Use of state-and-transition simulation modeling in National Forest planning in the Pacific Northwest, U.S.A

Treesearch

Ayn J. Shlisky; Don Vandendriesche

2012-01-01

Effective national forest planning depends on scientifically sound analyses of land management alternatives relative to desired future conditions and environmental effects. The USDA Forest Service Pacific Northwest Region is currently using state-and-transition simulation models (STMs) to simulate changes in forest composition and structure for the revisions of five...

Calibration of a γ- Re θ transition model and its application in low-speed flows

NASA Astrophysics Data System (ADS)

Wang, YunTao; Zhang, YuLun; Meng, DeHong; Wang, GunXue; Li, Song

2014-12-01

The prediction of laminar-turbulent transition in boundary layer is very important for obtaining accurate aerodynamic characteristics with computational fluid dynamic (CFD) tools, because laminar-turbulent transition is directly related to complex flow phenomena in boundary layer and separated flow in space. Unfortunately, the transition effect isn't included in today's major CFD tools because of non-local calculations in transition modeling. In this paper, Menter's γ- Re θ transition model is calibrated and incorporated into a Reynolds-Averaged Navier-Stokes (RANS) code — Trisonic Platform (TRIP) developed in China Aerodynamic Research and Development Center (CARDC). Based on the experimental data of flat plate from the literature, the empirical correlations involved in the transition model are modified and calibrated numerically. Numerical simulation for low-speed flow of Trapezoidal Wing (Trap Wing) is performed and compared with the corresponding experimental data. It is indicated that the γ- Re θ transition model can accurately predict the location of separation-induced transition and natural transition in the flow region with moderate pressure gradient. The transition model effectively imporves the simulation accuracy of the boundary layer and aerodynamic characteristics.

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

PubMed Central

Okazaki, Kei-ichi; Koga, Nobuyasu; Takada, Shoji; Onuchic, Jose N.; Wolynes, Peter G.

2006-01-01

Biomolecules often undergo large-amplitude motions when they bind or release other molecules. Unlike macroscopic machines, these biomolecular machines can partially disassemble (unfold) and then reassemble (fold) during such transitions. Here we put forward a minimal structure-based model, the “multiple-basin model,” that can directly be used for molecular dynamics simulation of even very large biomolecular systems so long as the endpoints of the conformational change are known. We investigate the model by simulating large-scale motions of four proteins: glutamine-binding protein, S100A6, dihydrofolate reductase, and HIV-1 protease. The mechanisms of conformational transition depend on the protein basin topologies and change with temperature near the folding transition. The conformational transition rate varies linearly with driving force over a fairly large range. This linearity appears to be a consequence of partial unfolding during the conformational transition. PMID:16877541

Encapsulating model complexity and landscape-scale analyses of state-and-transition simulation models: an application of ecoinformatics and juniper encroachment in sagebrush steppe ecosystems

USGS Publications Warehouse

O'Donnell, Michael

2015-01-01

State-and-transition simulation modeling relies on knowledge of vegetation composition and structure (states) that describe community conditions, mechanistic feedbacks such as fire that can affect vegetation establishment, and ecological processes that drive community conditions as well as the transitions between these states. However, as the need for modeling larger and more complex landscapes increase, a more advanced awareness of computing resources becomes essential. The objectives of this study include identifying challenges of executing state-and-transition simulation models, identifying common bottlenecks of computing resources, developing a workflow and software that enable parallel processing of Monte Carlo simulations, and identifying the advantages and disadvantages of different computing resources. To address these objectives, this study used the ApexRMS® SyncroSim software and embarrassingly parallel tasks of Monte Carlo simulations on a single multicore computer and on distributed computing systems. The results demonstrated that state-and-transition simulation models scale best in distributed computing environments, such as high-throughput and high-performance computing, because these environments disseminate the workloads across many compute nodes, thereby supporting analysis of larger landscapes, higher spatial resolution vegetation products, and more complex models. Using a case study and five different computing environments, the top result (high-throughput computing versus serial computations) indicated an approximate 96.6% decrease of computing time. With a single, multicore compute node (bottom result), the computing time indicated an 81.8% decrease relative to using serial computations. These results provide insight into the tradeoffs of using different computing resources when research necessitates advanced integration of ecoinformatics incorporating large and complicated data inputs and models. - See more at: http://aimspress.com/aimses/ch/reader/view_abstract.aspx?file_no=Environ2015030&flag=1#sthash.p1XKDtF8.dpuf

Turbulence Modeling for the Simulation of Transition in Wall Shear Flows

NASA Technical Reports Server (NTRS)

Crawford, Michael E.

2007-01-01

Our research involves study of the behavior of k-epsilon turbulence models for simulation of bypass-level transition over flat surfaces and turbine blades. One facet of the research has been to assess the performance of a multitude of k-epsilon models in what we call "natural transition", i.e. no modifications to the k-e models. The study has been to ascertain what features in the dynamics of the model affect the start and end of the transition. Some of the findings are in keeping with those reported by others (e.g. ERCOFTAC). A second facet of the research has been to develop and benchmark a new multi-time scale k-epsilon model (MTS) for use in simulating bypass-level transition. This model has certain features of the published MTS models by Hanjalic, Launder, and Schiestel, and by Kim and his coworkers. The major new feature of our MTS model is that it can be used to compute wall shear flows as a low-turbulence Reynolds number type of model, i.e. there is no required partition with patching a one-equation k model in the near-wall region to a two-equation k-epsilon model in the outer part of the flow. Our MTS model has been studied extensively to understand its dynamics in predicting the onset of transition and the end-stage of the transition. Results to date indicate that it far superior to the standard unmodified k-epsilon models. The effects of protracted pressure gradients on the model behavior are currently being investigated.

State-and-transition simulation models: a framework for forecasting landscape change

USGS Publications Warehouse

Daniel, Colin; Frid, Leonardo; Sleeter, Benjamin M.; Fortin, Marie-Josée

2016-01-01

SummaryA wide range of spatially explicit simulation models have been developed to forecast landscape dynamics, including models for projecting changes in both vegetation and land use. While these models have generally been developed as separate applications, each with a separate purpose and audience, they share many common features.We present a general framework, called a state-and-transition simulation model (STSM), which captures a number of these common features, accompanied by a software product, called ST-Sim, to build and run such models. The STSM method divides a landscape into a set of discrete spatial units and simulates the discrete state of each cell forward as a discrete-time-inhomogeneous stochastic process. The method differs from a spatially interacting Markov chain in several important ways, including the ability to add discrete counters such as age and time-since-transition as state variables, to specify one-step transition rates as either probabilities or target areas, and to represent multiple types of transitions between pairs of states.We demonstrate the STSM method using a model of land-use/land-cover (LULC) change for the state of Hawai'i, USA. Processes represented in this example include expansion/contraction of agricultural lands, urbanization, wildfire, shrub encroachment into grassland and harvest of tree plantations; the model also projects shifts in moisture zones due to climate change. Key model output includes projections of the future spatial and temporal distribution of LULC classes and moisture zones across the landscape over the next 50 years.State-and-transition simulation models can be applied to a wide range of landscapes, including questions of both land-use change and vegetation dynamics. Because the method is inherently stochastic, it is well suited for characterizing uncertainty in model projections. When combined with the ST-Sim software, STSMs offer a simple yet powerful means for developing a wide range of models of landscape dynamics.

Using the Weak-Temperature Gradient Approximation to Evaluate Parameterizations: An Example of the Transition From Suppressed to Active Convection

NASA Astrophysics Data System (ADS)

Daleu, C. L.; Plant, R. S.; Woolnough, S. J.

2017-10-01

Two single-column models are fully coupled via the weak-temperature gradient approach. The coupled-SCM is used to simulate the transition from suppressed to active convection under the influence of an interactive large-scale circulation. The sensitivity of this transition to the value of mixing entrainment within the convective parameterization is explored. The results from these simulations are compared with those from equivalent simulations using coupled cloud-resolving models. Coupled-column simulations over nonuniform surface forcing are used to initialize the simulations of the transition, in which the column with suppressed convection is forced to undergo a transition to active convection by changing the local and/or remote surface forcings. The direct contributions from the changes in surface forcing are to induce a weakening of the large-scale circulation which systematically modulates the transition. In the SCM, the contributions from the large-scale circulation are dominated by the heating effects, while in the CRM the heating and moistening effects are about equally divided. A transition time is defined as the time when the rain rate in the dry column is halfway to the value at equilibrium after the transition. For the control value of entrainment, the order of the transition times is identical to that obtained in the CRM, but the transition times are markedly faster. The locally forced transition is strongly delayed by a higher entrainment. A consequence is that for a 50% higher entrainment the transition times are reordered. The remotely forced transition remains fast while the locally forced transition becomes slow, compared to the CRM.

Deflagration to Detonation Transition (DDT) Simulations of HMX Powder Using the HERMES Model

NASA Astrophysics Data System (ADS)

White, Bradley; Reaugh, John; Tringe, Joseph

2017-06-01

We performed computer simulations of DDT experiments with Class I HMX powder using the HERMES model (High Explosive Response to MEchanical Stimulus) in ALE3D. Parameters for the model were fitted to the limited available mechanical property data of the low-density powder, and to the Shock to Detonation Transition (SDT) test results. The DDT tests were carried out in steel-capped polycarbonate tubes. This arrangement permits direct observation of the event using both flash X-ray radiography and high speed camera imaging, and provides a stringent test of the model. We found the calculated detonation transition to be qualitatively similar to experiment. Through simulation we also explored the effects of confinement strength, the HMX particle size distribution and porosity on the computed detonation transition location. This work was performed under the auspices of the US DOE by LLNL under Contract DE-AC52-07NA27344.

Center for Modeling of Turbulence and Transition (CMOTT). Research briefs: 1990

NASA Technical Reports Server (NTRS)

Povinelli, Louis A. (Compiler); Liou, Meng-Sing (Compiler); Shih, Tsan-Hsing (Compiler)

1991-01-01

Brief progress reports of the Center for Modeling of Turbulence and Transition (CMOTT) research staff from May 1990 to May 1991 are given. The objectives of the CMOTT are to develop, validate, and implement the models for turbulence and boundary layer transition in the practical engineering flows. The flows of interest are three dimensional, incompressible, and compressible flows with chemistry. The schemes being studied include the two-equation and algebraic Reynolds stress models, the full Reynolds stress (or second moment closure) models, the probability density function models, the Renormalization Group Theory (RNG) and Interaction Approximation (DIA), the Large Eddy Simulation (LES) and Direct Numerical Simulation (DNS).

Analysis of flow disturbance in a stenosed carotid artery bifurcation using two-equation transitional and turbulence models.

PubMed

Tan, F P P; Soloperto, G; Bashford, S; Wood, N B; Thom, S; Hughes, A; Xu, X Y

2008-12-01

In this study, newly developed two-equation turbulence models and transitional variants are employed for the prediction of blood flow patterns in a diseased carotid artery where the growth, progression, and structure of the plaque at rupture are closely linked to low and oscillating wall shear stresses. Moreover, the laminar-turbulent transition in the poststenotic zone can alter the separation zone length, wall shear stress, and pressure distribution over the plaque, with potential implications for stresses within the plaque. Following the validation with well established experimental measurements and numerical studies, a magnetic-resonance (MR) image-based model of the carotid bifurcation with 70% stenosis was reconstructed and simulated using realistic patient-specific conditions. Laminar flow, a correlation-based transitional version of Menter's hybrid k-epsilon/k-omega shear stress transport (SST) model and its "scale adaptive simulation" (SAS) variant were implemented in pulsatile simulations from which analyses of velocity profiles, wall shear stress, and turbulence intensity were conducted. In general, the transitional version of SST and its SAS variant are shown to give a better overall agreement than their standard counterparts with experimental data for pulsatile flow in an axisymmetric stenosed tube. For the patient-specific case reported, the wall shear stress analysis showed discernable differences between the laminar flow and SST transitional models but virtually no difference between the SST transitional model and its SAS variant.

State-to-state models of vibrational relaxation in Direct Simulation Monte Carlo (DSMC)

NASA Astrophysics Data System (ADS)

Oblapenko, G. P.; Kashkovsky, A. V.; Bondar, Ye A.

2017-02-01

In the present work, the application of state-to-state models of vibrational energy exchanges to the Direct Simulation Monte Carlo (DSMC) is considered. A state-to-state model for VT transitions of vibrational energy in nitrogen and oxygen, based on the application of the inverse Laplace transform to results of quasiclassical trajectory calculations (QCT) of vibrational energy transitions, along with the Forced Harmonic Oscillator (FHO) state-to-state model is implemented in DSMC code and applied to flows around blunt bodies. Comparisons are made with the widely used Larsen-Borgnakke model and the in uence of multi-quantum VT transitions is assessed.

Elastic Model Transitions: a Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

NASA Technical Reports Server (NTRS)

Jurenko, Robert J.; Bush, T. Jason; Ottander, John A.

2014-01-01

A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes both quadratically constrained least squares (LSQI) and Direct Shape Mapping (DSM) algorithms to determine physical displacements. This approach is applicable to the simulation of the elastic behavior of launch vehicles and other structures that utilize multiple LTI finite element model (FEM) derived mode sets that are propagated throughout time. The time invariant nature of the elastic data for discrete segments of the launch vehicle trajectory presents a problem of how to properly transition between models while preserving motion across the transition. In addition, energy may vary between flex models when using a truncated mode set. The LSQI-DSM algorithm can accommodate significant changes in energy between FEM models and carries elastic motion across FEM model transitions. Compared with previous approaches, the LSQI-DSM algorithm shows improvements ranging from a significant reduction to a complete removal of transients across FEM model transitions as well as maintaining elastic motion from the prior state.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

A phenomenological model for simulating the chemo-responsive shape memory effect in polymers undergoing a permeation transition

NASA Astrophysics Data System (ADS)

Lu, Haibao; Huang, Wei Min; Leng, Jinsong

2014-04-01

We present a phenomenological model for studying the constitutive relations and working mechanism of the chemo-responsive shape memory effect (SME) in shape memory polymers (SMPs). On the basis of the solubility parameter equation, diffusion model and permeation transition model, a phenomenological model is derived for quantitatively identifying the influential factors in the chemically induced SME in SMPs. After this, a permeability parallel model and series model are implemented in order to couple the constitutive relations of the permeability coefficient, stress and relaxation time as a function of stretch, separately. The inductive effect of the permeability transition on the transition temperature is confirmed as the driving force for the chemo-responsive SME. Furthermore, the analytical result from the phenomenological model is compared with the available experimental results and the simulation of a semi-empirical model reported in the literature for verification.

Large-eddy simulation of laminar-turbulent breakdown at high speeds with dynamic subgrid-scale modeling

NASA Technical Reports Server (NTRS)

El-Hady, Nabil M.

1993-01-01

The laminar-turbulent breakdown of a boundary-layer flow along a hollow cylinder at Mach 4.5 is investigated with large-eddy simulation. The subgrid scales are modeled dynamically, where the model coefficients are determined from the local resolved field. The behavior of the dynamic-model coefficients is investigated through both an a priori test with direct numerical simulation data for the same case and a complete large-eddy simulation. Both formulations proposed by Germano et al. and Lilly are used for the determination of unique coefficients for the dynamic model and their results are compared and assessed. The behavior and the energy cascade of the subgrid-scale field structure are investigated at various stages of the transition process. The investigations are able to duplicate a high-speed transition phenomenon observed in experiments and explained only recently by the direct numerical simulations of Pruett and Zang, which is the appearance of 'rope-like' waves. The nonlinear evolution and breakdown of the laminar boundary layer and the structure of the flow field during the transition process were also investigated.

Calibration of the 7—Equation Transition Model for High Reynolds Flows at Low Mach

NASA Astrophysics Data System (ADS)

Colonia, S.; Leble, V.; Steijl, R.; Barakos, G.

2016-09-01

The numerical simulation of flows over large-scale wind turbine blades without considering the transition from laminar to fully turbulent flow may result in incorrect estimates of the blade loads and performance. Thanks to its relative simplicity and promising results, the Local-Correlation based Transition Modelling concept represents a valid way to include transitional effects into practical CFD simulations. However, the model involves coefficients that need tuning. In this paper, the γ—equation transition model is assessed and calibrated, for a wide range of Reynolds numbers at low Mach, as needed for wind turbine applications. An aerofoil is used to evaluate the original model and calibrate it; while a large scale wind turbine blade is employed to show that the calibrated model can lead to reliable solutions for complex three-dimensional flows. The calibrated model shows promising results for both two-dimensional and three-dimensional flows, even if cross-flow instabilities are neglected.

Transition to parenthood: the role of social interaction and endogenous networks.

PubMed

Diaz, Belinda Aparicio; Fent, Thomas; Prskawetz, Alexia; Bernardi, Laura

2011-05-01

Empirical studies indicate that the transition to parenthood is influenced by an individual's peer group. To study the mechanisms creating interdependencies across individuals' transition to parenthood and its timing, we apply an agent-based simulation model. We build a one-sex model and provide agents with three different characteristics: age, intended education, and parity. Agents endogenously form their network based on social closeness. Network members may then influence the agents' transition to higher parity levels. Our numerical simulations indicate that accounting for social interactions can explain the shift of first-birth probabilities in Austria during the period 1984 to 2004. Moreover, we apply our model to forecast age-specific fertility rates up to 2016.

The Kepler End-to-End Model: Creating High-Fidelity Simulations to Test Kepler Ground Processing

NASA Technical Reports Server (NTRS)

Bryson, Stephen T.; Jenkins, Jon M.; Peters, Dan J.; Tenenbaum, Peter P.; Klaus, Todd C.; Gunter, Jay P.; Cote, Miles T.; Caldwell, Douglas A.

2010-01-01

The Kepler mission is designed to detect the transit of Earth-like planets around Sun-like stars by observing 100,000 stellar targets. Developing and testing the Kepler ground-segment processing system, in particular the data analysis pipeline, requires high-fidelity simulated data. This simulated data is provided by the Kepler End-to-End Model (ETEM). ETEM simulates the astrophysics of planetary transits and other phenomena, properties of the Kepler spacecraft and the format of the downlinked data. Major challenges addressed by ETEM include the rapid production of large amounts of simulated data, extensibility and maintainability.

Implementation of a Transition Model in a NASA Code and Validation Using Heat Transfer Data on a Turbine Blade

NASA Technical Reports Server (NTRS)

Ameri, Ali A.

2012-01-01

The purpose of this report is to summarize and document the work done to enable a NASA CFD code to model laminar-turbulent transition process on an isolated turbine blade. The ultimate purpose of the present work is to down-select a transition model that would allow the flow simulation of a variable speed power turbine to be accurately performed. The flow modeling in its final form will account for the blade row interactions and their effects on transition which would lead to accurate accounting for losses. The present work only concerns itself with steady flows of variable inlet turbulence. The low Reynolds number k- model of Wilcox and a modified version of the same model will be used for modeling of transition on experimentally measured blade pressure and heat transfer. It will be shown that the k- model and its modified variant fail to simulate the transition with any degree of accuracy. A case is thus made for the adoption of more accurate transition models. Three-equation models based on the work of Mayle on Laminar Kinetic Energy were explored. The three-equation model of Walters and Leylek was thought to be in a relatively mature state of development and was implemented in the Glenn-HT code. Two-dimensional heat transfer predictions of flat plate flow and two-dimensional and three-dimensional heat transfer predictions on a turbine blade were performed and reported herein. Surface heat transfer rate serves as sensitive indicator of transition. With the newly implemented model, it was shown that the simulation of transition process is much improved over the baseline k- model for the single Reynolds number and pressure ratio attempted; while agreement with heat transfer data became more satisfactory. Armed with the new transition model, total-pressure losses of computed three-dimensional flow of E3 tip section cascade were compared to the experimental data for a range of incidence angles. The results obtained, form a partial loss bucket for the chosen blade. In time the loss bucket will be populated with losses at additional incidences. Results obtained thus far will be discussed herein.

Dicke-model simulation via cavity-assisted Raman transitions

NASA Astrophysics Data System (ADS)

Zhang, Zhiqiang; Lee, Chern Hui; Kumar, Ravi; Arnold, K. J.; Masson, Stuart J.; Grimsmo, A. L.; Parkins, A. S.; Barrett, M. D.

2018-04-01

The Dicke model is of fundamental importance in quantum mechanics for understanding the collective behavior of atoms coupled to a single electromagnetic mode. Here, we demonstrate a Dicke-model simulation via cavity-assisted Raman transitions in a configuration using counterpropagating laser beams. The observations indicate that motional effects should be included to fully account for the results. These results are contrary to experiments using single-beam and copropagating configurations. We give a theoretical description that accounts for the beam geometries used in the experiments and indicates the potential role of motional effects. In particular, a model is given that highlights the influence of Doppler broadening on the observed phase-transition thresholds.

An Introduction to the Transition to Work Simulator.

ERIC Educational Resources Information Center

Conroy, William G., Jr.

