpin. We sample the free-energy landscapes of both hairpins with Replica Exchange Molecular Dynamics (REMD) and identify the four (meta)stable states (U, H, F, and N). Using Transition Path Sampling (TPS), we then harvest ensembles of unbiased pathways between the H and F states and between the F and N states to investigate the unbiased folding mechanisms. In both hairpins, the hydrophobic collapse (U-H) is followed by the middle hydrogen bond formation (H-F), and finally a closing of the strands in a zipper-like fashion (F-N). For the Trpzip4, the path ensembles indicate that the final F-N step is much more difficult than for GB1 and involves partial unfolding, rezipping of hydrogen bonds, and rearrangement of the Trp-14 side chain. For the rate-limiting (H-F) step, the path ensembles show that in GB1 desolvation and strand closure go hand in hand, while in Trpzip4 desolvation is decoupled from strand closure. Nevertheless, likelihood maximization shows that the reaction coordinate for both hairpins remains the interstrand distance. We conclude that the folding mechanism of both hairpins is a combination of hydrophobic collapse and zipping of hydrogen bonds but that the zipper mechanism is more visible in Trpzip4. A major difference between the two hairpins is that in the transition state of the rate-limiting step for Trpzip4 one tryptophan is exposed to the solvent due to steric hindrance, making the folding mechanism more complex and leading to an increased F-N barrier. Thus, our results show in atomistic detail how a mutation leads to a different folding mechanism and results in a more frustrated folding free-energy landscape.

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

The allosteric switching mechanism in bacteriophage MS2

NASA Astrophysics Data System (ADS)

Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F.

2016-07-01

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

The allosteric switching mechanism in bacteriophage MS2

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

Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F., E-mail: hagan@brandeis.edu

2016-07-21

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we usemore » all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.« less

The allosteric switching mechanism in bacteriophage MS2

PubMed Central

Perkett, Matthew R.; Mirijanian, Dina T.

2016-01-01

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates. PMID:27448905

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

On the efficacy of spatial sampling using manual scanning paths to determine the spatial average sound pressure level in rooms.

PubMed

Hopkins, Carl

2011-05-01

In architectural acoustics, noise control and environmental noise, there are often steady-state signals for which it is necessary to measure the spatial average, sound pressure level inside rooms. This requires using fixed microphone positions, mechanical scanning devices, or manual scanning. In comparison with mechanical scanning devices, the human body allows manual scanning to trace out complex geometrical paths in three-dimensional space. To determine the efficacy of manual scanning paths in terms of an equivalent number of uncorrelated samples, an analytical approach is solved numerically. The benchmark used to assess these paths is a minimum of five uncorrelated fixed microphone positions at frequencies above 200 Hz. For paths involving an operator walking across the room, potential problems exist with walking noise and non-uniform scanning speeds. Hence, paths are considered based on a fixed standing position or rotation of the body about a fixed point. In empty rooms, it is shown that a circle, helix, or cylindrical-type path satisfy the benchmark requirement with the latter two paths being highly efficient at generating large number of uncorrelated samples. In furnished rooms where there is limited space for the operator to move, an efficient path comprises three semicircles with 45°-60° separations.

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

Near-Surface Profiles of Water Stable Isotope Components and Indicated Transitional History of Ice-Wedge Polygons Near Barrow

NASA Astrophysics Data System (ADS)

Iwahana, G.; Wilson, C.; Newman, B. D.; Heikoop, J. M.; Busey, R.

2017-12-01

Wetlands associated with ice-wedge polygons are commonly distributed across the Arctic Coastal Plain of northern Alaska, a region underlain by continuous permafrost. Micro-topography of the ice-wedge polygons controls local hydrology, and the micro-topography could be altered due to factors such like surface vegetation, wetness, freeze-thaw cycles, and permafrost degradation/aggradation under climate change. Understanding status of the wetlands in the near future is important because it determines biogeochemical cycle, which drives release of greenhouse gases from the ground. However, transitional regime of the ice-wedge polygons under the changing climate is not fully understood. In this study, we analyzed geochemistry of water extracted from frozen soil cores sampled down to about 1m depth in 2014 March at NGEE-Arctic sites in the Barrow Environmental Observatory. The cores were sampled from troughs/rims/centers of five different low-centered or flat-centered polygons. The frozen cores are divided into 5-10cm cores for each location, thawed in sealed plastic bags, and then extracted water was stored in vials. Comparison between the profiles of geochemistry indicated connection of soil water in the active layer at different location in a polygon, while it revealed that distinctly different water has been stored in permafrost layer at troughs/rims/centers of some polygons. Profiles of volumetric water content (VWC) showed clear signals of freeze-up desiccation in the middle of saturated active layers as low VWC anomalies at most sampling points. Water in the active layer and near-surface permafrost was classified into four categories: ice wedge / fresh meteoric / transitional / highly fractionated water. The overall results suggested prolonged separation of water in the active layer at the center of low-centered polygons without lateral connection in water path in the past.

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

NASA Astrophysics Data System (ADS)

McGibbon, J.; Bretherton, C. S.

2017-06-01

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