The transition to work simulator (TWS) was developed as a policy tool for education and manpower planning. It was designed in anticipation of the Education Amendments of 1976 and the Youth Employment and Demonstration Projects Act of 1977 to facilitate comprehensive planning. TWS is a computerized simulation model of the stream of important…

Simulation of Shallow Cumuli and Their Transition to Deep Convective Clouds by Cloud-resolving Models with Different Third-order Turbulence Closures

NASA Technical Reports Server (NTRS)

Cheng, Anning; Xu, Kuan-Man

2006-01-01

The abilities of cloud-resolving models (CRMs) with the double-Gaussian based and the single-Gaussian based third-order closures (TOCs) to simulate the shallow cumuli and their transition to deep convective clouds are compared in this study. The single-Gaussian based TOC is fully prognostic (FP), while the double-Gaussian based TOC is partially prognostic (PP). The latter only predicts three important third-order moments while the former predicts all the thirdorder moments. A shallow cumulus case is simulated by single-column versions of the FP and PP TOC models. The PP TOC improves the simulation of shallow cumulus greatly over the FP TOC by producing more realistic cloud structures. Large differences between the FP and PP TOC simulations appear in the cloud layer of the second- and third-order moments, which are related mainly to the underestimate of the cloud height in the FP TOC simulation. Sensitivity experiments and analysis of probability density functions (PDFs) used in the TOCs show that both the turbulence-scale condensation and higher-order moments are important to realistic simulations of the boundary-layer shallow cumuli. A shallow to deep convective cloud transition case is also simulated by the 2-D versions of the FP and PP TOC models. Both CRMs can capture the transition from the shallow cumuli to deep convective clouds. The PP simulations produce more and deeper shallow cumuli than the FP simulations, but the FP simulations produce larger and wider convective clouds than the PP simulations. The temporal evolutions of cloud and precipitation are closely related to the turbulent transport, the cold pool and the cloud-scale circulation. The large amount of turbulent mixing associated with the shallow cumuli slows down the increase of the convective available potential energy and inhibits the early transition to deep convective clouds in the PP simulation. When the deep convective clouds fully develop and the precipitation is produced, the cold pools produced by the evaporation of the precipitation are not favorable to the formation of shallow cumuli.

CONFIG: Qualitative simulation tool for analyzing behavior of engineering devices

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Basham, Bryan D.; Harris, Richard A.

1987-01-01

To design failure management expert systems, engineers mentally analyze the effects of failures and procedures as they propagate through device configurations. CONFIG is a generic device modeling tool for use in discrete event simulation, to support such analyses. CONFIG permits graphical modeling of device configurations and qualitative specification of local operating modes of device components. Computation requirements are reduced by focussing the level of component description on operating modes and failure modes, and specifying qualitative ranges of variables relative to mode transition boundaries. Simulation processing occurs only when modes change or variables cross qualitative boundaries. Device models are built graphically, using components from libraries. Components are connected at ports by graphical relations that define data flow. The core of a component model is its state transition diagram, which specifies modes of operation and transitions among them.

Application of renormalization group theory to the large-eddy simulation of transitional boundary layers

NASA Technical Reports Server (NTRS)

Piomelli, Ugo; Zang, Thomas A.; Speziale, Charles G.; Lund, Thomas S.

1990-01-01

An eddy viscosity model based on the renormalization group theory of Yakhot and Orszag (1986) is applied to the large-eddy simulation of transition in a flat-plate boundary layer. The simulation predicts with satisfactory accuracy the mean velocity and Reynolds stress profiles, as well as the development of the important scales of motion. The evolution of the structures characteristic of the nonlinear stages of transition is also predicted reasonably well.

Computational Fluid Dynamics (CFD) Simulation of Hypersonic Turbine-Based Combined-Cycle (TBCC) Inlet Mode Transition

NASA Technical Reports Server (NTRS)

Slater, John W.; Saunders, John D.

2010-01-01

Methods of computational fluid dynamics were applied to simulate the aerodynamics within the turbine flowpath of a turbine-based combined-cycle propulsion system during inlet mode transition at Mach 4. Inlet mode transition involved the rotation of a splitter cowl to close the turbine flowpath to allow the full operation of a parallel dual-mode ramjet/scramjet flowpath. Steady-state simulations were performed at splitter cowl positions of 0deg, -2deg, -4deg, and -5.7deg, at which the turbine flowpath was closed half way. The simulations satisfied one objective of providing a greater understanding of the flow during inlet mode transition. Comparisons of the simulation results with wind-tunnel test data addressed another objective of assessing the applicability of the simulation methods for simulating inlet mode transition. The simulations showed that inlet mode transition could occur in a stable manner and that accurate modeling of the interactions among the shock waves, boundary layers, and porous bleed regions was critical for evaluating the inlet static and total pressures, bleed flow rates, and bleed plenum pressures. The simulations compared well with some of the wind-tunnel data, but uncertainties in both the windtunnel data and simulations prevented a formal evaluation of the accuracy of the simulation methods.

Urban public transit systems modeling capabilities

DOT National Transportation Integrated Search

1995-02-01

Current national transportation policy places increasing emphasis on multi-modal : solutions involving public transit and high-occupancy vehicle (HOV) facilities : and services. Current traffic simulation/assignment models, however, have only : limit...

Assessing the effects of rural livelihood transition on non-point source pollution: a coupled ABM-IECM model.

PubMed

Yuan, Chengcheng; Liu, Liming; Ye, Jinwei; Ren, Guoping; Zhuo, Dong; Qi, Xiaoxing

2017-05-01

Water pollution caused by anthropogenic activities and driven by changes in rural livelihood strategies in an agricultural system has received increasing attention in recent decades. To simulate the effects of rural household livelihood transition on non-point source (NPS) pollution, a model combining an agent-based model (ABM) and an improved export coefficient model (IECM) was developed. The ABM was adopted to simulate the dynamic process of household livelihood transition, and the IECM was employed to estimate the effects of household livelihood transition on NPS pollution. The coupled model was tested in a small catchment in the Dongting Lake region, China. The simulated results reveal that the transition of household livelihood strategies occurred with the changes in the prices of rice, pig, and labor. Thus, the cropping system, land-use intensity, resident population, and number of pigs changed in the small catchment from 2000 to 2014. As a result of these changes, the total nitrogen load discharged into the river initially increased from 6841.0 kg in 2000 to 8446.3 kg in 2004 and then decreased to 6063.9 kg in 2014. Results also suggest that rural living, livestock, paddy field, and precipitation alternately became the main causes of NPS pollution in the small catchment, and the midstream region of the small catchment was the primary area for NPS pollution from 2000 to 2014. Despite some limitations, the coupled model provides an innovative way to simulate the effects of rural household livelihood transition on NPS pollution with the change of socioeconomic factors, and thereby identify the key factors influencing water pollution to provide valuable suggestions on how agricultural environmental risks can be reduced through the regulation of the behaviors of farming households in the future.

Transition in coupled replicas may not imply a finite-temperature ideal glass transition in glass-forming systems.

PubMed

Garrahan, Juan P

2014-03-01

A key open question in the glass transition field is whether a finite temperature thermodynamic transition to the glass state exists or not. Recent simulations of coupled replicas in atomistic models have found signatures of a static transition as a function of replica coupling. This can be viewed as evidence of an associated thermodynamic glass transition in the uncoupled system. We demonstrate here that a different interpretation is possible. We consider the triangular plaquette model, an interacting spin system which displays (East model-like) glassy dynamics in the absence of any static transition. We show that when two replicas are coupled, there is a curve of equilibrium phase transitions, between phases of small and large overlap, in the temperature-coupling plane (located on the self-dual line of an exact temperature-coupling duality of the system) which ends at a critical point. Crucially, in the limit of vanishing coupling the finite temperature transition disappears, and the uncoupled system is in the disordered phase at all temperatures. We discuss an interpretation of atomistic simulations in light of this result.

Hydrogeologic unit flow characterization using transition probability geostatistics.

PubMed

Jones, Norman L; Walker, Justin R; Carle, Steven F

2005-01-01

This paper describes a technique for applying the transition probability geostatistics method for stochastic simulation to a MODFLOW model. Transition probability geostatistics has some advantages over traditional indicator kriging methods including a simpler and more intuitive framework for interpreting geologic relationships and the ability to simulate juxtapositional tendencies such as fining upward sequences. The indicator arrays generated by the transition probability simulation are converted to layer elevation and thickness arrays for use with the new Hydrogeologic Unit Flow package in MODFLOW 2000. This makes it possible to preserve complex heterogeneity while using reasonably sized grids and/or grids with nonuniform cell thicknesses.

Application of global kinetic models to HMX beta-delta transition and cookoff processes.

PubMed

Wemhoff, Aaron P; Burnham, Alan K; Nichols, Albert L

2007-03-08

The reduction of the number of reactions in kinetic models for both the HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) beta-delta phase transition and thermal cookoff provides an attractive alternative to traditional multi-stage kinetic models due to reduced calibration effort requirements. In this study, we use the LLNL code ALE3D to provide calibrated kinetic parameters for a two-reaction bidirectional beta-delta HMX phase transition model based on Sandia instrumented thermal ignition (SITI) and scaled thermal explosion (STEX) temperature history curves, and a Prout-Tompkins cookoff model based on one-dimensional time to explosion (ODTX) data. Results show that the two-reaction bidirectional beta-delta transition model presented here agrees as well with STEX and SITI temperature history curves as a reversible four-reaction Arrhenius model yet requires an order of magnitude less computational effort. In addition, a single-reaction Prout-Tompkins model calibrated to ODTX data provides better agreement with ODTX data than a traditional multistep Arrhenius model and can contain up to 90% fewer chemistry-limited time steps for low-temperature ODTX simulations. Manual calibration methods for the Prout-Tompkins kinetics provide much better agreement with ODTX experimental data than parameters derived from differential scanning calorimetry (DSC) measurements at atmospheric pressure. The predicted surface temperature at explosion for STEX cookoff simulations is a weak function of the cookoff model used, and a reduction of up to 15% of chemistry-limited time steps can be achieved by neglecting the beta-delta transition for this type of simulation. Finally, the inclusion of the beta-delta transition model in the overall kinetics model can affect the predicted time to explosion by 1% for the traditional multistep Arrhenius approach, and up to 11% using a Prout-Tompkins cookoff model.

Implementation of a roughness element to trip transition in large-eddy simulation

NASA Astrophysics Data System (ADS)

Boudet, J.; Monier, J.-F.; Gao, F.

2015-02-01

In aerodynamics, the laminar or turbulent regime of a boundary layer has a strong influence on friction or heat transfer. In practical applications, it is sometimes necessary to trip the transition to turbulent, and a common way is by use of a roughness element ( e.g. a step) on the wall. The present paper is concerned with the numerical implementation of such a trip in large-eddy simulations. The study is carried out on a flat-plate boundary layer configuration, with Reynolds number Rex=1.3×106. First, this work brings the opportunity to introduce a practical methodology to assess convergence in large-eddy simulations. Second, concerning the trip implementation, a volume source term is proposed and is shown to yield a smoother and faster transition than a grid step. Moreover, it is easier to implement and more adaptable. Finally, two subgrid-scale models are tested: the WALE model of Nicoud and Ducros ( Flow Turbul. Combust., vol. 62, 1999) and the shear-improved Smagorinsky model of Lévêque et al. ( J. Fluid Mech., vol. 570, 2007). Both models allow transition, but the former appears to yield a faster transition and a better prediction of friction in the turbulent regime.

Effects of Pump-turbine S-shaped Characteristics on Transient Behaviours: Model Setup

NASA Astrophysics Data System (ADS)

Zeng, Wei; Yang, Jiandong; Hu, Jinhong

2017-04-01

Pumped storage stations undergo numerous transition processes, which make the pump turbines go through the unstable S-shaped region. The hydraulic transient in S-shaped region has normally been investigated through numerical simulations, while field experiments generally involve high risks and are difficult to perform. In this research, a pumped storage model composed of a piping system, two model units, two electrical control systems, a measurement system and a collection system was set up to study the transition processes. The model platform can be applied to simulate almost any hydraulic transition process that occurs in real power stations, such as load rejection, startup, frequency control and grid connection.

Stable lattice Boltzmann model for Maxwell equations in media

NASA Astrophysics Data System (ADS)

Hauser, A.; Verhey, J. L.

2017-12-01

The present work shows a method for stable simulations via the lattice Boltzmann (LB) model for electromagnetic waves (EM) transiting homogeneous media. LB models for such media were already presented in the literature, but they suffer from numerical instability when the media transitions are sharp. We use one of these models in the limit of pure vacuum derived from Liu and Yan [Appl. Math. Model. 38, 1710 (2014), 10.1016/j.apm.2013.09.009] and apply an extension that treats the effects of polarization and magnetization separately. We show simulations of simple examples in which EM waves travel into media to quantify error scaling, stability, accuracy, and time scaling. For conductive media, we use the Strang splitting and check the simulations accuracy at the example of the skin effect. Like pure EM propagation, the error for the static limits, which are constructed with a current density added in a first-order scheme, can be less than 1 % . The presented method is an easily implemented alternative for the stabilization of simulation for EM waves propagating in spatially complex structured media properties and arbitrary transitions.

Chapter 3: Simulating fire hazard across landscapes through time: integrating state-and-transition models with the Fuel Characteristic Classification System

Treesearch

Jessica E. Halofsky; Stephanie K. Hart; Miles A. Hemstrom; Joshua S. Halofsky; Morris C. Johnson

2014-01-01

Information on the effects of management activities such as fuel reduction treatments and of processes such as vegetation growth and disturbance on fire hazard can help land managers prioritize treatments across a landscape to best meet management goals. State-and-transition models (STMs) allow landscape-scale simulations that incorporate effects of succession,...

Statistical Analysis of Notational AFL Data Using Continuous Time Markov Chains

PubMed Central

Meyer, Denny; Forbes, Don; Clarke, Stephen R.

2006-01-01

Animal biologists commonly use continuous time Markov chain models to describe patterns of animal behaviour. In this paper we consider the use of these models for describing AFL football. In particular we test the assumptions for continuous time Markov chain models (CTMCs), with time, distance and speed values associated with each transition. Using a simple event categorisation it is found that a semi-Markov chain model is appropriate for this data. This validates the use of Markov Chains for future studies in which the outcomes of AFL matches are simulated. Key Points A comparison of four AFL matches suggests similarity in terms of transition probabilities for events and the mean times, distances and speeds associated with each transition. The Markov assumption appears to be valid. However, the speed, time and distance distributions associated with each transition are not exponential suggesting that semi-Markov model can be used to model and simulate play. Team identified events and directions associated with transitions are required to develop the model into a tool for the prediction of match outcomes. PMID:24357946

Statistical Analysis of Notational AFL Data Using Continuous Time Markov Chains.

PubMed

Meyer, Denny; Forbes, Don; Clarke, Stephen R

2006-01-01

Animal biologists commonly use continuous time Markov chain models to describe patterns of animal behaviour. In this paper we consider the use of these models for describing AFL football. In particular we test the assumptions for continuous time Markov chain models (CTMCs), with time, distance and speed values associated with each transition. Using a simple event categorisation it is found that a semi-Markov chain model is appropriate for this data. This validates the use of Markov Chains for future studies in which the outcomes of AFL matches are simulated. Key PointsA comparison of four AFL matches suggests similarity in terms of transition probabilities for events and the mean times, distances and speeds associated with each transition.The Markov assumption appears to be valid.However, the speed, time and distance distributions associated with each transition are not exponential suggesting that semi-Markov model can be used to model and simulate play.Team identified events and directions associated with transitions are required to develop the model into a tool for the prediction of match outcomes.

The behavior of commensurate-incommensurate transitions using the phase field crystal model

NASA Astrophysics Data System (ADS)

Zhang, Tinghui; Lu, Yanli; Chen, Zheng

2018-02-01

We study the behavior of the commensurate-incommensurate (CI) transitions by using a phase field crystal model. The model is capable of modeling both elastic and plastic deformation and can simulate the evolution of the microstructure of the material at the atomic scale and the diffusive time scale, such as for adsorbed monolayer. Specifically, we study the behavior of the CI transitions as a function of lattice mismatch and the amplitude of substrate pinning potential. The behavior of CI phase transitions is revealed with the increase of the amplitude of pinning potential in some certain lattice mismatches. We find that for the negative lattice mismatch absorbed monolayer undergoes division, reorganization and displacement as increasing the amplitude of substrate pinning potential. In addition, for the positive mismatch absorbed monolayer undergoes a progress of phase transformation after a complete grain is split. Our results accord with simulations for atomic models of absorbed monolayer on a substrate surface.

Modeling boundary-layer transition in direct and large-eddy simulations using parabolized stability equations

NASA Astrophysics Data System (ADS)

Lozano-Durán, A.; Hack, M. J. P.; Moin, P.

2018-02-01

We examine the potential of the nonlinear parabolized stability equations (PSE) to provide an accurate yet computationally efficient treatment of the growth of disturbances in H-type transition to turbulence. The PSE capture the nonlinear interactions that eventually induce breakdown to turbulence and can as such identify the onset of transition without relying on empirical correlations. Since the local PSE solution at the onset of transition is a close approximation of the Navier-Stokes equations, it provides a natural inflow condition for direct numerical simulations (DNS) and large-eddy simulations (LES) by avoiding nonphysical transients. We show that a combined PSE-DNS approach, where the pretransitional region is modeled by the PSE, can reproduce the skin-friction distribution and downstream turbulent statistics from a DNS of the full domain. When the PSE are used in conjunction with wall-resolved and wall-modeled LES, the computational cost in both the laminar and turbulent regions is reduced by several orders of magnitude compared to DNS.

Decadal shifts of East Asian summer monsoon in a climate model free of explicit GHGs and aerosols

NASA Astrophysics Data System (ADS)

Lin, Renping; Zhu, Jiang; Zheng, Fei

2016-12-01

The East Asian summer monsoon (EASM) experienced decadal transitions over the past few decades, and the associated "wetter-South-drier-North" shifts in rainfall patterns in China significantly affected the social and economic development in China. Two viewpoints stand out to explain these decadal shifts, regarding the shifts either a result of internal variability of climate system or that of external forcings (e.g. greenhouse gases (GHGs) and anthropogenic aerosols). However, most climate models, for example, the Atmospheric Model Intercomparison Project (AMIP)-type simulations and the Coupled Model Intercomparison Project (CMIP)-type simulations, fail to simulate the variation patterns, leaving the mechanisms responsible for these shifts still open to dispute. In this study, we conducted a successful simulation of these decadal transitions in a coupled model where we applied ocean data assimilation in the model free of explicit aerosols and GHGs forcing. The associated decadal shifts of the three-dimensional spatial structure in the 1990s, including the eastward retreat, the northward shift of the western Pacific subtropical high (WPSH), and the south-cool-north-warm pattern of the upper-level tropospheric temperature, were all well captured. Our simulation supports the argument that the variations of the oceanic fields are the dominant factor responsible for the EASM decadal transitions.

Decadal shifts of East Asian summer monsoon in a climate model free of explicit GHGs and aerosols

PubMed Central

Lin, Renping; Zhu, Jiang; Zheng, Fei

2016-01-01

The East Asian summer monsoon (EASM) experienced decadal transitions over the past few decades, and the associated "wetter-South-drier-North" shifts in rainfall patterns in China significantly affected the social and economic development in China. Two viewpoints stand out to explain these decadal shifts, regarding the shifts either a result of internal variability of climate system or that of external forcings (e.g. greenhouse gases (GHGs) and anthropogenic aerosols). However, most climate models, for example, the Atmospheric Model Intercomparison Project (AMIP)-type simulations and the Coupled Model Intercomparison Project (CMIP)-type simulations, fail to simulate the variation patterns, leaving the mechanisms responsible for these shifts still open to dispute. In this study, we conducted a successful simulation of these decadal transitions in a coupled model where we applied ocean data assimilation in the model free of explicit aerosols and GHGs forcing. The associated decadal shifts of the three-dimensional spatial structure in the 1990s, including the eastward retreat, the northward shift of the western Pacific subtropical high (WPSH), and the south-cool-north-warm pattern of the upper-level tropospheric temperature, were all well captured. Our simulation supports the argument that the variations of the oceanic fields are the dominant factor responsible for the EASM decadal transitions. PMID:27934933

Methods used to parameterize the spatially-explicit components of a state-and-transition simulation model

USGS Publications Warehouse

Sleeter, Rachel; Acevedo, William; Soulard, Christopher E.; Sleeter, Benjamin M.

2015-01-01

Spatially-explicit state-and-transition simulation models of land use and land cover (LULC) increase our ability to assess regional landscape characteristics and associated carbon dynamics across multiple scenarios. By characterizing appropriate spatial attributes such as forest age and land-use distribution, a state-and-transition model can more effectively simulate the pattern and spread of LULC changes. This manuscript describes the methods and input parameters of the Land Use and Carbon Scenario Simulator (LUCAS), a customized state-and-transition simulation model utilized to assess the relative impacts of LULC on carbon stocks for the conterminous U.S. The methods and input parameters are spatially explicit and describe initial conditions (strata, state classes and forest age), spatial multipliers, and carbon stock density. Initial conditions were derived from harmonization of multi-temporal data characterizing changes in land use as well as land cover. Harmonization combines numerous national-level datasets through a cell-based data fusion process to generate maps of primary LULC categories. Forest age was parameterized using data from the North American Carbon Program and spatially-explicit maps showing the locations of past disturbances (i.e. wildfire and harvest). Spatial multipliers were developed to spatially constrain the location of future LULC transitions. Based on distance-decay theory, maps were generated to guide the placement of changes related to forest harvest, agricultural intensification/extensification, and urbanization. We analyze the spatially-explicit input parameters with a sensitivity analysis, by showing how LUCAS responds to variations in the model input. This manuscript uses Mediterranean California as a regional subset to highlight local to regional aspects of land change, which demonstrates the utility of LUCAS at many scales and applications.

Aerodynamics Model for a Generic ASTOVL Lift-Fan Aircraft

DOT National Transportation Integrated Search

1995-04-01

This report describes the aerodynamics model used in a simulation model of : an advanced short takeoff and vertical landing lift-far fighter aircraft. The : simulation model was developed for use in piloted evaluations of transition and : hover fligh...

A dynamic population model to investigate effects of climate and climate-independent factors on the lifecycle of the tick Amblyomma americanum (Acari: Ixodidae)

USGS Publications Warehouse

Ludwig, Antoinette; Ginsberg, Howard; Hickling, Graham J.; Ogden, Nicholas H.

2016-01-01

The lone star tick, Amblyomma americanum, is a disease vector of significance for human and animal health throughout much of the eastern United States. To model the potential effects of climate change on this tick, a better understanding is needed of the relative roles of temperature-dependent and temperature-independent (day-length-dependent behavioral or morphogenetic diapause) processes acting on the tick lifecycle. In this study, we explored the roles of these processes by simulating seasonal activity patterns using models with site-specific temperature and day-length-dependent processes. We first modeled the transitions from engorged larvae to feeding nymphs, engorged nymphs to feeding adults, and engorged adult females to feeding larvae. The simulated seasonal patterns were compared against field observations at three locations in United States. Simulations suggested that 1) during the larva-to-nymph transition, some larvae undergo no diapause while others undergo morphogenetic diapause of engorged larvae; 2) molted adults undergo behavioral diapause during the transition from nymph-to-adult; and 3) there is no diapause during the adult-to-larva transition. A model constructed to simulate the full lifecycle of A. americanum successfully predicted observed tick activity at the three U.S. study locations. Some differences between observed and simulated seasonality patterns were observed, however, identifying the need for research to refine some model parameters. In simulations run using temperature data for Montreal, deterministic die-out of A. americanum populations did not occur, suggesting the possibility that current climate in parts of southern Canada is suitable for survival and reproduction of this tick.

A Dynamic Population Model to Investigate Effects of Climate and Climate-Independent Factors on the Lifecycle of Amblyomma americanum (Acari: Ixodidae).

PubMed

Ludwig, Antoinette; Ginsberg, Howard S; Hickling, Graham J; Ogden, Nicholas H

2016-01-01

The lone star tick, Amblyomma americanum, is a disease vector of significance for human and animal health throughout much of the eastern United States. To model the potential effects of climate change on this tick, a better understanding is needed of the relative roles of temperature-dependent and temperature-independent (day-length-dependent behavioral or morphogenetic diapause) processes acting on the tick lifecycle. In this study, we explored the roles of these processes by simulating seasonal activity patterns using models with site-specific temperature and day-length-dependent processes. We first modeled the transitions from engorged larvae to feeding nymphs, engorged nymphs to feeding adults, and engorged adult females to feeding larvae. The simulated seasonal patterns were compared against field observations at three locations in United States. Simulations suggested that 1) during the larva-to-nymph transition, some larvae undergo no diapause while others undergo morphogenetic diapause of engorged larvae; 2) molted adults undergo behavioral diapause during the transition from nymph-to-adult; and 3) there is no diapause during the adult-to-larva transition. A model constructed to simulate the full lifecycle of A. americanum successfully predicted observed tick activity at the three U.S. study locations. Some differences between observed and simulated seasonality patterns were observed, however, identifying the need for research to refine some model parameters. In simulations run using temperature data for Montreal, deterministic die-out of A. americanum populations did not occur, suggesting the possibility that current climate in parts of southern Canada is suitable for survival and reproduction of this tick. © Crown copyright 2015.

Simulating Society Transitions: Standstill, Collapse and Growth in an Evolving Network Model

PubMed Central

Xu, Guanghua; Yang, Junjie; Li, Guoqing

2013-01-01

We developed a model society composed of various occupations that interact with each other and the environment, with the capability of simulating three widely recognized societal transition patterns: standstill, collapse and growth, which are important compositions of society evolving dynamics. Each occupation is equipped with a number of inhabitants that may randomly flow to other occupations, during which process new occupations may be created and then interact with existing ones. Total population of society is associated with productivity, which is determined by the structure and volume of the society. We ran the model under scenarios such as parasitism, environment fluctuation and invasion, which correspond to different driving forces of societal transition, and obtained reasonable simulation results. This work adds to our understanding of societal evolving dynamics as well as provides theoretical clues to sustainable development. PMID:24086530

Bifurcation analysis and dimension reduction of a predator-prey model for the L-H transition

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

Dam, Magnus; Brøns, Morten; Juul Rasmussen, Jens

2013-10-15

The L-H transition denotes a shift to an improved confinement state of a toroidal plasma in a fusion reactor. A model of the L-H transition is required to simulate the time dependence of tokamak discharges that include the L-H transition. A 3-ODE predator-prey type model of the L-H transition is investigated with bifurcation theory of dynamical systems. The analysis shows that the model contains three types of transitions: an oscillating transition, a sharp transition with hysteresis, and a smooth transition. The model is recognized as a slow-fast system. A reduced 2-ODE model consisting of the full model restricted to themore » flow on the critical manifold is found to contain all the same dynamics as the full model. This means that all the dynamics in the system is essentially 2-dimensional, and a minimal model of the L-H transition could be a 2-ODE model.« less

Nonequilibrium Phase Transition in a Model for Social Influence

NASA Astrophysics Data System (ADS)

Castellano, Claudio; Marsili, Matteo; Vespignani, Alessandro

2000-10-01

We present extensive numerical simulations of the Axelrod's model for social influence, aimed at understanding the formation of cultural domains. This is a nonequilibrium model with short range interactions and a remarkably rich dynamical behavior. We study the phase diagram of the model and uncover a nonequilibrium phase transition separating an ordered (culturally polarized) phase from a disordered (culturally fragmented) one. The nature of the phase transition can be continuous or discontinuous depending on the model parameters. At the transition, the size of cultural regions is power-law distributed.

Velocity mode transition of dynamic crack propagation in hyperviscoelastic materials: A continuum model study.

PubMed

Kubo, Atsushi; Umeno, Yoshitaka

2017-02-10

Experiments of crack propagation in rubbers have shown that a discontinuous jump of crack propagation velocity can occur as energy release rate increases, which is known as the "mode transition" phenomenon. Although it is believed that the mode transition is strongly related to the mechanical properties, the nature of the mode transition had not been revealed. In this study, dynamic crack propagation on an elastomer was investigated using the finite element method (FEM) with a hyperviscoelastic material model. A series of pure shear test was carried out numerically with FEM simulations and crack velocities were measured under various values of tensile strain. As a result, our FEM simulations successfully reproduced the mode transition. The success of realising the mode transition phenomenon by a simple FEM model, which was achieved for the first time ever, helped to explain that the phenomenon occurs owing to a characteristic non-monotonic temporal development of principal stress near the crack tip.

Simulation of transonic flows through a turbine blade cascade with various prescription of outlet boundary conditions

NASA Astrophysics Data System (ADS)

Louda, Petr; Straka, Petr; Příhoda, Jaromír

2018-06-01

The contribution deals with the numerical simulation of transonic flows through a linear turbine blade cascade. Numerical simulations were carried partly for the standard computational domain with various outlet boundary conditions by the algebraic transition model of Straka and Příhoda [1] connected with the EARSM turbulence model of Hellsten [2] and partly for the computational domain corresponding to the geometrical arrangement in the wind tunnel by the γ-ζ transition model of Dick et al. [3] with the SST turbulence model. Numerical results were compared with experimental data. The agreement of numerical results with experimental results is acceptable through a complicated experimental configuration.

A Framework for Simulating Turbine-Based Combined-Cycle Inlet Mode-Transition

NASA Technical Reports Server (NTRS)

Le, Dzu K.; Vrnak, Daniel R.; Slater, John W.; Hessel, Emil O.

2012-01-01

A simulation framework based on the Memory-Mapped-Files technique was created to operate multiple numerical processes in locked time-steps and send I/O data synchronously across to one-another to simulate system-dynamics. This simulation scheme is currently used to study the complex interactions between inlet flow-dynamics, variable-geometry actuation mechanisms, and flow-controls in the transition from the supersonic to hypersonic conditions and vice-versa. A study of Mode-Transition Control for a high-speed inlet wind-tunnel model with this MMF-based framework is presented to illustrate this scheme and demonstrate its usefulness in simulating supersonic and hypersonic inlet dynamics and controls or other types of complex systems.

State-and-transition models: Conceptual versus simulation perspectives, usefulness and breadth of use, and land management applications

USGS Publications Warehouse

Provencher, Louis; Frid, Leonardo; Czembor, Christina; Morisette, Jeffrey T.

2016-01-01

State-and-Transition Simulation Modeling (STSM) is a quantitative analysis method that can consolidate a wide array of resource management issues under a “what-if” scenario exercise. STSM can be seen as an ensemble of models, such as climate models, ecological models, and economic models that incorporate human dimensions and management options. This chapter presents STSM as a tool to help synthesize information on social–ecological systems and to investigate some of the management issues associated with exotic annual Bromus species, which have been described elsewhere in this book. Definitions, terminology, and perspectives on conceptual and computer-simulated stochastic state-and-transition models are given first, followed by a brief review of past STSM studies relevant to the management of Bromus species. A detailed case study illustrates the usefulness of STSM for land management. As a whole, this chapter is intended to demonstrate how STSM can help both managers and scientists: (a) determine efficient resource allocation for monitoring nonnative grasses; (b) evaluate sources of uncertainty in model simulation results involving expert opinion, and their consequences for management decisions; and (c) provide insight into the consequences of predicted local climate change effects on ecological systems invaded by exotic annual Bromus species.

Semiempirical models of H-mode discharges

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

Singer, C.E.; Redi, M.; Boyd, D.

1985-05-01

The H-mode transition can lead to a rapid increase in tokamak plasma confinement. A semiempirical transport model was derived from global OH and L-mode confinement scalings and then applied to simulation of H-mode discharges. The radial diffusivities in the model also depend on local density and pressure gradients and satisfy an appropriate dimensional constraint. Examples are shown of the application of this and similar models to the detailed simulation of two discharges which exhibit an H-mode transition. The models reproduce essential features of plasma confinement in the ohmic heating, low and high confinement phases of these discharges. In particular, themore » evolution of plasma energy content through the H-mode transition can be reproduced without any sudden or ad hoc modification of the plasma transport formulation.« less

Statistic inversion of multi-zone transition probability models for aquifer characterization in alluvial fans

DOE PAGES

Zhu, Lin; Dai, Zhenxue; Gong, Huili; ...

2015-06-12

Understanding the heterogeneity arising from the complex architecture of sedimentary sequences in alluvial fans is challenging. This study develops a statistical inverse framework in a multi-zone transition probability approach for characterizing the heterogeneity in alluvial fans. An analytical solution of the transition probability matrix is used to define the statistical relationships among different hydrofacies and their mean lengths, integral scales, and volumetric proportions. A statistical inversion is conducted to identify the multi-zone transition probability models and estimate the optimal statistical parameters using the modified Gauss–Newton–Levenberg–Marquardt method. The Jacobian matrix is computed by the sensitivity equation method, which results in anmore » accurate inverse solution with quantification of parameter uncertainty. We use the Chaobai River alluvial fan in the Beijing Plain, China, as an example for elucidating the methodology of alluvial fan characterization. The alluvial fan is divided into three sediment zones. In each zone, the explicit mathematical formulations of the transition probability models are constructed with optimized different integral scales and volumetric proportions. The hydrofacies distributions in the three zones are simulated sequentially by the multi-zone transition probability-based indicator simulations. Finally, the result of this study provides the heterogeneous structure of the alluvial fan for further study of flow and transport simulations.« less

Probing the free energy landscape of the FBP28WW domain using multiple techniques.

PubMed

Periole, Xavier; Allen, Lucy R; Tamiola, Kamil; Mark, Alan E; Paci, Emanuele

2009-05-01

The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent. Sampling of conformation space was performed using both conventional and temperature-replica exchange MD simulations. Experimental chemical shifts and NOEs were used to validate the simulations, and experimental phi values both for validation and as restraints. This combination of different approaches has provided insight into the free energy landscape and barriers encountered by the protein during folding and enabled the characterization of native, denatured and transition states which are compatible with the available experimental data. All the molecular models used stabilize well defined native and denatured basins; however, the degree of agreement with the available experimental data varies. While the most detailed, explicit solvent model predicts the data reasonably accurately, it does not fold despite a simulation time 10 times that of the experimental folding time. The less detailed models performed poorly relative to the explicit solvent model: an implicit solvent model stabilizes a ground state which differs from the experimental native state, and a structure-based model underestimates the size of the barrier between the two states. The use of experimental phi values both as restraints, and to extract structures from unfolding simulations, result in conformations which, although not necessarily true transition states, appear to share the geometrical characteristics of transition state structures. In addition to characterizing the native, transition and denatured states of this particular system in this work, the advantages and limitations of using varying levels of representation are discussed. 2008 Wiley Periodicals, Inc.

Piloted Evaluation of an Integrated Methodology for Propulsion and Airframe Control Design

NASA Technical Reports Server (NTRS)

Bright, Michelle M.; Simon, Donald L.; Garg, Sanjay; Mattern, Duane L.; Ranaudo, Richard J.; Odonoghue, Dennis P.

1994-01-01

An integrated methodology for propulsion and airframe control has been developed and evaluated for a Short Take-Off Vertical Landing (STOVL) aircraft using a fixed base flight simulator at NASA Lewis Research Center. For this evaluation the flight simulator is configured for transition flight using a STOVL aircraft model, a full nonlinear turbofan engine model, simulated cockpit and displays, and pilot effectors. The paper provides a brief description of the simulation models, the flight simulation environment, the displays and symbology, the integrated control design, and the piloted tasks used for control design evaluation. In the simulation, the pilots successfully completed typical transition phase tasks such as combined constant deceleration with flight path tracking, and constant acceleration wave-off maneuvers. The pilot comments of the integrated system performance and the display symbology are discussed and analyzed to identify potential areas of improvement.

A Spalart-Allmaras local correlation-based transition model for Thermo-fuid dynamics

NASA Astrophysics Data System (ADS)

D'Alessandro, V.; Garbuglia, F.; Montelpare, S.; Zoppi, A.

2017-11-01

The study of innovative energy systems often involves complex fluid flows problems and the Computational Fluid-Dynamics (CFD) is one of the main tools of analysis. It is important to put in evidence that in several energy systems the flow field experiences the laminar-to-turbulent transition. Direct Numerical Simulations (DNS) or Large Eddy Simulation (LES) are able to predict the flow transition but they are still inapplicable to the study of real problems due to the significant computational resources requirements. Differently standard Reynolds Averaged Navier Stokes (RANS) approaches are not always reliable since they assume a fully turbulent regime. In order to overcome this drawback in the recent years some locally formulated transition RANS models have been developed. In this work, we present a local correlation-based transition approach adding two equations that control the laminar-toturbulent transition process -γ and \\[\\overset{}{\\mathop{{{\\operatorname{Re}}θ, \\text{t}}}} \\] - to the well-known Spalart-Allmaras (SA) turbulence model. The new model was implemented within OpenFOAM code. The energy equation is also implemented in order to evaluate the model performance in thermal-fluid dynamics applications. In all the considered cases a very good agreement between numerical and experimental data was observed.

V/STOL propulsion control analysis: Phase 2, task 5-9

NASA Technical Reports Server (NTRS)

1981-01-01

Typical V/STOL propulsion control requirements were derived for transition between vertical and horizontal flight using the General Electric RALS (Remote Augmented Lift System) concept. Steady-state operating requirements were defined for a typical Vertical-to-Horizontal transition and for a typical Horizontal-to-Vertical transition. Control mode requirements were established and multi-variable regulators developed for individual operating conditions. Proportional/Integral gain schedules were developed and were incorporated into a transition controller with capabilities for mode switching and manipulated variable reassignment. A non-linear component-level transient model of the engine was developed and utilized to provide a preliminary check-out of the controller logic. An inlet and nozzle effects model was developed for subsequent incorporation into the engine model and an aircraft model was developed for preliminary flight transition simulations. A condition monitoring development plan was developed and preliminary design requirements established. The Phase 1 long-range technology plan was refined and restructured toward the development of a real-time high fidelity transient model of a supersonic V/STOL propulsion system and controller for use in a piloted simulation program at NASA-Ames.

One-Dimensional Collision Carts Computer Model and Its Design Ideas for Productive Experiential Learning

ERIC Educational Resources Information Center

Wee, Loo Kang

2012-01-01

We develop an Easy Java Simulation (EJS) model for students to experience the physics of idealized one-dimensional collision carts. The physics model is described and simulated by both continuous dynamics and discrete transition during collision. In designing the simulations, we discuss briefly three pedagogical considerations namely (1) a…

Modeling crystal growth from solution with molecular dynamics simulations: approaches to transition rate constants.

PubMed

Reilly, Anthony M; Briesen, Heiko

2012-01-21

The feasibility of using the molecular dynamics (MD) simulation technique to study crystal growth from solution quantitatively, as well as to obtain transition rate constants, has been studied. The dynamics of an interface between a solution of Lennard-Jones particles and the (100) face of an fcc lattice comprised of solute particles have been studied using MD simulations, showing that MD is, in principle, capable of following growth behavior over large supersaturation and temperature ranges. Using transition state theory, and a nearest-neighbor approximation growth and dissolution rate constants have been extracted from equilibrium MD simulations at a variety of temperatures. The temperature dependence of the rates agrees well with the expected transition state theory behavior. © 2012 American Institute of Physics

Extinction phase transitions in a model of ecological and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Barghathi, Hatem; Tackkett, Skye; Vojta, Thomas

2017-07-01

We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental conditions, i.e., temporal disorder. Using large-scale Monte-Carlo simulations of up to 3 × 107 organisms and 105 generations, we find the extinction transition in time-independent environments to be in the well-known directed percolation universality class. In contrast, temporal disorder leads to a highly unusual extinction transition characterized by logarithmically slow population decay and enormous fluctuations even for large populations. The simulations provide strong evidence for this transition to be of exotic infinite-noise type, as recently predicted by a renormalization group theory. The transition is accompanied by temporal Griffiths phases featuring a power-law dependence of the life time on the population size.

Extending the Operational Envelope of a Turbofan Engine Simulation into the Sub-Idle Region

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Hamley, Andrew J.; Guo, Ten-Huei; Litt, Jonathan S.

2016-01-01

In many non-linear gas turbine simulations, operation in the sub-idle region can lead to model instability. This paper lays out a method for extending the operational envelope of a map based gas turbine simulation to include the sub-idle region. This method develops a multi-simulation solution where the baseline component maps are extrapolated below the idle level and an alternate model is developed to serve as a safety net when the baseline model becomes unstable or unreliable. Sub-idle model development takes place in two distinct operational areas, windmilling/shutdown and purge/cranking/ startup. These models are based on derived steady state operating points with transient values extrapolated between initial (known) and final (assumed) states. Model transitioning logic is developed to predict baseline model sub-idle instability, and transition smoothly and stably to the backup sub-idle model. Results from the simulation show a realistic approximation of sub-idle behavior as compared to generic sub-idle engine performance that allows the engine to operate continuously and stably from shutdown to full power.

Extending the Operational Envelope of a Turbofan Engine Simulation into the Sub-Idle Region

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes Walter; Hamley, Andrew J.; Guo, Ten-Huei; Litt, Jonathan S.

2016-01-01

In many non-linear gas turbine simulations, operation in the sub-idle region can lead to model instability. This paper lays out a method for extending the operational envelope of a map based gas turbine simulation to include the sub-idle region. This method develops a multi-simulation solution where the baseline component maps are extrapolated below the idle level and an alternate model is developed to serve as a safety net when the baseline model becomes unstable or unreliable. Sub-idle model development takes place in two distinct operational areas, windmilling/shutdown and purge/cranking/startup. These models are based on derived steady state operating points with transient values extrapolated between initial (known) and final (assumed) states. Model transitioning logic is developed to predict baseline model sub-idle instability, and transition smoothly and stably to the backup sub-idle model. Results from the simulation show a realistic approximation of sub-idle behavior as compared to generic sub-idle engine performance that allows the engine to operate continuously and stably from shutdown to full power.

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

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

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much lessmore » computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.« less

Validating clustering of molecular dynamics simulations using polymer models.

PubMed

Phillips, Joshua L; Colvin, Michael E; Newsam, Shawn

2011-11-14

Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers.

Validating clustering of molecular dynamics simulations using polymer models

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers. PMID:22082218

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

Wemhoff, A P; Burnham, A K; Nichols III, A L

The reduction of the number of reactions in kinetic models for both the HMX beta-delta phase transition and thermal cookoff provides an attractive alternative to traditional multi-stage kinetic models due to reduced calibration effort requirements. In this study, we use the LLNL code ALE3D to provide calibrated kinetic parameters for a two-reaction bidirectional beta-delta HMX phase transition model based on Sandia Instrumented Thermal Ignition (SITI) and Scaled Thermal Explosion (STEX) temperature history curves, and a Prout-Tompkins cookoff model based on One-Dimensional Time to Explosion (ODTX) data. Results show that the two-reaction bidirectional beta-delta transition model presented here agrees as wellmore » with STEX and SITI temperature history curves as a reversible four-reaction Arrhenius model, yet requires an order of magnitude less computational effort. In addition, a single-reaction Prout-Tompkins model calibrated to ODTX data provides better agreement with ODTX data than a traditional multi-step Arrhenius model, and can contain up to 90% less chemistry-limited time steps for low-temperature ODTX simulations. Manual calibration methods for the Prout-Tompkins kinetics provide much better agreement with ODTX experimental data than parameters derived from Differential Scanning Calorimetry (DSC) measurements at atmospheric pressure. The predicted surface temperature at explosion for STEX cookoff simulations is a weak function of the cookoff model used, and a reduction of up to 15% of chemistry-limited time steps can be achieved by neglecting the beta-delta transition for this type of simulation. Finally, the inclusion of the beta-delta transition model in the overall kinetics model can affect the predicted time to explosion by 1% for the traditional multi-step Arrhenius approach, while up to 11% using a Prout-Tompkins cookoff model.« less

Extension of the quantum-kinetic model to lunar and Mars return physics

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

Liechty, D. S.; Lewis, M. J.

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high-mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. A recently introduced molecular-level chemistry model, the quantum-kinetic, or Q-K, model that predicts reaction rates for gases in thermal equilibrium and non-equilibrium using only kinetic theory and fundamental molecular properties, is extended in the current work to include electronic energy level transitions and reactions involving charged particles. Like the Q-K procedures for neutral species chemical reactions, these new models are phenomenological procedures that aimmore » to reproduce the reaction/transition rates but do not necessarily capture the exact physics. These engineering models are necessarily efficient due to the requirement to compute billions of simulated collisions in direct simulation Monte Carlo (DSMC) simulations. The new models are shown to generally agree within the spread of reported transition and reaction rates from the literature for near equilibrium conditions.« less

The democracy ochlocracy dictatorship transition in the Sznajd model and in the Ising model

NASA Astrophysics Data System (ADS)

Schneider, Johannes J.; Hirtreiter, Christian

2005-08-01

Since its introduction in 2000, the Sznajd model has been assumed to simulate a democratic community with two parties. The main flaw in this model is that a Sznajd system freezes in the long term in a non-democratic state, which can be either a dictatorship or a stalemate configuration. Here we show that the Sznajd model has better to be considered as a transition model, transferring a democratic system already at the beginning of a simulation via an ochlocratic scenario, i.e., a regime in which several mobs rule, to a dictatorship, thus reproducing the corresponding Aristotelian theory.

The use of transition region characteristics to improve the numerical simulation of heat transfer in bypass transitional flows

NASA Technical Reports Server (NTRS)

Simon, Frederick F.

1993-01-01

A method is presented for improving the numerical prediction of bypass transition heat transfer on a flat plate in a high-disturbance environment with zero or favorable pressure gradient. The method utilizes low Reynolds number k-epsilon turbulence models in combination with the characteristic parameters of the transition region. The parameters representing the characteristics of the transition region used are the intermittency, transition length and turbulent spot properties. An analysis is made of the transition length in terms of turbulent spot variables. The nondimensional spot formation rate, required for the prediction of the transition length, is shown by the analysis to be a function of the spot spreading angle, the dimensionless spot velocity ratio and the dimensionless spot area ratio. The intermittency form of the k-epsilon equations were derived from conditionally averaged equations which have been shown to be an improvement over global-time-averaged equations for the numerical calculation of the transition region. The numerical predictions are in general good agreement with the experimental data and indicate the potential use of the method in accelerating flows. Turbulence models of the k-epsilon type are known to underpredict the transition length. The present work demonstrates how incorporating transition region characteristics improves the ability of two-equation turbulence models to simulate bypass transition for flat plates with potential application to turbine vanes and blades.

CAFE simulation of columnar-to-equiaxed transition in Al-7wt%Si alloys directionally solidified under microgravity

NASA Astrophysics Data System (ADS)

Liu, D. R.; Mangelinck-Noël, N.; Gandin, Ch-A.; Zimmermann, G.; Sturz, L.; Nguyen Thi, H.; Billia, B.

2016-03-01

A two-dimensional multi-scale cellular automaton - finite element (CAFE) model is used to simulate grain structure evolution and microsegregation formation during solidification of refined Al-7wt%Si alloys under microgravity. The CAFE simulations are first qualitatively compared with the benchmark experimental data under microgravity. Qualitative agreement is obtained for the position of columnar to equiaxed transition (CET) and the CET transition mode (sharp or progressive). Further comparisons of the distributions of grain elongation factor and equivalent diameter are conducted and reveal a fair quantitative agreement.

Velocity mode transition of dynamic crack propagation in hyperviscoelastic materials: A continuum model study

PubMed Central

Kubo, Atsushi; Umeno, Yoshitaka

2017-01-01

Experiments of crack propagation in rubbers have shown that a discontinuous jump of crack propagation velocity can occur as energy release rate increases, which is known as the “mode transition” phenomenon. Although it is believed that the mode transition is strongly related to the mechanical properties, the nature of the mode transition had not been revealed. In this study, dynamic crack propagation on an elastomer was investigated using the finite element method (FEM) with a hyperviscoelastic material model. A series of pure shear test was carried out numerically with FEM simulations and crack velocities were measured under various values of tensile strain. As a result, our FEM simulations successfully reproduced the mode transition. The success of realising the mode transition phenomenon by a simple FEM model, which was achieved for the first time ever, helped to explain that the phenomenon occurs owing to a characteristic non-monotonic temporal development of principal stress near the crack tip. PMID:28186205

Velocity mode transition of dynamic crack propagation in hyperviscoelastic materials: A continuum model study

NASA Astrophysics Data System (ADS)

Kubo, Atsushi; Umeno, Yoshitaka

2017-02-01

Experiments of crack propagation in rubbers have shown that a discontinuous jump of crack propagation velocity can occur as energy release rate increases, which is known as the “mode transition” phenomenon. Although it is believed that the mode transition is strongly related to the mechanical properties, the nature of the mode transition had not been revealed. In this study, dynamic crack propagation on an elastomer was investigated using the finite element method (FEM) with a hyperviscoelastic material model. A series of pure shear test was carried out numerically with FEM simulations and crack velocities were measured under various values of tensile strain. As a result, our FEM simulations successfully reproduced the mode transition. The success of realising the mode transition phenomenon by a simple FEM model, which was achieved for the first time ever, helped to explain that the phenomenon occurs owing to a characteristic non-monotonic temporal development of principal stress near the crack tip.

Mode transition coordinated control for a compound power-split hybrid car

NASA Astrophysics Data System (ADS)

Wang, Chen; Zhao, Zhiguo; Zhang, Tong; Li, Mengna

2017-03-01

With a compound power-split transmission directly connected to the engine in hybrid cars, dramatic fluctuations in engine output torque result in noticeable jerks when the car is in mode transition from electric drive mode to hybrid drive mode. This study designed a mode transition coordinated control strategy, and verified that strategy's effectiveness with both simulations and experiments. Firstly, the mode transition process was analyzed, and ride comfort issues during the mode transition process were demonstrated. Secondly, engine ripple torque was modeled using the measured cylinder pumping pressure when the engine was not in operation. The complete dynamic plant model of the power-split hybrid car was deduced, and its effectiveness was validated by a comparison of experimental and simulation results. Thirdly, a coordinated control strategy was designed to determine the desired engine torque, motor torque, and the moment of fuel injection. Active damping control with two degrees of freedom, based on reference output shaft speed estimation, was designed to mitigate driveline speed oscillations. Carrier torque estimation based on transmission kinematics and dynamics was used to suppress torque disturbance during engine cranking. The simulation and experimental results indicate that the proposed strategy effectively suppressed vehicle jerks and improved ride comfort during mode transition.

Effective equilibrium picture in the x y model with exponentially correlated noise

NASA Astrophysics Data System (ADS)

Paoluzzi, Matteo; Marconi, Umberto Marini Bettolo; Maggi, Claudio

2018-02-01

We study the effect of exponentially correlated noise on the x y model in the limit of small correlation time, discussing the order-disorder transition in the mean field and the topological transition in two dimensions. We map the steady states of the nonequilibrium dynamics into an effective equilibrium theory. In the mean field, the critical temperature increases with the noise correlation time τ , indicating that memory effects promote ordering. This finding is confirmed by numerical simulations. The topological transition temperature in two dimensions remains untouched. However, finite-size effects induce a crossover in the vortices proliferation that is confirmed by numerical simulations.

Effective equilibrium picture in the xy model with exponentially correlated noise.

PubMed

Paoluzzi, Matteo; Marconi, Umberto Marini Bettolo; Maggi, Claudio

2018-02-01

We study the effect of exponentially correlated noise on the xy model in the limit of small correlation time, discussing the order-disorder transition in the mean field and the topological transition in two dimensions. We map the steady states of the nonequilibrium dynamics into an effective equilibrium theory. In the mean field, the critical temperature increases with the noise correlation time τ, indicating that memory effects promote ordering. This finding is confirmed by numerical simulations. The topological transition temperature in two dimensions remains untouched. However, finite-size effects induce a crossover in the vortices proliferation that is confirmed by numerical simulations.

Comparative empirical analysis of flow-weighted transit route networks in R-space and evolution modeling

NASA Astrophysics Data System (ADS)

Huang, Ailing; Zang, Guangzhi; He, Zhengbing; Guan, Wei

2017-05-01

Urban public transit system is a typical mixed complex network with dynamic flow, and its evolution should be a process coupling topological structure with flow dynamics, which has received little attention. This paper presents the R-space to make a comparative empirical analysis on Beijing’s flow-weighted transit route network (TRN) and we found that both the Beijing’s TRNs in the year of 2011 and 2015 exhibit the scale-free properties. As such, we propose an evolution model driven by flow to simulate the development of TRNs with consideration of the passengers’ dynamical behaviors triggered by topological change. The model simulates that the evolution of TRN is an iterative process. At each time step, a certain number of new routes are generated driven by travel demands, which leads to dynamical evolution of new routes’ flow and triggers perturbation in nearby routes that will further impact the next round of opening new routes. We present the theoretical analysis based on the mean-field theory, as well as the numerical simulation for this model. The results obtained agree well with our empirical analysis results, which indicate that our model can simulate the TRN evolution with scale-free properties for distributions of node’s strength and degree. The purpose of this paper is to illustrate the global evolutional mechanism of transit network that will be used to exploit planning and design strategies for real TRNs.

System Operations Studies for Automated Guideway Transit Systems : Discrete Event Simulation Model Programmer's Manual

DOT National Transportation Integrated Search

1982-07-01

In order to examine specific automated guideway transit (AGT) developments and concepts, UMTA undertook a program of studies and technology investigations called Automated Guideway Transit Technology (AGTT) Program. The objectives of one segment of t...

Correlating Free-Volume Hole Distribution to the Glass Transition Temperature of Epoxy Polymers.

PubMed

Aramoon, Amin; Breitzman, Timothy D; Woodward, Christopher; El-Awady, Jaafar A

2017-09-07

A new algorithm is developed to quantify the free-volume hole distribution and its evolution in coarse-grained molecular dynamics simulations of polymeric networks. This is achieved by analyzing the geometry of the network rather than a voxelized image of the structure to accurately and efficiently find and quantify free-volume hole distributions within large scale simulations of polymer networks. The free-volume holes are quantified by fitting the largest ellipsoids and spheres in the free-volumes between polymer chains. The free-volume hole distributions calculated from this algorithm are shown to be in excellent agreement with those measured from positron annihilation lifetime spectroscopy (PALS) experiments at different temperature and pressures. Based on the results predicted using this algorithm, an evolution model is proposed for the thermal behavior of an individual free-volume hole. This model is calibrated such that the average radius of free-volumes holes mimics the one predicted from the simulations. The model is then employed to predict the glass-transition temperature of epoxy polymers with different degrees of cross-linking and lengths of prepolymers. Comparison between the predicted glass-transition temperatures and those measured from simulations or experiments implies that this model is capable of successfully predicting the glass-transition temperature of the material using only a PDF of the initial free-volume holes radii of each microstructure. This provides an effective approach for the optimized design of polymeric systems on the basis of the glass-transition temperature, degree of cross-linking, and average length of prepolymers.

Stimulated neutrino transformation through turbulence on a changing density profile and application to supernovae

DOE PAGES

Patton, Kelly M.; Kneller, James P.; McLaughlin, Gail C.

2015-01-06

We apply the model of stimulated neutrino transitions to neutrinos travelling through turbulence on a non constant density profile. We describe a method to predict the location of large amplitude transitions and demonstrate the effectiveness of this method by comparing to numerical calculations using a model supernova (SN) profile. The important wavelength scales of turbulence, both those that stimulate neutrino transformations and those that suppress them, are presented and discussed. We then examine the effects of changing the parameters of the turbulent spectrum, specifically the root-mean-square amplitude and cutoff wavelength, and show how the stimulated transitions model offers an explanationmore » for the increase in both the amplitude and number of transitions with large amplitude turbulence, as well as a suppression or absence of transitions for long cutoff wavelengths. The method can also be used to predict the location of transitions between anti-neutrino states which, in the normal hierarchy we are using, will not undergo Mikheev-Smirnov-Wolfenstein transitions. Lastly, the stimulated neutrino transitions method is applied to a turbulent 2D supernova simulation and explains the minimal observed effect on neutrino oscillations in the simulation as being due to excessive long wavelength modes suppressing transitions and the absence of modes that fulfill the parametric resonance condition.« less

Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions.

PubMed

Vosmeer, C Ruben; Kooi, Derk P; Capoferri, Luigi; Terpstra, Margreet M; Vermeulen, Nico P E; Geerke, Daan P

2016-01-01

Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was shown to decrease the root-mean-square error and standard deviation of error prediction by combining interaction energies of simulations starting from different conformations. Thereby, different parts of protein-ligand conformational space are sampled in parallel simulations. The iterative LIE framework relies on the assumption that separate simulations explore different local parts of phase space, and do not show transitions to other parts of configurational space that are already covered in parallel simulations. In this work, a method is proposed to (automatically) detect such transitions during the simulations that are performed to construct LIE models and to predict binding affinities. Using noise-canceling techniques and splines to fit time series of the raw data for the interaction energies, transitions during simulation between different parts of phase space are identified. Boolean selection criteria are then applied to determine which parts of the interaction energy trajectories are to be used as input for the LIE calculations. Here we show that this filtering approach benefits the predictive quality of our previous CYP 2D6-aryloxypropanolamine LIE model. In addition, an analysis is performed of the gain in computational efficiency that can be obtained from monitoring simulations using the proposed filtering method and by prematurely terminating simulations accordingly.

Phase transitions and thermodynamic properties of antiferromagnetic Ising model with next-nearest-neighbor interactions on the Kagomé lattice

NASA Astrophysics Data System (ADS)

Ramazanov, M. K.; Murtazaev, A. K.; Magomedov, M. A.; Badiev, M. K.

2018-06-01

We study phase transitions and thermodynamic properties in the two-dimensional antiferromagnetic Ising model with next-nearest-neighbor interaction on a Kagomé lattice by Monte Carlo simulations. A histogram data analysis shows that a second-order transition occurs in the model. From the analysis of obtained data, we can assume that next-nearest-neighbor ferromagnetic interactions in two-dimensional antiferromagnetic Ising model on a Kagomé lattice excite the occurrence of a second-order transition and unusual behavior of thermodynamic properties on the temperature dependence.

Modeling and Simulation of Quenching and Tempering Process in steels

NASA Astrophysics Data System (ADS)

Deng, Xiaohu; Ju, Dongying

Quenching and tempering (Q&T) is a combined heat treatment process to achieve maximum toughness and ductility at a specified hardness and strength. It is important to develop a mathematical model for quenching and tempering process for satisfy requirement of mechanical properties with low cost. This paper presents a modified model to predict structural evolution and hardness distribution during quenching and tempering process of steels. The model takes into account tempering parameters, carbon content, isothermal and non-isothermal transformations. Moreover, precipitation of transition carbides, decomposition of retained austenite and precipitation of cementite can be simulated respectively. Hardness distributions of quenched and tempered workpiece are predicted by experimental regression equation. In order to validate the model, it is employed to predict the tempering of 80MnCr5 steel. The predicted precipitation dynamics of transition carbides and cementite is consistent with the previous experimental and simulated results from literature. Then the model is implemented within the framework of the developed simulation code COSMAP to simulate microstructure, stress and distortion in the heat treated component. It is applied to simulate Q&T process of J55 steel. The calculated results show a good agreement with the experimental ones. This agreement indicates that the model is effective for simulation of Q&T process of steels.

Development of state and transition model assumptions used in National Forest Plan revision

Treesearch

Eric B. Henderson

2008-01-01

State and transition models are being utilized in forest management analysis processes to evaluate assumptions about disturbances and succession. These models assume valid information about seral class successional pathways and timing. The Forest Vegetation Simulator (FVS) was used to evaluate seral class succession assumptions for the Hiawatha National Forest in...

Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions.

PubMed

Aoun, Bachir; Pellegrini, Eric; Trapp, Marcus; Natali, Francesca; Cantù, Laura; Brocca, Paola; Gerelli, Yuri; Demé, Bruno; Marek Koza, Michael; Johnson, Mark; Peters, Judith

2016-04-01

Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn -glycero-3-phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.

Hydrogeologic Unit Flow Characterization Using Transition Probability Geostatistics

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

Jones, N L; Walker, J R; Carle, S F

2003-11-21

This paper describes a technique for applying the transition probability geostatistics method for stochastic simulation to a MODFLOW model. Transition probability geostatistics has several advantages over traditional indicator kriging methods including a simpler and more intuitive framework for interpreting geologic relationships and the ability to simulate juxtapositional tendencies such as fining upwards sequences. The indicator arrays generated by the transition probability simulation are converted to layer elevation and thickness arrays for use with the new Hydrogeologic Unit Flow (HUF) package in MODFLOW 2000. This makes it possible to preserve complex heterogeneity while using reasonably sized grids. An application of themore » technique involving probabilistic capture zone delineation for the Aberjona Aquifer in Woburn, Ma. is included.« less

Sitewise manipulations and Mott insulator-superfluid transition of interacting photons using superconducting circuit simulators

DOE PAGES

Deng, Xiuhao; Jia, Chunjing; Chien, Chih-Chun

2015-02-23

We report that the Bose Hubbard model (BHM) of interacting bosons in a lattice has been a paradigm in many-body physics, and it exhibits a Mott insulator (MI)-superfluid (SF) transition at integer filling. Here a quantum simulator of the BHM using a superconducting circuit is proposed. Specifically, a superconducting transmission line resonator supporting microwave photons is coupled to a charge qubit to form one site of the BHM, and adjacent sites are connected by a tunable coupler. To obtain a mapping from the superconducting circuit to the BHM, we focus on the dispersive regime where the excitations remain photonlike. Standardmore » perturbation theory is implemented to locate the parameter range where the MI-SF transition may be simulated. This simulator allows single-site manipulations and we illustrate this feature by considering two scenarios where a single-site manipulation can drive a MI-SF transition. The transition can be analyzed by mean-field analyses, and the exact diagonalization was implemented to provide accurate results. The variance of the photon density and the fidelity metric clearly show signatures of the transition. Lastly, experimental realizations and other possible applications of this simulator are also discussed.« less

Piloted evaluation of an integrated propulsion and flight control simulator

NASA Technical Reports Server (NTRS)

Bright, Michelle M.; Simon, Donald L.

1992-01-01

A piloted evaluation of the integrated flight and propulsion control simulator for advanced integrated propulsion and airframe control design is described. The evaluation will cover control effector gains and deadbands, control effectiveness and control authority, and heads up display functionality. For this evaluation the flight simulator is configured for transition flight using an advanced Short Take-Off and Vertical Landing fighter aircraft model, a simplified high-bypass turbofan engine model, fighter cockpit displays, and pilot effectors. The piloted tasks used for rating displays and control effector gains are described. Pilot comments and simulation results confirm that the display symbology and control gains are very adequate for the transition flight task. Additionally, it is demonstrated that this small-scale, fixed base flight simulator facility can adequately perform a real time, piloted control evaluation.

Simulation of an epidemic model with vector transmission

NASA Astrophysics Data System (ADS)

Dickman, Adriana G.; Dickman, Ronald

2015-03-01

We study a lattice model for vector-mediated transmission of a disease in a population consisting of two species, A and B, which contract the disease from one another. Individuals of species A are sedentary, while those of species B (the vector) diffuse in space. Examples of such diseases are malaria, dengue fever, and Pierce's disease in vineyards. The model exhibits a phase transition between an absorbing (infection free) phase and an active one as parameters such as infection rates and vector density are varied. We study the static and dynamic critical behavior of the model using initial spreading, initial decay, and quasistationary simulations. Simulations are checked against mean-field analysis. Although phase transitions to an absorbing state fall generically in the directed percolation universality class, this appears not to be the case for the present model.

Validation of Potential Models for Li2O in Classical Molecular Dynamics Simulation

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

Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru

2007-08-01

Four Buckingham-type pairwise potential models for Li2O were assessed by molecular static and dynamics simulations. In the static simulation, all models afforded acceptable agreement with experimental values and ab initio calculation results for the crystalline properties. Moreover, the superionic phase transition was realized in the dynamics simulation. However, the Li diffusivity and the lattice expansion were not adequately reproduced at the same time by any model. When using these models in future radiation simulation, these features should be taken into account, in order to reduce the model dependency of the results.

Shock Position Control for Mode Transition in a Turbine Based Combined Cycle Engine Inlet Model

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Stueber, Thomas J.

2013-01-01

A dual flow-path inlet for a turbine based combined cycle (TBCC) propulsion system is to be tested in order to evaluate methodologies for performing a controlled inlet mode transition. Prior to experimental testing, simulation models are used to test, debug, and validate potential control algorithms which are designed to maintain shock position during inlet disturbances. One simulation package being used for testing is the High Mach Transient Engine Cycle Code simulation, known as HiTECC. This paper discusses the development of a mode transition schedule for the HiTECC simulation that is analogous to the development of inlet performance maps. Inlet performance maps, derived through experimental means, describe the performance and operability of the inlet as the splitter closes, switching power production from the turbine engine to the Dual Mode Scram Jet. With knowledge of the operability and performance tradeoffs, a closed loop system can be designed to optimize the performance of the inlet. This paper demonstrates the design of the closed loop control system and benefit with the implementation of a Proportional-Integral controller, an H-Infinity based controller, and a disturbance observer based controller; all of which avoid inlet unstart during a mode transition with a simulated disturbance that would lead to inlet unstart without closed loop control.

Experimental testing of a new integrated model of the budding yeast Start transition

PubMed Central

Adames, Neil R.; Schuck, P. Logan; Chen, Katherine C.; Murali, T. M.; Tyson, John J.; Peccoud, Jean

2015-01-01

The cell cycle is composed of bistable molecular switches that govern the transitions between gap phases (G1 and G2) and the phases in which DNA is replicated (S) and partitioned between daughter cells (M). Many molecular details of the budding yeast G1–S transition (Start) have been elucidated in recent years, especially with regard to its switch-like behavior due to positive feedback mechanisms. These results led us to reevaluate and expand a previous mathematical model of the yeast cell cycle. The new model incorporates Whi3 inhibition of Cln3 activity, Whi5 inhibition of SBF and MBF transcription factors, and feedback inhibition of Whi5 by G1–S cyclins. We tested the accuracy of the model by simulating various mutants not described in the literature. We then constructed these novel mutant strains and compared their observed phenotypes to the model’s simulations. The experimental results reported here led to further changes of the model, which will be fully described in a later article. Our study demonstrates the advantages of combining model design, simulation, and testing in a coordinated effort to better understand a complex biological network. PMID:26310445

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin

PubMed Central

Savol, Andrej J.; Burger, Virginia M.; Agarwal, Pratul K.; Ramanathan, Arvind; Chennubhotla, Chakra S.

2011-01-01

Motivation: Molecular dynamics (MD) simulations have dramatically improved the atomistic understanding of protein motions, energetics and function. These growing datasets have necessitated a corresponding emphasis on trajectory analysis methods for characterizing simulation data, particularly since functional protein motions and transitions are often rare and/or intricate events. Observing that such events give rise to long-tailed spatial distributions, we recently developed a higher-order statistics based dimensionality reduction method, called quasi-anharmonic analysis (QAA), for identifying biophysically-relevant reaction coordinates and substates within MD simulations. Further characterization of conformation space should consider the temporal dynamics specific to each identified substate. Results: Our model uses hierarchical clustering to learn energetically coherent substates and dynamic modes of motion from a 0.5 μs ubiqutin simulation. Autoregressive (AR) modeling within and between states enables a compact and generative description of the conformational landscape as it relates to functional transitions between binding poses. Lacking a predictive component, QAA is extended here within a general AR model appreciative of the trajectory's temporal dependencies and the specific, local dynamics accessible to a protein within identified energy wells. These metastable states and their transition rates are extracted within a QAA-derived subspace using hierarchical Markov clustering to provide parameter sets for the second-order AR model. We show the learned model can be extrapolated to synthesize trajectories of arbitrary length. Contact: ramanathana@ornl.gov; chakracs@pitt.edu PMID:21685101

Integrating continuous stocks and flows into state-and-transition simulation models of landscape change

USGS Publications Warehouse

Daniel, Colin J.; Sleeter, Benjamin M.; Frid, Leonardo; Fortin, Marie-Josée

2018-01-01

State-and-transition simulation models (STSMs) provide a general framework for forecasting landscape dynamics, including projections of both vegetation and land-use/land-cover (LULC) change. The STSM method divides a landscape into spatially-referenced cells and then simulates the state of each cell forward in time, as a discrete-time stochastic process using a Monte Carlo approach, in response to any number of possible transitions. A current limitation of the STSM method, however, is that all of the state variables must be discrete.Here we present a new approach for extending a STSM, in order to account for continuous state variables, called a state-and-transition simulation model with stocks and flows (STSM-SF). The STSM-SF method allows for any number of continuous stocks to be defined for every spatial cell in the STSM, along with a suite of continuous flows specifying the rates at which stock levels change over time. The change in the level of each stock is then simulated forward in time, for each spatial cell, as a discrete-time stochastic process. The method differs from the traditional systems dynamics approach to stock-flow modelling in that the stocks and flows can be spatially-explicit, and the flows can be expressed as a function of the STSM states and transitions.We demonstrate the STSM-SF method by integrating a spatially-explicit carbon (C) budget model with a STSM of LULC change for the state of Hawai'i, USA. In this example, continuous stocks are pools of terrestrial C, while the flows are the possible fluxes of C between these pools. Importantly, several of these C fluxes are triggered by corresponding LULC transitions in the STSM. Model outputs include changes in the spatial and temporal distribution of C pools and fluxes across the landscape in response to projected future changes in LULC over the next 50 years.The new STSM-SF method allows both discrete and continuous state variables to be integrated into a STSM, including interactions between them. With the addition of stocks and flows, STSMs provide a conceptually simple yet powerful approach for characterizing uncertainties in projections of a wide range of questions regarding landscape change.

Piloted evaluation of an integrated propulsion and flight control simulator

NASA Technical Reports Server (NTRS)

Bright, Michelle M.; Simon, Donald L.

1992-01-01

This paper describes a piloted evaluation of the integrated flight and propulsion control simulator at NASA Lewis Research Center. The purpose of this evaluation is to demonstrate the suitability and effectiveness of this fixed based simulator for advanced integrated propulsion and airframe control design. The evaluation will cover control effector gains and deadbands, control effectiveness and control authority, and heads up display functionality. For this evaluation the flight simulator is configured for transition flight using an advanced Short Take-Off and vertical Landing fighter aircraft model, a simplified high-bypass turbofan engine model, fighter cockpit, displays, and pilot effectors. The paper describes the piloted tasks used for rating displays and control effector gains. Pilot comments and simulation results confirm that the display symbology and control gains are very adequate for the transition flight task. Additionally, it is demonstrated that this small-scale, fixed base flight simulator facility can adequately perform a real time, piloted control evaluation.

Controlling protein molecular dynamics: How to accelerate folding while preserving the native state

NASA Astrophysics Data System (ADS)

Jensen, Christian H.; Nerukh, Dmitry; Glen, Robert C.

2008-12-01

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1μs. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

Kinetics from Replica Exchange Molecular Dynamics Simulations.

PubMed

Stelzl, Lukas S; Hummer, Gerhard

2017-08-08

Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

Emergence of coherence and the dynamics of quantum phase transitions

PubMed Central

Braun, Simon; Friesdorf, Mathis; Hodgman, Sean S.; Schreiber, Michael; Ronzheimer, Jens Philipp; Riera, Arnau; del Rey, Marco; Bloch, Immanuel; Eisert, Jens

2015-01-01

The dynamics of quantum phase transitions pose one of the most challenging problems in modern many-body physics. Here, we study a prototypical example in a clean and well-controlled ultracold atom setup by observing the emergence of coherence when crossing the Mott insulator to superfluid quantum phase transition. In the 1D Bose–Hubbard model, we find perfect agreement between experimental observations and numerical simulations for the resulting coherence length. We, thereby, perform a largely certified analog quantum simulation of this strongly correlated system reaching beyond the regime of free quasiparticles. Experimentally, we additionally explore the emergence of coherence in higher dimensions, where no classical simulations are available, as well as for negative temperatures. For intermediate quench velocities, we observe a power-law behavior of the coherence length, reminiscent of the Kibble–Zurek mechanism. However, we find nonuniversal exponents that cannot be captured by this mechanism or any other known model. PMID:25775515

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

Zhu, Lin; Dai, Zhenxue; Gong, Huili

Understanding the heterogeneity arising from the complex architecture of sedimentary sequences in alluvial fans is challenging. This study develops a statistical inverse framework in a multi-zone transition probability approach for characterizing the heterogeneity in alluvial fans. An analytical solution of the transition probability matrix is used to define the statistical relationships among different hydrofacies and their mean lengths, integral scales, and volumetric proportions. A statistical inversion is conducted to identify the multi-zone transition probability models and estimate the optimal statistical parameters using the modified Gauss–Newton–Levenberg–Marquardt method. The Jacobian matrix is computed by the sensitivity equation method, which results in anmore » accurate inverse solution with quantification of parameter uncertainty. We use the Chaobai River alluvial fan in the Beijing Plain, China, as an example for elucidating the methodology of alluvial fan characterization. The alluvial fan is divided into three sediment zones. In each zone, the explicit mathematical formulations of the transition probability models are constructed with optimized different integral scales and volumetric proportions. The hydrofacies distributions in the three zones are simulated sequentially by the multi-zone transition probability-based indicator simulations. Finally, the result of this study provides the heterogeneous structure of the alluvial fan for further study of flow and transport simulations.« less

Transition model for ricin-aptamer interactions with multiple pathways and energy barriers

NASA Astrophysics Data System (ADS)

Wang, Bin; Xu, Bingqian

2014-02-01

We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.

Modeling the polydomain-monodomain transition of liquid crystal elastomers.

PubMed

Whitmer, Jonathan K; Roberts, Tyler F; Shekhar, Raj; Abbott, Nicholas L; de Pablo, Juan J

2013-02-01

We study the mechanism of the polydomain-monodomain transition in liquid crystalline elastomers at the molecular scale. A coarse-grained model is proposed in which mesogens are described as ellipsoidal particles. Molecular dynamics simulations are used to examine the transition from a polydomain state to a monodomain state in the presence of uniaxial strain. Our model demonstrates soft elasticity, similar to that exhibited by side-chain elastomers in the literature. By analyzing the growth dynamics of nematic domains during uniaxial extension, we provide direct evidence that at a molecular level the polydomain-monodomain transition proceeds through cluster rotation and domain growth.

A Closed-Loop Model of Operator Visual Attention, Situation Awareness, and Performance Across Automation Mode Transitions.

PubMed

Johnson, Aaron W; Duda, Kevin R; Sheridan, Thomas B; Oman, Charles M

2017-03-01

This article describes a closed-loop, integrated human-vehicle model designed to help understand the underlying cognitive processes that influenced changes in subject visual attention, mental workload, and situation awareness across control mode transitions in a simulated human-in-the-loop lunar landing experiment. Control mode transitions from autopilot to manual flight may cause total attentional demands to exceed operator capacity. Attentional resources must be reallocated and reprioritized, which can increase the average uncertainty in the operator's estimates of low-priority system states. We define this increase in uncertainty as a reduction in situation awareness. We present a model built upon the optimal control model for state estimation, the crossover model for manual control, and the SEEV (salience, effort, expectancy, value) model for visual attention. We modify the SEEV attention executive to direct visual attention based, in part, on the uncertainty in the operator's estimates of system states. The model was validated using the simulated lunar landing experimental data, demonstrating an average difference in the percentage of attention ≤3.6% for all simulator instruments. The model's predictions of mental workload and situation awareness, measured by task performance and system state uncertainty, also mimicked the experimental data. Our model supports the hypothesis that visual attention is influenced by the uncertainty in system state estimates. Conceptualizing situation awareness around the metric of system state uncertainty is a valuable way for system designers to understand and predict how reallocations in the operator's visual attention during control mode transitions can produce reallocations in situation awareness of certain states.

Integrating Ecosystem Carbon Dynamics into State-and-Transition Simulation Models of Land Use/Land Cover Change

NASA Astrophysics Data System (ADS)

Sleeter, B. M.; Daniel, C.; Frid, L.; Fortin, M. J.

2016-12-01

State-and-transition simulation models (STSMs) provide a general approach for incorporating uncertainty into forecasts of landscape change. Using a Monte Carlo approach, STSMs generate spatially-explicit projections of the state of a landscape based upon probabilistic transitions defined between states. While STSMs are based on the basic principles of Markov chains, they have additional properties that make them applicable to a wide range of questions and types of landscapes. A current limitation of STSMs is that they are only able to track the fate of discrete state variables, such as land use/land cover (LULC) classes. There are some landscape modelling questions, however, for which continuous state variables - for example carbon biomass - are also required. Here we present a new approach for integrating continuous state variables into spatially-explicit STSMs. Specifically we allow any number of continuous state variables to be defined for each spatial cell in our simulations; the value of each continuous variable is then simulated forward in discrete time as a stochastic process based upon defined rates of change between variables. These rates can be defined as a function of the realized states and transitions of each cell in the STSM, thus providing a connection between the continuous variables and the dynamics of the landscape. We demonstrate this new approach by (1) developing a simple IPCC Tier 3 compliant model of ecosystem carbon biomass, where the continuous state variables are defined as terrestrial carbon biomass pools and the rates of change as carbon fluxes between pools, and (2) integrating this carbon model with an existing LULC change model for the state of Hawaii, USA.

A simulation study on the constancy of cardiac energy metabolites during workload transition.

PubMed

Saito, Ryuta; Takeuchi, Ayako; Himeno, Yukiko; Inagaki, Nobuya; Matsuoka, Satoshi

2016-12-01

The cardiac energy metabolites such as ATP, phosphocreatine, ADP and NADH are kept relatively constant during physiological cardiac workload transition. How this is accomplished is not yet clarified, though Ca 2+ has been suggested to be one of the possible mechanisms. We constructed a detailed mathematical model of cardiac mitochondria based on experimental data and studied whether known Ca 2+ -dependent regulation mechanisms play roles in the metabolite constancy. Model simulations revealed that the Ca 2+ -dependent regulation mechanisms have important roles under the in vitro condition of isolated mitochondria where malate and glutamate were mitochondrial substrates, while they have only a minor role and the composition of substrates has marked influence on the metabolite constancy during workload transition under the simulated in vivo condition where many substrates exist. These results help us understand the regulation mechanisms of cardiac energy metabolism during physiological cardiac workload transition. The cardiac energy metabolites such as ATP, phosphocreatine, ADP and NADH are kept relatively constant over a wide range of cardiac workload, though the mechanisms are not yet clarified. One possible regulator of mitochondrial metabolism is Ca 2+ , because it activates several mitochondrial enzymes and transporters. Here we constructed a mathematical model of cardiac mitochondria, including oxidative phosphorylation, substrate metabolism and ion/substrate transporters, based on experimental data, and studied whether the Ca 2+ -dependent activation mechanisms play roles in metabolite constancy. Under the in vitro condition of isolated mitochondria, where malate and glutamate were used as mitochondrial substrates, the model well reproduced the Ca 2+ and inorganic phosphate (P i ) dependences of oxygen consumption, NADH level and mitochondrial membrane potential. The Ca 2+ -dependent activations of the aspartate/glutamate carrier and the F 1 F o -ATPase, and the P i -dependent activation of Complex III were key factors in reproducing the experimental data. When the mitochondrial model was implemented in a simple cardiac cell model, simulation of workload transition revealed that cytoplasmic Ca 2+ concentration ([Ca 2+ ] cyt ) within the physiological range markedly increased NADH level. However, the addition of pyruvate or citrate attenuated the Ca 2+ dependence of NADH during the workload transition. Under the simulated in vivo condition where malate, glutamate, pyruvate, citrate and 2-oxoglutarate were used as mitochondrial substrates, the energy metabolites were more stable during the workload transition and NADH level was almost insensitive to [Ca 2+ ] cyt . It was revealed that mitochondrial substrates have a significant influence on metabolite constancy during cardiac workload transition, and Ca 2+ has only a minor role under physiological conditions. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Modeling of turbulence and transition

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing

1992-01-01

The first objective is to evaluate current two-equation and second order closure turbulence models using available direct numerical simulations and experiments, and to identify the models which represent the state of the art in turbulence modeling. The second objective is to study the near-wall behavior of turbulence, and to develop reliable models for an engineering calculation of turbulence and transition. The third objective is to develop a two-scale model for compressible turbulence.

Superfluid--Solid Quantum Phase Transitions and Landau-Ginzburg-Wilson Paradigm

NASA Astrophysics Data System (ADS)

Kuklov, A. B.; Prokof'ev, N. V.

2005-03-01

We study superfluid (SF)--solid zero-temperature transitions in 2d lattice boson/spin models by Worm-Algorithm Monte Carlo simulations. The SF -- Valence Bond Solid (VBS) transition was recently argued to be generically of II order in violation of the Ginzburg-Landau- Wilson (GLW) paradigm [1]. We simulate the J-current model on lattices up to 64x64x64, and observe that SF- columnar VBS and SF-checkerboard solid transitions are typically weak I-order ones and in small systems they may be confused with the continuous or high-symmetry points [2]. Thus, in the simulated model, the SF-VBS transition proceeds in agreement with the GLW paradigm. We explain this by dominance of standard particle and hole excitations, as opposed to fractionalized (spinon) excitations [1]. We developed a technique based on tunneling events (instantons) in the insulating phase which reveals charges of the revelant long-wave modes. While in 1d systems spinons are clearly seen in tunneling events, in two spatial dimensions tunneling is solely controlled by particles and holes in our system. This work is supported by NSF grant ITR-405460001 and PSC-CUNY- 665560035. [1] T. Senthil, A. Vishwanath, L. Balents, S. Sachdev, and M.P.A. Fisher, Science 303, 1490 (2004); [2] A.B. Kuklov, N.V. Prokof'ev, B.V. Svistunov, condmat/0406061; PRL, to be published.

A general stochastic model for studying time evolution of transition networks

NASA Astrophysics Data System (ADS)

Zhan, Choujun; Tse, Chi K.; Small, Michael

2016-12-01

We consider a class of complex networks whose nodes assume one of several possible states at any time and may change their states from time to time. Such networks represent practical networks of rumor spreading, disease spreading, language evolution, and so on. Here, we derive a model describing the dynamics of this kind of network and a simulation algorithm for studying the network evolutionary behavior. This model, derived at a microscopic level, can reveal the transition dynamics of every node. A numerical simulation is taken as an ;experiment; or ;realization; of the model. We use this model to study the disease propagation dynamics in four different prototypical networks, namely, the regular nearest-neighbor (RN) network, the classical Erdös-Renyí (ER) random graph, the Watts-Strogátz small-world (SW) network, and the Barabási-Albert (BA) scalefree network. We find that the disease propagation dynamics in these four networks generally have different properties but they do share some common features. Furthermore, we utilize the transition network model to predict user growth in the Facebook network. Simulation shows that our model agrees with the historical data. The study can provide a useful tool for a more thorough understanding of the dynamics networks.

The transition of a real-time single-rotor helicopter simulation program to a supercomputer

NASA Technical Reports Server (NTRS)

Martinez, Debbie

1995-01-01

This report presents the conversion effort and results of a real-time flight simulation application transition to a CONVEX supercomputer. Enclosed is a detailed description of the conversion process and a brief description of the Langley Research Center's (LaRC) flight simulation application program structure. Currently, this simulation program may be configured to represent Sikorsky S-61 helicopter (a five-blade, single-rotor, commercial passenger-type helicopter) or an Army Cobra helicopter (either the AH-1 G or AH-1 S model). This report refers to the Sikorsky S-61 simulation program since it is the most frequently used configuration.

Some Recent Developments in Turbulence Closure Modeling

NASA Astrophysics Data System (ADS)

Durbin, Paul A.

2018-01-01

Turbulence closure models are central to a good deal of applied computational fluid dynamical analysis. Closure modeling endures as a productive area of research. This review covers recent developments in elliptic relaxation and elliptic blending models, unified rotation and curvature corrections, transition prediction, hybrid simulation, and data-driven methods. The focus is on closure models in which transport equations are solved for scalar variables, such as the turbulent kinetic energy, a timescale, or a measure of anisotropy. Algebraic constitutive representations are reviewed for their role in relating scalar closures to the Reynolds stress tensor. Seamless and nonzonal methods, which invoke a single closure model, are reviewed, especially detached eddy simulation (DES) and adaptive DES. Other topics surveyed include data-driven modeling and intermittency and laminar fluctuation models for transition prediction. The review concludes with an outlook.

Seasonal Transitions and the Westerly Jet in the Holocene East Asian Summer Monsoon

NASA Astrophysics Data System (ADS)

Kong, W.; Chiang, J. C. H.

2015-12-01

The Holocene East Asian Summer Monsoon (EASM) was characterized by a trend to weaker monsoon intensity paced by orbital insolation. Here, we attribute the stronger EASM intensity in the early-mid Holocene to changes in the timing of the transition between the EASM seasonal stages - Spring, pre Mei- Yu, Mei-Yu, and Summer - during that time. Following the recent 'jet transition hypothesis' (Chiang et al., 2015), we explore the role of north-south displacement of the westerlies relative to the Tibetan Plateau that is hypothesized to control the downstream EASM seasonality changes across the Holocene. To this end, we analyze model simulations of the Holocene EASM, compare the simulated Holocene climate with the paleodata observations, and examine the role of atmospheric circulation and specifically the westerlies in modulating the East Asia summer climate. The PMIP3 climate model simulations suggest that, compared to the pre-industrial, the Mei-Yu onset and the transition from Mei-Yu to Summer rainfall occur earlier in the mid-Holocene. The advanced seasonal rainfall transition is accompanied by the weakened and northward-shifted upstream westerlies. In our atmospheric general circulation model (coupled to a slab ocean) simulations of various time periods across the Holocene (9ka, 6ka, 3ka, and pre-industrial), we quantitatively show that the timing and the length of each rainfall stage are closely related to the jet position over East Asia. We also show that the simulated changes in the maximum annual rainfall band and dust emission over East Asia largely agree with the paleo-proxy observations. In addition, we find that changes to the seasonal rainfall transitions, latitudinal westerly position, and stationary eddy activity over East Asia co-vary across the Holocene. In particular, we argue that the changes in the rainfall seasonal transitions are tied to an altered stationary wave pattern, resembling today's the so-called 'Silk Road Pattern', riding along the westerly jet. We end by discussing the mechanism that is proposed to explain the changed EASM seasonality across the Holocene.

Atomistic Simulations of the pH Induced Functional Rearrangement of Influenza Hemagglutinin

NASA Astrophysics Data System (ADS)

Lin, Xingcheng; Noel, Jeffrey; Wang, Qinghua; Ma, Jianpeng; Onuchic, Jose

Influenza hemagglutinin (HA), a surface glycoprotein responsible for the entry and replication of flu viruses in their host cells, functions by starting a dramatic conformational rearrangement, which leads to a fusion of the viral and endosomal membranes. It has been claimed that a loop-to-coiled-coil transition of the B-loop domain of HA drives the HA-induced membrane fusion. On the lack of dynamical details, however, the microscopic picture for this proposed ``spring-loaded'' movement is missing. To elaborate on the transition of the B-loop, we performed a set of unbiased all-atom molecular dynamics simulations of the full B-loop structure with the CHARMM36 force field. The complete free-energy profile constructed from our simulations reveals a slow transition rate for the B-loop that is incompatible with a downhill process. Additionally, our simulations indicate two potential sources of kinetic traps in the structural switch of the B-loop: Desolvation barriers and non-native secondary structure formation. The slow timescale of the B-loop transition also confirms our previous discovery from simulations using a coarse-grained structure-based model, which identified two competitive pathways both with a slow B-loop transition for HA to guide the membrane fusion.

Economic Theory and Management Games II.

ERIC Educational Resources Information Center

Zernik, Wolfgang

1988-01-01

Description of management games continues a previous article's discussion of how mathematical modeling and microeconomic concepts can be used by players. Highlights include an initial condition simulating a profit-maximizing monopoly; simulating the transition from monopoly to oligopoly; and how mathematical properties of the model affect final…

Numerical simulation of flow for viscoelastic neutrophil models in a rectangular capillary network: effects of capillary shape and cell stiffness on transit time.

PubMed

Shirai, Atsushi; Fujita, Ryo; Hayase, Toshiyuki

2007-01-01

The concentration of neutrophils in the pulmonary microvasculature is higher than in large systemic vessels. It is thought that the high concentration of neutrophils facilitates their effective recruitment to sites of inflammation. Thus, in order to understand the role of neutrophils in the immune system, it is important to clarify their flow characteristics in the pulmonary microvasculature. In a previous study, we developed a model to simulate the flow of neutrophils in a capillary network, in which the cells were modeled as spheres of a Maxwell material with a cortical tension and the capillary segments were modeled as arc-shaped constrictions in straight pipes. In the present paper, the flow of neutrophils in a simplified alveolar capillary network model is investigated for various constriction shapes and cell stiffnesses. Finally, it is shown that both the coefficient of variation of the transit time of the cells, which is the standard deviation divided by the mean transit time, and the mean transit time increase as the capillary segments become steep or tight, or when the cells become hard. The mean value of the transit time exceeds the median for all of the conditions that occur in real lungs, although the difference between them is small.

Single-Column Model Simulations of Subtropical Marine Boundary-Layer Cloud Transitions Under Weakening Inversions: SCM SIMULATIONS OF CLOUD TRANSITIONS

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

Neggers, R. A. J.; Ackerman, A. S.; Angevine, W. M.

Results are presented of the GASS/EUCLIPSE single-column model inter-comparison study on the subtropical marine low-level cloud transition. A central goal is to establish the performance of state-of-the-art boundary-layer schemes for weather and climate mod- els for this cloud regime, using large-eddy simulations of the same scenes as a reference. A novelty is that the comparison covers four different cases instead of one, in order to broaden the covered parameter space. Three cases are situated in the North-Eastern Pa- cific, while one reflects conditions in the North-Eastern Atlantic. A set of variables is considered that reflects key aspects of the transitionmore » process, making use of simple met- rics to establish the model performance. Using this method some longstanding problems in low level cloud representation are identified. Considerable spread exists among models concerning the cloud amount, its vertical structure and the associated impact on radia- tive transfer. The sign and amplitude of these biases differ somewhat per case, depending on how far the transition has progressed. After cloud breakup the ensemble median ex- hibits the well-known “too few too bright” problem. The boundary layer deepening rate and its state of decoupling are both underestimated, while the representation of the thin capping cloud layer appears complicated by a lack of vertical resolution. Encouragingly, some models are successful in representing the full set of variables, in particular the verti- cal structure and diurnal cycle of the cloud layer in transition. An intriguing result is that the median of the model ensemble performs best, inspiring a new approach in subgrid pa- rameterization.« less

Transition Heat Transfer Modeling Based on the Characteristics of Turbulent Spots

NASA Technical Reports Server (NTRS)

Simon, Fred; Boyle, Robert

1998-01-01

While turbulence models are being developed which show promise for simulating the transition region on a turbine blade or vane, it is believed that the best approach with the greatest potential for practical use is the use of models which incorporate the physics of turbulent spots present in the transition region. This type of modeling results in the prediction of transition region intermittency which when incorporated in turbulence models give a good to excellent prediction of the transition region heat transfer. Some models are presented which show how turbulent spot characteristics and behavior can be employed to predict the effect of pressure gradient and Mach number on the transition region. The models predict the spot formation rate which is needed, in addition to the transition onset location, in the Narasimha concentrated breakdown intermittency equation. A simplified approach is taken for modeling turbulent spot growth and interaction in the transition region which utilizes the turbulent spot variables governing transition length and spot generation rate. The models are expressed in terms of spot spreading angle, dimensionless spot velocity, dimensionless spot area, disturbance frequency and Mach number. The models are used in conjunction with a computer code to predict the effects of pressure gradient and Mach number on the transition region and compared with VKI experimental turbine data.

Sabin-to-Mahoney Transition Model of Quasispecies Replication

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

2009-05-31

Qspp is an agent-based stochastic simulation model of the Poliovirus Sabin-to-Mahoney transition. This code simulates a cell-to-cell model of Poliovirus replication. The model tracks genotypes (virus genomes) as they are replicated in cells, and as the cells burst and release particles into the medium of a culture dish. An inoculum is then taken from the pool of virions and is used to inoculate cells on a new dish. This process repeats. The Sabin genotype comprises the initial inoculum. Nucleotide positions that match the Sabin1 (vaccine strain) and Mahoney (wild type) genotypes, as well as the neurovirulent phenotype (from the literature)more » are enumerated as constants.« less

Utilizing Direct Numerical Simulations of Transition and Turbulence in Design Optimization

NASA Technical Reports Server (NTRS)

Rai, Man M.

2015-01-01

Design optimization methods that use the Reynolds-averaged Navier-Stokes equations with the associated turbulence and transition models, or other model-based forms of the governing equations, may result in aerodynamic designs with actual performance levels that are noticeably different from the expected values because of the complexity of modeling turbulence/transition accurately in certain flows. Flow phenomena such as wake-blade interaction and trailing edge vortex shedding in turbines and compressors (examples of such flows) may require a computational approach that is free of transition/turbulence models, such as direct numerical simulations (DNS), for the underlying physics to be computed accurately. Here we explore the possibility of utilizing DNS data in designing a turbine blade section. The ultimate objective is to substantially reduce differences between predicted performance metrics and those obtained in reality. The redesign of a typical low-pressure turbine blade section with the goal of reducing total pressure loss in the row is provided as an example. The basic ideas presented here are of course just as applicable elsewhere in aerodynamic shape optimization as long as the computational costs are not excessive.

Employment, Production and Consumption model: Patterns of phase transitions

NASA Astrophysics Data System (ADS)

Lavička, H.; Lin, L.; Novotný, J.

2010-04-01

We have simulated the model of Employment, Production and Consumption (EPC) using Monte Carlo. The EPC model is an agent based model that mimics very basic rules of industrial economy. From the perspective of physics, the nature of the interactions in the EPC model represents multi-agent interactions where the relations among agents follow the key laws for circulation of capital and money. Monte Carlo simulations of the stochastic model reveal phase transition in the model economy. The two phases are the phase with full unemployment and the phase with nearly full employment. The economy switches between these two states suddenly as a reaction to a slight variation in the exogenous parameter, thus the system exhibits strong non-linear behavior as a response to the change of the exogenous parameters.

Developing a Policy Flight Simulator to Facilitate the Adoption of an Evidence-Based Intervention

PubMed Central

Yu, Zhongyuan; Hirschman, Karen B.; Pepe, Kara; Pauly, Mark V.; Naylor, Mary D.; Rouse, William B.

2018-01-01

While the use of evidence-based interventions (EBIs) has been advocated by the medical research community for quite some time, uptake of these interventions by healthcare providers has been slow. One possible explanation is that it is challenging for providers to estimate impacts of a specific EBI on their particular organization. To address that concern, we developed and evaluated a type of simulation called a policy flight simulator to determine if it could improve the adoption decision about a specific EBI, the transitional care model (TCM). The TCM uses an advanced practice nurse-led model of care to transition older adults with multiple chronic conditions from a hospitalization to home. An evaluation by a National Advisory Committee, made up of senior representatives from various stakeholders in the U.S. healthcare system, found the policy flight simulator to be a useful tool that has the potential to better inform adoption decisions. This paper describes the simulation development effort and documents lessons learned that may be useful to the healthcare modeling community and those interested in using simulation to support decisions based on EBIs. PMID:29805921

Simple Model of Sickle Hemoglobin

NASA Astrophysics Data System (ADS)

Shiryayev, Andrey; Li, Xiaofei; Gunton, James

2006-03-01

A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of understanding fiber formation. A gradual transition from monomers to one dimensional chains is observed as one varies the density of molecules at fixed temperature, somewhat similar to the transition from monomers to polymer fibers in sickle hemoglobin molecules in solution. An observed competition between chain formation and crystallization for the model is also discussed. The results of the simulation of the equation of state are shown to be in excellent agreement with a theory for a model of globular proteins, for the case of two interacting sites.

Urban Growth Modeling Using Cellular Automata with Multi-Temporal Remote Sensing Images Calibrated by the Artificial Bee Colony Optimization Algorithm.

PubMed

Naghibi, Fereydoun; Delavar, Mahmoud Reza; Pijanowski, Bryan

2016-12-14

Cellular Automata (CA) is one of the most common techniques used to simulate the urbanization process. CA-based urban models use transition rules to deliver spatial patterns of urban growth and urban dynamics over time. Determining the optimum transition rules of the CA is a critical step because of the heterogeneity and nonlinearities existing among urban growth driving forces. Recently, new CA models integrated with optimization methods based on swarm intelligence algorithms were proposed to overcome this drawback. The Artificial Bee Colony (ABC) algorithm is an advanced meta-heuristic swarm intelligence-based algorithm. Here, we propose a novel CA-based urban change model that uses the ABC algorithm to extract optimum transition rules. We applied the proposed ABC-CA model to simulate future urban growth in Urmia (Iran) with multi-temporal Landsat images from 1997, 2006 and 2015. Validation of the simulation results was made through statistical methods such as overall accuracy, the figure of merit and total operating characteristics (TOC). Additionally, we calibrated the CA model by ant colony optimization (ACO) to assess the performance of our proposed model versus similar swarm intelligence algorithm methods. We showed that the overall accuracy and the figure of merit of the ABC-CA model are 90.1% and 51.7%, which are 2.9% and 8.8% higher than those of the ACO-CA model, respectively. Moreover, the allocation disagreement of the simulation results for the ABC-CA model is 9.9%, which is 2.9% less than that of the ACO-CA model. Finally, the ABC-CA model also outperforms the ACO-CA model with fewer quantity and allocation errors and slightly more hits.

Urban Growth Modeling Using Cellular Automata with Multi-Temporal Remote Sensing Images Calibrated by the Artificial Bee Colony Optimization Algorithm

PubMed Central

Naghibi, Fereydoun; Delavar, Mahmoud Reza; Pijanowski, Bryan

2016-01-01

Cellular Automata (CA) is one of the most common techniques used to simulate the urbanization process. CA-based urban models use transition rules to deliver spatial patterns of urban growth and urban dynamics over time. Determining the optimum transition rules of the CA is a critical step because of the heterogeneity and nonlinearities existing among urban growth driving forces. Recently, new CA models integrated with optimization methods based on swarm intelligence algorithms were proposed to overcome this drawback. The Artificial Bee Colony (ABC) algorithm is an advanced meta-heuristic swarm intelligence-based algorithm. Here, we propose a novel CA-based urban change model that uses the ABC algorithm to extract optimum transition rules. We applied the proposed ABC-CA model to simulate future urban growth in Urmia (Iran) with multi-temporal Landsat images from 1997, 2006 and 2015. Validation of the simulation results was made through statistical methods such as overall accuracy, the figure of merit and total operating characteristics (TOC). Additionally, we calibrated the CA model by ant colony optimization (ACO) to assess the performance of our proposed model versus similar swarm intelligence algorithm methods. We showed that the overall accuracy and the figure of merit of the ABC-CA model are 90.1% and 51.7%, which are 2.9% and 8.8% higher than those of the ACO-CA model, respectively. Moreover, the allocation disagreement of the simulation results for the ABC-CA model is 9.9%, which is 2.9% less than that of the ACO-CA model. Finally, the ABC-CA model also outperforms the ACO-CA model with fewer quantity and allocation errors and slightly more hits. PMID:27983633

MOSES: A Matlab-based open-source stochastic epidemic simulator.

PubMed

Varol, Huseyin Atakan

2016-08-01

This paper presents an open-source stochastic epidemic simulator. Discrete Time Markov Chain based simulator is implemented in Matlab. The simulator capable of simulating SEQIJR (susceptible, exposed, quarantined, infected, isolated and recovered) model can be reduced to simpler models by setting some of the parameters (transition probabilities) to zero. Similarly, it can be extended to more complicated models by editing the source code. It is designed to be used for testing different control algorithms to contain epidemics. The simulator is also designed to be compatible with a network based epidemic simulator and can be used in the network based scheme for the simulation of a node. Simulations show the capability of reproducing different epidemic model behaviors successfully in a computationally efficient manner.

Universal monopole scaling near transitions from the Coulomb phase.

PubMed

Powell, Stephen

2012-08-10

Certain frustrated systems, including spin ice and dimer models, exhibit a Coulomb phase at low temperatures, with power-law correlations and fractionalized monopole excitations. Transitions out of this phase, at which the effective gauge theory becomes confining, provide examples of unconventional criticality. This Letter studies the behavior at nonzero monopole density near such transitions, using scaling theory to arrive at universal expressions for the crossover phenomena. For a particular transition in spin ice, quantitative predictions are made by mapping to the XY model and confirmed using Monte Carlo simulations.

Folding thermodynamics of model four-strand antiparallel beta-sheet proteins.

PubMed Central

Jang, Hyunbum; Hall, Carol K; Zhou, Yaoqi

2002-01-01

The thermodynamic properties for three different types of off-lattice four-strand antiparallel beta-strand protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration R(g)(2), the root-mean-squared pair separation fluctuation Delta(B), the specific heat C(v), the internal energy of the system E, and the Lindemann disorder parameter Delta(L). Despite these models' simplicity, they exhibit a complex set of protein transitions, consistent with those observed in experimental studies on real proteins. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. The high temperature transitions, i.e., the collapse transition and the disordered-to-ordered globule transition, exist for all three beta-strand proteins, although the native-state geometry of the three model proteins is different. However the low temperature transitions, i.e., the folding transition and the liquid-to-solid transition, strongly depend on the native-state geometry of the model proteins and the size of the bias gap. PMID:11806908

The validation and preference among different EAM potentials to describe the solid-liquid transition of aluminum

NASA Astrophysics Data System (ADS)

Jiang, Yewei; Luo, Jie; Wu, Yongquan

2017-06-01

Empirical potential is vital to the classic atomic simulation, especially for the study of phase transitions, as well as the solid-interface. In this paper, we attempt to set up a uniform procedure for the validation among different potentials before the formal simulation study of phase transitions of metals. Two main steps are involved: (1) the prediction of the structures of both solid and liquid phases and their mutual transitions, i.e. melting and crystallization; (2) the prediction of vital thermodynamic (the equilibrium melting point at ambient pressure) and dynamic properties (the degrees of superheating and undercooling). We applied this procedure to the testing of seven published embedded-atom potentials (MKBA (Mendelev et al 2008 Philos. Mag. 88 1723), MFMP (Mishin et al 1999 Phys. Rev. B 59 3393), MDSL (Sturgeon and Laird 2000 Phys. Rev. B 62 14720), ZM (Zope and Mishin 2003 Phys. Rev. B 68 024102), LEA (Liu et al 2004 Model. Simul. Mater. Sci. Eng. 12 665), WKG (Winey et al 2009 Model. Simul. Mater. Sci. Eng. 17 055004) and ZJW (Zhou et al 2004 Phys. Rev. B 69 144113)) for the description of the solid-liquid transition of Al. All the predictions of structure, melting point and superheating/undercooling degrees were compared with the experiments or theoretical calculations. Then, two of them, MKBA and MDSL, were proven suitable for the study of the solid-liquid transition of Al while the residuals were unqualified. However, potential MKBA is more accurate to predict the structures of solid and liquid, while MDSL works a little better in the thermodynamic and dynamic predictions of solid-liquid transitions.

Biome changes in Asia since the mid-Holocene - an analysis of different transient Earth system model simulations

NASA Astrophysics Data System (ADS)

Dallmeyer, Anne; Claussen, Martin; Ni, Jian; Cao, Xianyong; Wang, Yongbo; Fischer, Nils; Pfeiffer, Madlene; Jin, Liya; Khon, Vyacheslav; Wagner, Sebastian; Haberkorn, Kerstin; Herzschuh, Ulrike

2017-02-01

The large variety of atmospheric circulation systems affecting the eastern Asian climate is reflected by the complex Asian vegetation distribution. Particularly in the transition zones of these circulation systems, vegetation is supposed to be very sensitive to climate change. Since proxy records are scarce, hitherto a mechanistic understanding of the past spatio-temporal climate-vegetation relationship is lacking. To assess the Holocene vegetation change and to obtain an ensemble of potential mid-Holocene biome distributions for eastern Asia, we forced the diagnostic biome model BIOME4 with climate anomalies of different transient Holocene climate simulations performed in coupled atmosphere-ocean(-vegetation) models. The simulated biome changes are compared with pollen-based biome records for different key regions.In all simulations, substantial biome shifts during the last 6000 years are confined to the high northern latitudes and the monsoon-westerly wind transition zone, but the temporal evolution and amplitude of change strongly depend on the climate forcing. Large parts of the southern tundra are replaced by taiga during the mid-Holocene due to a warmer growing season and the boreal treeline in northern Asia is shifted northward by approx. 4° in the ensemble mean, ranging from 1.5 to 6° in the individual simulations, respectively. This simulated treeline shift is in agreement with pollen-based reconstructions from northern Siberia. The desert fraction in the transition zone is reduced by 21 % during the mid-Holocene compared to pre-industrial due to enhanced precipitation. The desert-steppe margin is shifted westward by 5° (1-9° in the individual simulations). The forest biomes are expanded north-westward by 2°, ranging from 0 to 4° in the single simulations. These results corroborate pollen-based reconstructions indicating an extended forest area in north-central China during the mid-Holocene. According to the model, the forest-to-non-forest and steppe-to-desert changes in the climate transition zones are spatially not uniform and not linear since the mid-Holocene.

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

Parlinski, K.; Hashi, Y.; Tsunekawa, S.

A model of lanthanum orthoniobate which possesses a ferroelastic tetragonal-monoclinic phase transition is proposed. It contains only one particle per unit cell, but it is constructed consistently with symmetry changes at the phase transition. The model parameters are chosen to reproduce the bare soft mode, degree of deformation of the tetragonal unit cell to monoclinic one, and the phase transition temperature. The ferroelastic system with free boundary conditions was simulated by the molecular dynamics technique, and the second order phase transition was reproduced. The studied annealing process shows formation of the stripe lenticular domain pattern, which has been interrupted bymore » appearance of a temporary band of perpendicularly oriented lenticular domains. The maps contain W{sup {prime}}-type domain walls whose orientations are fixed only by interplay of potential parameters and not by symmetry elements. The simulated domain pattern has the same features as those observed by transmission electron microscopy. {copyright} {ital 1997 Materials Research Society.}« less

Statistical mechanics of protein structural transitions: Insights from the island model

PubMed Central

Kobayashi, Yukio

2016-01-01

The so-called island model of protein structural transition holds that hydrophobic interactions are the key to both the folding and function of proteins. Herein, the genesis and statistical mechanical basis of the island model of transitions are reviewed, by presenting the results of simulations of such transitions. Elucidating the physicochemical mechanism of protein structural formation is the foundation for understanding the hierarchical structure of life at the microscopic level. Based on the results obtained to date using the island model, remaining problems and future work in the field of protein structures are discussed, referencing Professor Saitô’s views on the hierarchic structure of science. PMID:28409078

Towards a Sufficient Theory of Transition in Cognitive Development.

ERIC Educational Resources Information Center

Wallace, J. G.

The work reported aims at the construction of a sufficient theory of transition in cognitive development. The method of theory construction employed is computer simulation of cognitive process. The core of the model of transition presented comprises self-modification processes that, as a result of continuously monitoring an exhaustive record of…

Modeling and Simulating Passenger Behavior for a Station Closure in a Rail Transit Network

PubMed Central

Yin, Haodong; Han, Baoming; Li, Dewei; Wu, Jianjun; Sun, Huijun

2016-01-01

A station closure is an abnormal operational situation in which the entrances or exits of a rail transit station have to be closed for some time due to an unexpected incident. A novel approach is developed to estimate the impacts of the alternative station closure scenarios on both passenger behavioral choices at the individual level and passenger demand at the disaggregate level in a rail transit network. Therefore, the contributions of this study are two-fold: (1) A basic passenger behavior optimization model is mathematically constructed based on 0–1 integer programming to describe passengers’ responses to alternative origin station closure scenarios and destination station closure scenarios; this model also considers the availability of multi-mode transportation and the uncertain duration of the station closure; (2) An integrated solution algorithm based on the passenger simulation is developed to solve the proposed model and to estimate the effects of a station closure on passenger demand in a rail transit network. Furthermore, 13 groups of numerical experiments based on the Beijing rail transit network are performed as case studies with 2,074,267 records of smart card data. The comparisons of the model outputs and the manual survey show that the accuracy of our proposed behavior optimization model is approximately 80%. The results also show that our model can be used to capture the passenger behavior and to quantitatively estimate the effects of alternative closure scenarios on passenger flow demand for the rail transit network. Moreover, the closure duration and its overestimation greatly influence the individual behavioral choices of the affected passengers and the passenger demand. Furthermore, if the rail transit operator can more accurately estimate the closure duration (namely, as g approaches 1), the impact of the closure can be somewhat mitigated. PMID:27935963

Modeling and Simulating Passenger Behavior for a Station Closure in a Rail Transit Network.

PubMed

Yin, Haodong; Han, Baoming; Li, Dewei; Wu, Jianjun; Sun, Huijun

2016-01-01

A station closure is an abnormal operational situation in which the entrances or exits of a rail transit station have to be closed for some time due to an unexpected incident. A novel approach is developed to estimate the impacts of the alternative station closure scenarios on both passenger behavioral choices at the individual level and passenger demand at the disaggregate level in a rail transit network. Therefore, the contributions of this study are two-fold: (1) A basic passenger behavior optimization model is mathematically constructed based on 0-1 integer programming to describe passengers' responses to alternative origin station closure scenarios and destination station closure scenarios; this model also considers the availability of multi-mode transportation and the uncertain duration of the station closure; (2) An integrated solution algorithm based on the passenger simulation is developed to solve the proposed model and to estimate the effects of a station closure on passenger demand in a rail transit network. Furthermore, 13 groups of numerical experiments based on the Beijing rail transit network are performed as case studies with 2,074,267 records of smart card data. The comparisons of the model outputs and the manual survey show that the accuracy of our proposed behavior optimization model is approximately 80%. The results also show that our model can be used to capture the passenger behavior and to quantitatively estimate the effects of alternative closure scenarios on passenger flow demand for the rail transit network. Moreover, the closure duration and its overestimation greatly influence the individual behavioral choices of the affected passengers and the passenger demand. Furthermore, if the rail transit operator can more accurately estimate the closure duration (namely, as g approaches 1), the impact of the closure can be somewhat mitigated.

Validation of a RANS transition model using a high-order weighted compact nonlinear scheme

NASA Astrophysics Data System (ADS)

Tu, GuoHua; Deng, XiaoGang; Mao, MeiLiang

2013-04-01

A modified transition model is given based on the shear stress transport (SST) turbulence model and an intermittency transport equation. The energy gradient term in the original model is replaced by flow strain rate to saving computational costs. The model employs local variables only, and then it can be conveniently implemented in modern computational fluid dynamics codes. The fifth-order weighted compact nonlinear scheme and the fourth-order staggered scheme are applied to discrete the governing equations for the purpose of minimizing discretization errors, so as to mitigate the confusion between numerical errors and transition model errors. The high-order package is compared with a second-order TVD method on simulating the transitional flow of a flat plate. Numerical results indicate that the high-order package give better grid convergence property than that of the second-order method. Validation of the transition model is performed for transitional flows ranging from low speed to hypersonic speed.

An Exercise Health Simulation Method Based on Integrated Human Thermophysiological Model

PubMed Central

Chen, Xiaohui; Yu, Liang; Yang, Kaixing

2017-01-01

Research of healthy exercise has garnered a keen research for the past few years. It is known that participation in a regular exercise program can help improve various aspects of cardiovascular function and reduce the risk of suffering from illness. But some exercise accidents like dehydration, exertional heatstroke, and even sudden death need to be brought to attention. If these exercise accidents can be analyzed and predicted before they happened, it will be beneficial to alleviate or avoid disease or mortality. To achieve this objective, an exercise health simulation approach is proposed, in which an integrated human thermophysiological model consisting of human thermal regulation model and a nonlinear heart rate regulation model is reported. The human thermoregulatory mechanism as well as the heart rate response mechanism during exercise can be simulated. On the basis of the simulated physiological indicators, a fuzzy finite state machine is constructed to obtain the possible health transition sequence and predict the exercise health status. The experiment results show that our integrated exercise thermophysiological model can numerically simulate the thermal and physiological processes of the human body during exercise and the predicted exercise health transition sequence from finite state machine can be used in healthcare. PMID:28702074

Twist-writhe partitioning in a coarse-grained DNA minicircle model

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Avşaroǧlu, Barış; Kabakçıoǧlu, Alkan

2010-04-01

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.

MHD Simulation for Investigating the Dynamic State Transition Responsible for a Solar Eruption in Active Region 12158

NASA Astrophysics Data System (ADS)

Lee, Hwanhee; Magara, Tetsuya

2018-06-01

We present a magnetohydrodynamic model of solar eruption based on the dynamic state transition from the quasi-static state to the eruptive state of an active region (AR) magnetic field. For the quasi-static state before an eruption, we consider the existence of a slow solar wind originating from an AR, which may continuously make the AR magnetic field deviate from mechanical equilibrium. In this model, we perform a three-dimensional magnetohydrodynamic simulation of AR 12158 producing a coronal mass ejection, where the initial magnetic structure of the simulation is given by a nonlinear force-free field derived from an observed photospheric vector magnetic field. We then apply a pressure-driven outflow to the upper part of the magnetic structure to achieve a quasi-static pre-eruptive state. The simulation shows that the eruptive process observed in this AR may be caused by the dynamic state transition of an AR magnetic field, which is essentially different from the destabilization of a static magnetic field. The dynamic state transition is determined from the shape evolution of the magnetic field line according to the κH-mechanism. This work demonstrates how the mechanism works to produce a solar eruption in the dynamic solar corona governed by the gravitational field and the continuous outflows of solar wind.

The remarkable ability of turbulence model equations to describe transition

NASA Technical Reports Server (NTRS)

Wilcox, David C.

1992-01-01

This paper demonstrates how well the k-omega turbulence model describes the nonlinear growth of flow instabilities from laminar flow into the turbulent flow regime. Viscous modifications are proposed for the k-omega model that yield close agreement with measurements and with Direct Numerical Simulation results for channel and pipe flow. These modifications permit prediction of subtle sublayer details such as maximum dissipation at the surface, k approximately y(exp 2) as y approaches 0, and the sharp peak value of k near the surface. With two transition specific closure coefficients, the model equations accurately predict transition for an incompressible flat-plate boundary layer. The analysis also shows why the k-epsilon model is so difficult to use for predicting transition.

Analysis of the Assignment Scheduling Capability for Unmanned Aerial Vehicles (ASC-U) Simulation Tool

DTIC Science & Technology

2006-06-01

dynamic programming approach known as a “rolling horizon” approach. This method accounts for state transitions within the simulation rather than modeling ... model is based on the framework developed for Dynamic Allocation of Fires and Sensors used to evaluate factors associated with networking assets in the...of UAVs required by all types of maneuver and support brigades. (Witsken, 2004) The Modeling , Virtual Environments, and Simulations Institute

Genetic Algorithms and Nucleation in VIH-AIDS transition.

NASA Astrophysics Data System (ADS)

Barranon, Armando

2003-03-01

VIH to AIDS transition has been modeled via a genetic algorithm that uses boom-boom principle and where population evolution is simulated with a cellular automaton based on SIR model. VIH to AIDS transition is signed by nucleation of infected cells and low probability of infection are obtained for different mutation rates in agreement with clinical results. A power law is obtained with a critical exponent close to the critical exponent of cubic, spherical percolation, colossal magnetic resonance, Ising Model and liquid-gas phase transition in heavy ion collisions. Computations were carried out at UAM-A Supercomputing Lab and author acknowledges financial support from Division of CBI at UAM-A.

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

NASA Astrophysics Data System (ADS)

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

2007-03-01

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

Phase transition in conservative diffusive contact processes

NASA Astrophysics Data System (ADS)

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

2004-10-01

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

Three-dimensional characterisation and simulation of deformation and damage during Taylor impact in PTFE

NASA Astrophysics Data System (ADS)

Resnyansky, A. D.; McDonald, S. A.; Withers, P. J.; Bourne, N. K.; Millett, J. C. F.; Brown, E. N.; Rae, P. J.

2014-05-01

The current work presents Taylor impact experiments interrogating the effect of dynamic, high-pressure loading on polytetrafluoroethylene (PTFE). In particular, X-ray microtomography has been used to characterise the damage imparted to cylindrical samples due to impact at different velocities. Distinct regions of deformation are present and controlled by fracture within the polymer, with the extent of the deformed region and increasing propagation of fractures from the impact face showing a clear trend with increasing impact velocity. A two-phase rate sensitive strength model is implemented in the CTH hydrocode and used for simulation of the problem. The high-pressure phase transition of PTFE into Phase III within the crystalline domains from the polymer at normal conditions is managed by suitable phase transition kinetics within the model. The experimental observations are discussed with respect to the multi-phase model hydrocode predictions of the shock response from Taylor impact simulations. The damage and its progress are shown to correlate well with the onset of the phase transition and its evolution following the impact velocity increase.

Markov state models from short non-equilibrium simulations—Analysis and correction of estimation bias

NASA Astrophysics Data System (ADS)

Nüske, Feliks; Wu, Hao; Prinz, Jan-Hendrik; Wehmeyer, Christoph; Clementi, Cecilia; Noé, Frank

2017-03-01

Many state-of-the-art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are integrated. In this context, Markov state models (MSMs) are extremely popular because they can be used to compute stationary quantities and long-time kinetics from ensembles of short simulations, provided that these short simulations are in "local equilibrium" within the MSM states. However, over the last 15 years since the inception of MSMs, it has been controversially discussed and not yet been answered how deviations from local equilibrium can be detected, whether these deviations induce a practical bias in MSM estimation, and how to correct for them. In this paper, we address these issues: We systematically analyze the estimation of MSMs from short non-equilibrium simulations, and we provide an expression for the error between unbiased transition probabilities and the expected estimate from many short simulations. We show that the unbiased MSM estimate can be obtained even from relatively short non-equilibrium simulations in the limit of long lag times and good discretization. Further, we exploit observable operator model (OOM) theory to derive an unbiased estimator for the MSM transition matrix that corrects for the effect of starting out of equilibrium, even when short lag times are used. Finally, we show how the OOM framework can be used to estimate the exact eigenvalues or relaxation time scales of the system without estimating an MSM transition matrix, which allows us to practically assess the discretization quality of the MSM. Applications to model systems and molecular dynamics simulation data of alanine dipeptide are included for illustration. The improved MSM estimator is implemented in PyEMMA of version 2.3.

Flywheel Propulsion Simulation

DOT National Transportation Integrated Search

1977-05-01

This report develops and describes the analytical models and digital computer simulations that can be used for the evaluation of flywheel-electric propulsion systems employed with urban transit vehicles operating over specified routes and with predet...

Global two-fluid turbulence simulations of L-H transitions and edge localized mode dynamics in the COMPASS-D tokamak

NASA Astrophysics Data System (ADS)

Thyagaraja, A.; Valovič, M.; Knight, P. J.

2010-04-01

It is shown that the transition from L-mode to H-mode regimes in tokamaks can be reproduced using a two-fluid, fully electromagnetic, plasma model when a suitable particle sink is added at the edge. Such a model is implemented in the CUTIE code [A. Thyagaraja et al., Eur. J. Mech. B/Fluids 23, 475 (2004)] and is illustrated on plasma parameters that mimic those in the COMPASS-D tokamak with electron cyclotron resonance heating [Fielding et al., Plasma Phys. Contr. Fusion 42, A191 (2000)]. In particular, it is shown that holding the heating power, current, and magnetic field constant and increasing the fuelling rate to raise the plasma density leads spontaneously to the formation of an edge transport barrier (ETB) which occurs going from low to higher density experimentally. In the following quiescent period in which the stored energy of the plasma rises linearly with time, a dynamical transition occurs in the simulation with the appearance of features resembling strong edge localized modes. The simulation qualitatively reproduces many features observed in the experiment. Its relative robustness suggests that some, at least of the observed characteristics of ETBs and L-H transitions, can be captured in the global electromagnetic turbulence model.

Galactic wind X-ray heating of the intergalactic medium during the Epoch of Reionization

NASA Astrophysics Data System (ADS)

Meiksin, Avery; Khochfar, Sadegh; Paardekooper, Jan-Pieter; Dalla Vecchia, Claudio; Kohn, Saul

2017-11-01

The diffuse soft X-ray emissivity from galactic winds is computed during the Epoch of Reionization (EoR). We consider two analytic models, a pressure-driven wind and a superbubble model, and a 3D cosmological simulation including gas dynamics from the First Billion Years (FiBY) project. The analytic models are normalized to match the diffuse X-ray emissivity of star-forming galaxies in the nearby Universe. The cosmological simulation uses physically motivated star formation and wind prescriptions, and includes radiative transfer corrections. The models and the simulation all are found to produce sufficient heating of the intergalactic medium to be detectable by current and planned radio facilities through 21 cm measurements during the EoR. While the analytic models predict a 21 cm emission signal relative to the cosmic microwave backgroundsets in by ztrans ≃ 8-10, the predicted signal in the FiBY simulation remains in absorption until reionization completes. The 21 cm absorption differential brightness temperature reaches a minimum of ΔT ≃ -130 to -200 mK, depending on model. Allowing for additional heat from high-mass X-ray binaries pushes the transition to emission to ztrans ≃ 10-12, with shallower absorption signatures having a minimum of ΔT ≃ -110 to -140 mK. The 21 cm signal may be a means of distinguishing between the wind models, with the superbubble model favouring earlier reheating. While an early transition to emission may indicate X-ray binaries dominate the reheating, a transition to emission as early as ztrans > 12 would suggest the presence of additional heat sources.

Network traffic behaviour near phase transition point

NASA Astrophysics Data System (ADS)

Lawniczak, A. T.; Tang, X.

2006-03-01

We explore packet traffic dynamics in a data network model near phase transition point from free flow to congestion. The model of data network is an abstraction of the Network Layer of the OSI (Open Systems Interconnect) Reference Model of packet switching networks. The Network Layer is responsible for routing packets across the network from their sources to their destinations and for control of congestion in data networks. Using the model we investigate spatio-temporal packets traffic dynamics near the phase transition point for various network connection topologies, and static and adaptive routing algorithms. We present selected simulation results and analyze them.

Application of stochastic weighted algorithms to a multidimensional silica particle model

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

Menz, William J.; Patterson, Robert I.A.; Wagner, Wolfgang

2013-09-01

Highlights: •Stochastic weighted algorithms (SWAs) are developed for a detailed silica model. •An implementation of SWAs with the transition kernel is presented. •The SWAs’ solutions converge to the direct simulation algorithm’s (DSA) solution. •The efficiency of SWAs is evaluated for this multidimensional particle model. •It is shown that SWAs can be used for coagulation problems in industrial systems. -- Abstract: This paper presents a detailed study of the numerical behaviour of stochastic weighted algorithms (SWAs) using the transition regime coagulation kernel and a multidimensional silica particle model. The implementation in the SWAs of the transition regime coagulation kernel and associatedmore » majorant rates is described. The silica particle model of Shekar et al. [S. Shekar, A.J. Smith, W.J. Menz, M. Sander, M. Kraft, A multidimensional population balance model to describe the aerosol synthesis of silica nanoparticles, Journal of Aerosol Science 44 (2012) 83–98] was used in conjunction with this coagulation kernel to study the convergence properties of SWAs with a multidimensional particle model. High precision solutions were calculated with two SWAs and also with the established direct simulation algorithm. These solutions, which were generated using large number of computational particles, showed close agreement. It was thus demonstrated that SWAs can be successfully used with complex coagulation kernels and high dimensional particle models to simulate real-world systems.« less

Aerodynamic heating effects on wall-modeled large-eddy simulations of high-speed flows

NASA Astrophysics Data System (ADS)

Yang, Xiang; Urzay, Javier; Moin, Parviz

2017-11-01

Aerospace vehicles flying at high speeds are subject to increased wall-heating rates because of strong aerodynamic heating in the near-wall region. In wall-modeled large-eddy simulations (WMLES), this near-wall region is typically not resolved by the computational grid. As a result, the effects of aerodynamic heating need to be modeled using an LES wall model. In this investigation, WMLES of transitional and fully turbulent high-speed flows are conducted to address this issue. In particular, an equilibrium wall model is employed in high-speed turbulent Couette flows subject to different combinations of thermal boundary conditions and grid sizes, and in transitional hypersonic boundary layers interacting with incident shock waves. Specifically, the WMLES of the Couette-flow configuration demonstrate that the shear-stress and heat-flux predictions made by the wall model show only a small sensitivity to the grid resolution even in the most adverse case where aerodynamic heating prevails near the wall and generates a sharp temperature peak there. In the WMLES of shock-induced transition in boundary layers, the wall model is tested against DNS and experiments, and it is shown to capture the post-transition aerodynamic heating and the overall heat transfer rate around the shock-impingement zone. This work is supported by AFOSR.

Exploring first-order phase transitions with population annealing

NASA Astrophysics Data System (ADS)

Barash, Lev Yu.; Weigel, Martin; Shchur, Lev N.; Janke, Wolfhard

2017-03-01

Population annealing is a hybrid of sequential and Markov chain Monte Carlo methods geared towards the efficient parallel simulation of systems with complex free-energy landscapes. Systems with first-order phase transitions are among the problems in computational physics that are difficult to tackle with standard methods such as local-update simulations in the canonical ensemble, for example with the Metropolis algorithm. It is hence interesting to see whether such transitions can be more easily studied using population annealing. We report here our preliminary observations from population annealing runs for the two-dimensional Potts model with q > 4, where it undergoes a first-order transition.

Using Hand Grip Force as a Correlate of Longitudinal Acceleration Comfort for Rapid Transit Trains

PubMed Central

Guo, Beiyuan; Gan, Weide; Fang, Weining

2015-01-01

Longitudinal acceleration comfort is one of the essential metrics used to evaluate the ride comfort of train. The aim of this study was to investigate the effectiveness of using hand grip force as a correlate of longitudinal acceleration comfort of rapid transit trains. In the paper, a motion simulation system was set up and a two-stage experiment was designed to investigate the role of the grip force on the longitudinal comfort of rapid transit trains. The results of the experiment show that the incremental grip force was linearly correlated with the longitudinal acceleration value, while the incremental grip force had no correlation with the direction of the longitudinal acceleration vector. The results also show that the effects of incremental grip force and acceleration duration on the longitudinal comfort of rapid transit trains were significant. Based on multiple regression analysis, a step function model was established to predict the longitudinal comfort of rapid transit trains using the incremental grip force and the acceleration duration. The feasibility and practicably of the model was verified by a field test. Furthermore, a comparative analysis shows that the motion simulation system and the grip force based model were valid to support the laboratory studies on the longitudinal comfort of rapid transit trains. PMID:26147730

Machine learning in sentiment reconstruction of the simulated stock market

NASA Astrophysics Data System (ADS)

Goykhman, Mikhail; Teimouri, Ali

2018-02-01

In this paper we continue the study of the simulated stock market framework defined by the driving sentiment processes. We focus on the market environment driven by the buy/sell trading sentiment process of the Markov chain type. We apply the methodology of the Hidden Markov Models and the Recurrent Neural Networks to reconstruct the transition probabilities matrix of the Markov sentiment process and recover the underlying sentiment states from the observed stock price behavior. We demonstrate that the Hidden Markov Model can successfully recover the transition probabilities matrix for the hidden sentiment process of the Markov Chain type. We also demonstrate that the Recurrent Neural Network can successfully recover the hidden sentiment states from the observed simulated stock price time series.

Topological phase transition in the two-dimensional anisotropic Heisenberg model: A study using the Replica Exchange Wang-Landau sampling

NASA Astrophysics Data System (ADS)

Figueiredo, T. P.; Rocha, J. C. S.; Costa, B. V.

2017-12-01

Although the topological Berezinskii-Kosterlitz-Thouless transition was for the first time described by 40 years ago, it is still a matter of discussion. It has been used to explain several experiments in the most diverse physical systems. In contrast with the ordinary continuous phase transitions the BKT-transition does not break any symmetry. However, in some contexts it can easily be confused with other continuous transitions, in general due to an insufficient data analysis. The two-dimensional XY (or sometimes called planar rotator) spin model is the fruit fly model describing the BKT transition. As demonstrated by Bramwell and Holdsworth (1993) the finite-size effects are more important in two-dimensions than in others due to the logarithmic system size dependence of the properties of the system. Closely related is the anisotropic two dimensional Heisenberg model (AH). Although they have the same Hamiltonian the spin variable in the former has only two degrees of freedom while the AH has three. Many works treat the AH model as undergoing a transition in the same universality class as the XY model. However, its characterization as being in the BKT class of universality deserve some investigation. This paper has two goals. First, we describe an analytical evidence showing that the AH model is in the BKT class of universality. Second, we make an extensive simulation, using the numerical Replica Exchange Wang-Landau method that corroborate our analytical calculations. From our simulation we obtain the BKT transition temperature as TBKT = 0 . 6980(10) by monitoring the susceptibility, the two point correlation function and the helicity modulus. We discuss the misuse of the fourth order Binder's cumulant to locate the transition temperature. The specific heat is shown to have a non-critical behavior as expected in the BKT transition. An analysis of the two point correlation function at low temperature, C(r) ∝r - η(T), shows that the exponent, η, is consistent with an exponential law η =η0eζT, with η0 = 0 . 025(5) and ζ = 3 . 25(10) in close agreement with the results of Cardy (1981) for the p-state clock model.

Phase transitions in a multistate majority-vote model on complex networks

NASA Astrophysics Data System (ADS)

Chen, Hanshuang; Li, Guofeng

2018-06-01

We generalize the original majority-vote (MV) model from two states to arbitrary p states and study the order-disorder phase transitions in such a p -state MV model on complex networks. By extensive Monte Carlo simulations and a mean-field theory, we show that for p ≥3 the order of phase transition is essentially different from a continuous second-order phase transition in the original two-state MV model. Instead, for p ≥3 the model displays a discontinuous first-order phase transition, which is manifested by the appearance of the hysteresis phenomenon near the phase transition. Within the hysteresis loop, the ordered phase and disordered phase are coexisting, and rare flips between the two phases can be observed due to the finite-size fluctuation. Moreover, we investigate the type of phase transition under a slightly modified dynamics [Melo et al., J. Stat. Mech. (2010) P11032, 10.1088/1742-5468/2010/11/P11032]. We find that the order of phase transition in the three-state MV model depends on the degree heterogeneity of networks. For p ≥4 , both dynamics produce the first-order phase transitions.

Folding domain B of protein A on a dynamically partitioned free energy landscape.

PubMed

Nelson, Erik D; Grishin, Nick V

2008-02-05

The B domain of staphylococcal protein A (BdpA) is a small helical protein that has been studied intensively in kinetics experiments and detailed computer simulations that include explicit water. The simulations indicate that BdpA needs to reorganize in crossing the transition barrier to facilitate folding its C-terminal helix (H3) onto the nucleus formed from helices H1 and H2. This process suggests frustration between two partially ordered forms of the protein, but recent varphi value measurements indicate that the transition structure is relatively constant over a broad range of temperatures. Here we develop a simplistic model to investigate the folding transition in which properties of the free energy landscape can be quantitatively compared with experimental data. The model is a continuation of the Muñoz-Eaton model to include the intermittency of contacts between structured parts of the protein, and the results compare variations in the landscape with denaturant and temperature to varphi value measurements and chevron plots of the kinetic rates. The topography of the model landscape (in particular, the feature of frustration) is consistent with detailed simulations even though variations in the varphi values are close to measured values. The transition barrier is smaller than indicated by the chevron data, but it agrees in order of magnitude with a similar alpha-carbon type of model. Discrepancies with the chevron plots are investigated from the point of view of solvent effects, and an approach is suggested to account for solvent participation in the model.

Modeling forest dynamics along climate gradients in Bolivia

NASA Astrophysics Data System (ADS)

Seiler, C.; Hutjes, R. W. A.; Kruijt, B.; Quispe, J.; Añez, S.; Arora, V. K.; Melton, J. R.; Hickler, T.; Kabat, P.

2014-05-01

Dynamic vegetation models have been used to assess the resilience of tropical forests to climate change, but the global application of these modeling experiments often misrepresents carbon dynamics at a regional level, limiting the validity of future projections. Here a dynamic vegetation model (Lund Potsdam Jena General Ecosystem Simulator) was adapted to simulate present-day potential vegetation as a baseline for climate change impact assessments in the evergreen and deciduous forests of Bolivia. Results were compared to biomass measurements (819 plots) and remote sensing data. Using regional parameter values for allometric relations, specific leaf area, wood density, and disturbance interval, a realistic transition from the evergreen Amazon to the deciduous dry forest was simulated. This transition coincided with threshold values for precipitation (1400 mm yr-1) and water deficit (i.e., potential evapotranspiration minus precipitation) (-830 mm yr-1), beyond which leaf abscission became a competitive advantage. Significant correlations were found between modeled and observed values of seasonal leaf abscission (R2 = 0.6, p <0.001) and vegetation carbon (R2 = 0.31, p <0.01). Modeled Gross Primary Productivity (GPP) and remotely sensed normalized difference vegetation index showed that dry forests were more sensitive to rainfall anomalies than wet forests. GPP was positively correlated to the El Niño-Southern Oscillation index in the Amazon and negatively correlated to consecutive dry days. Decreasing rainfall trends were simulated to reduce GPP in the Amazon. The current model setup provides a baseline for assessing the potential impacts of climate change in the transition zone from wet to dry tropical forests in Bolivia.

Numerical simulation of dune-flat bed transition and stage‐discharge relationship with hysteresis effect

USGS Publications Warehouse

Shimizu, Yasuyuki; Giri, Sanjay; Yamaguchi, Satomi; Nelson, Jonathan M.

2009-01-01

This work presents recent advances on morphodynamic modeling of bed forms under unsteady discharge. This paper includes further development of a morphodynamic model proposed earlier by Giri and Shimizu (2006a). This model reproduces the temporal development of river dunes and accurately replicates the physical properties associated with bed form evolution. Model results appear to provide accurate predictions of bed form geometry and form drag over bed forms for arbitrary steady flows. However, accurate predictions of temporal changes of form drag are key to the prediction of stage‐discharge relation during flood events. Herein, the model capability is extended to replicate the dune–flat bed transition, and in turn, the variation of form drag produced by the temporal growth or decay of bed forms under unsteady flow conditions. Some numerical experiments are performed to analyze hysteresis of the stage‐discharge relationship caused by the transition between dune and flat bed regimes during rising and falling stages of varying flows. The numerical model successfully simulates dune–flat bed transition and the associated hysteresis of the stage‐discharge relationship; this is in good agreement with physical observations but has been treated in the past only using empirical methods. A hypothetical relationship for a sediment parameter (the mean step length) is proposed to a first level of approximation that enables reproduction of the dune–flat bed transition. The proposed numerical model demonstrates its ability to address an important practical problem associated with bed form evolution and flow resistance in varying flows.

A Global Model Simulation of Aerosol Effects of Surface Radiation Budget- Toward Understanding of the "Dimming to Brightening" Transition

NASA Technical Reports Server (NTRS)

Chin, Mian; Diehl, Thomas; Bian, Huisheng; Yu, Hongbin

2008-01-01

We present a global model study on the role aerosols play in the change of solar radiation at Earth's surface that transitioned from a decreasing (dimming) trend to an increasing (brightening) trend. Our primary objective is to understand the relationship between the long-term trends of aerosol emission, atmospheric burden, and surface solar radiation. More specifically, we use the recently compiled comprehensive global emission datasets of aerosols and precursors from fuel combustion, biomass burning, volcanic eruptions and other sources from 1980 to 2006 to simulate long-term variations of aerosol distributions and optical properties, and then calculate the multi-decadal changes of short-wave radiative fluxes at the surface and at the top of the atmosphere by coupling the GOCART model simulated aerosols with the Goddard radiative transfer model. The model results are compared with long-term observational records from ground-based networks and satellite data. We will address the following critical questions: To what extent can the observed surface solar radiation trends, known as the transition from dimming to brightening, be explained by the changes of anthropogenic and natural aerosol loading on global and regional scales? What are the relative contributions of local emission and long-range transport to the surface radiation budget and how do these contributions change with time?

Free Energy Minimization by Simulated Annealing with Applications to Lithospheric Slabs and Mantle Plumes

NASA Astrophysics Data System (ADS)

Bina, C. R.

An optimization algorithm based upon the method of simulated annealing is of utility in calculating equilibrium phase assemblages as functions of pressure, temperature, and chemical composi tion. Operating by analogy to the statistical mechanics of the chemical system, it is applicable both to problems of strict chemical equilibrium and to problems involving metastability. The method reproduces known phase diagrams and illustrates the expected thermal deflection of phase transitions in thermal models of subducting lithospheric slabs and buoyant mantle plumes. It reveals temperature-induced changes in phase transition sharpness and the stability of Fe-rich γ phase within an α+γ field in cold slab thermal models, and it suggests that transitions such as the possible breakdown of silicate perovskite to mixed oxides can amplify velocity anomalies.

Numerical modeling of laboratory-scale surface-to-crown fire transition

NASA Astrophysics Data System (ADS)

Castle, Drew Clayton

Understanding the conditions leading to the transition of fire spread from a surface fuel to an elevated (crown) fuel is critical to effective fire risk assessment and management. Surface fires that successfully transition to crown fires can be very difficult to suppress, potentially leading to damages in the natural and built environments. This is relevant to chaparral shrub lands which are common throughout parts of the Southwest U.S. and represent a significant part of the wildland urban interface. The ability of the Wildland-Urban Interface Fire Dynamic Simulator (WFDS) to model surface-to-crown fire transition was evaluated through comparison to laboratory experiments. The WFDS model is being developed by the U.S. Forest Service (USFS) and the National Institute of Standards and Technology. The experiments were conducted at the USFS Forest Fire Laboratory in Riverside, California. The experiments measured the ignition of chamise (Adenostoma fasciculatum) crown fuel held above a surface fire spreading through excelsior fuel. Cases with different crown fuel bulk densities, crown fuel base heights, and imposed wind speeds were considered. Cold-flow simulations yielded wind speed profiles that closely matched the experimental measurements. Next, fire simulations with only the surface fuel were conducted to verify the rate of spread while factors such as substrate properties were varied. Finally, simulations with both a surface fuel and a crown fuel were completed. Examination of specific surface fire characteristics (rate of spread, flame angle, etc.) and the corresponding experimental surface fire behavior provided a basis for comparison of the factors most responsible for transition from a surface fire to the raised fuel ignition. The rate of spread was determined by tracking the flame in the Smokeview animations using a tool developed for tracking an actual flame in a video. WFDS simulations produced results in both surface fire spread and raised fuel bed ignition which closely matched the trends reported in the laboratory experiments.

Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Hao, Ming-Hong; Scheraga, Harold A.

1995-01-01

A comparative study of protein folding with an analytical theory and computer simulations, respectively, is reported. The theory is based on an improved mean-field formalism which, in addition to the usual mean-field approximations, takes into account the distributions of energies in the subsets of conformational states. Sequence-specific properties of proteins are parametrized in the theory by two sets of variables, one for the energetics of mean-field interactions and one for the distribution of energies. Simulations are carried out on model polypeptides with different sequences, with different chain lengths, and with different interaction potentials, ranging from strong biases towards certain local chain states (bond angles and torsional angles) to complete absence of local conformational preferences. Theoretical analysis of the simulation results for the model polypeptides reveals three different types of behavior in the folding transition from the statistical coiled state to the compact globular state; these include a cooperative two-state transition, a continuous folding, and a glasslike transition. It is found that, with the fitted theoretical parameters which are specific for each polypeptide under a different potential, the mean-field theory can describe the thermodynamic properties and folding behavior of the different polypeptides accurately. By comparing the theoretical descriptions with simulation results, we verify the basic assumptions of the theory and, thereby, obtain new insights about the folding transitions of proteins. It is found that the cooperativity of the first-order folding transition of the model polypeptides is determined mainly by long-range interactions, in particular the dipolar orientation; the local interactions (e.g., bond-angle and torsion-angle potentials) have only marginal effect on the cooperative characteristic of the folding, but have a large impact on the difference in energy between the folded lowest-energy structure and the unfolded conformations of a protein.

Initial Conceptualization and Application of the Alaska Thermokarst Model

NASA Astrophysics Data System (ADS)

Bolton, W. R.; Lara, M. J.; Genet, H.; Romanovsky, V. E.; McGuire, A. D.

2015-12-01

Thermokarst topography forms whenever ice-rich permafrost thaws and the ground subsides due to the volume loss when ground ice transitions to water. The Alaska Thermokarst Model (ATM) is a large-scale, state-and-transition model designed to simulate transitions between landscape units affected by thermokarst disturbance. The ATM uses a frame-based methodology to track transitions and proportion of cohorts within a 1-km2 grid cell. In the arctic tundra environment, the ATM tracks thermokarst-related transitions among wetland tundra, graminoid tundra, shrub tundra, and thermokarst lakes. In the boreal forest environment, the ATM tracks transitions among forested permafrost plateau, thermokarst lakes, collapse scar fens and bogs. The transition from one cohort to another due to thermokarst processes can take place if thaw reaches ice-rich ground layers either due to pulse disturbance (i.e. large precipitation event or fires), or due to gradual active layer deepening that eventually results in penetration of the protective layer. The protective layer buffers the ice-rich soils from the land surface and is critical to determine how susceptible an area is to thermokarst degradation. The rate of terrain transition in our model is determined by a set of rules that are based upon the ice-content of the soil, the drainage efficiency (or the ability of the landscape to store or transport water), the cumulative probability of thermokarst initiation, distance from rivers, lake dynamics (increasing, decreasing, or stable), and other factors. Tundra types are allowed to transition from one type to another (for example, wetland tundra to graminoid tundra) under favorable climatic conditions. In this study, we present our conceptualization and initial simulation results from in the arctic (the Barrow Peninsula) and boreal (the Tanana Flats) regions of Alaska.

Measuring stellar granulation during planet transits

NASA Astrophysics Data System (ADS)

Chiavassa, A.; Caldas, A.; Selsis, F.; Leconte, J.; Von Paris, P.; Bordé, P.; Magic, Z.; Collet, R.; Asplund, M.

2017-01-01

Context. Stellar activity and convection-related surface structures might cause bias in planet detection and characterization that use these transits. Surface convection simulations help to quantify the granulation signal. Aims: We used realistic three-dimensional (3D) radiative hydrodynamical (RHD) simulations from the Stagger grid and synthetic images computed with the radiative transfer code Optim3D to model the transits of three prototype planets: a hot Jupiter, a hot Neptune, and a terrestrial planet. Methods: We computed intensity maps from RHD simulations of the Sun and a K-dwarf star at different wavelength bands from optical to far-infrared that cover the range of several ground- and space-based telescopes which observe exoplanet transits. We modeled the transit using synthetic stellar-disk images obtained with a spherical-tile imaging method and emulated the temporal variation of the granulation intensity generating random images covering a granulation time-series of 13.3 h. We measured the contribution of the stellar granulation on the light curves during the planet transit. Results: We identified two types of granulation noise that act simultaneously during the planet transit: (I) the intrinsic change in the granulation pattern with timescale (e.g., 10 min for solar-type stars assumed in this work) is smaller than the usual planet transit ( hours as in our prototype cases); and (II) the fact that the transiting planet occults isolated regions of the photosphere that differ in local surface brightness as a result of convective-related surface structures. First, we showed that our modeling approach returns granulation timescale fluctuations that are comparable with what has been observed for the Sun. Then, our statistical approach shows that the granulation pattern of solar and K-dwarf-type stars have a non-negligible effect of the light curve depth during the transit, and, consequentially on the determination of the planet transit parameters such as the planet radius (up to 0.90% and 0.47% for terrestrial and gaseous planets, respectively). We also showed that larger (or smaller) orbital inclination angles with respect to values corresponding to transit at the stellar center display a shallower transit depth and longer ingress and egress times, but also granulation fluctuations that are correlated to the center-to-limb variation: they increase (or decrease) the value of the inclination, which amplifies the fluctuations. The granulation noise appears to be correlated among the different wavelength ranges either in the visible or in the infrared regions. Conclusions: The prospects for planet detection and characterization with transiting methods are excellent with access to large amounts of data for stars. The granulation has to be considered as an intrinsic uncertainty (as a result of stellar variability) on the precise measurements of exoplanet transits of planets. The full characterization of the granulation is essential for determining the degree of uncertainty on the planet parameters. In this context, the use of 3D RHD simulations is important to measure the convection-related fluctuations. This can be achieved by performing precise and continuous observations of stellar photometry and radial velocity, as we explained with RHD simulations, before, after, and during the transit periods.

A study of two subgrid-scale models and their effects on wake breakdown behind a wind turbine in uniform inflow

NASA Astrophysics Data System (ADS)

Martinez, Luis; Meneveau, Charles

2014-11-01

Large Eddy Simulations (LES) of the flow past a single wind turbine with uniform inflow have been performed. A goal of the simulations is to compare two turbulence subgrid-scale models and their effects in predicting the initial breakdown, transition and evolution of the wake behind the turbine. Prior works have often observed negligible sensitivities to subgrid-scale models. The flow is modeled using an in-house LES with pseudo-spectral discretization in horizontal planes and centered finite differencing in the vertical direction. Turbines are represented using the actuator line model. We compare the standard constant-coefficient Smagorinsky subgrid-scale model with the Lagrangian Scale Dependent Dynamic model (LSDM). The LSDM model predicts faster transition to turbulence in the wake, whereas the standard Smagorinsky model predicts significantly delayed transition. The specified Smagorinsky coefficient is larger than the dynamic one on average, increasing diffusion thus delaying transition. A second goal is to compare the resulting near-blade properties such as local aerodynamic forces from the LES with Blade Element Momentum Theory. Results will also be compared with those of the SOWFA package, the wind energy CFD framework from NREL. This work is supported by NSF (IGERT and IIA-1243482) and computations use XSEDE resources, and has benefitted from interactions with Dr. M. Churchfield of NREL.

Control of Tollmien-Schlichting instabilities by finite distributed wall actuation

NASA Astrophysics Data System (ADS)

Losse, Nikolas R.; King, Rudibert; Zengl, Marcus; Rist, Ulrich; Noack, Bernd R.

2011-06-01

Tollmien-Schlichting waves are one of the key mechanisms triggering the laminar-turbulent transition in a flat-plate boundary-layer flow. By damping these waves and thus delaying transition, skin friction drag can be significantly decreased. In this simulation study, a wall segment is actuated according to a control scheme based on a POD-Galerkin model driven extended Kalman filter for state estimation and a model predictive controller to dampen TS waves by negative superposition based on this information. The setup of the simulation is chosen to resemble actuation with a driven compliant wall, such as a membrane actuator. Most importantly, a method is proposed to integrate such a localized wall actuation into a Galerkin model.

From scale-free to Erdos-Rényi networks.

PubMed

Gómez-Gardeñes, Jesús; Moreno, Yamir

2006-05-01

We analyze a model that interpolates between scale-free and Erdos-Rényi networks. The model introduced generates a one-parameter family of networks and allows one to analyze the role of structural heterogeneity. Analytical calculations are compared with extensive numerical simulations in order to describe the transition between these two important classes of networks. Finally, an application of the proposed model to the study of the percolation transition is presented.

Combining state-and-transition simulations and species distribution models to anticipate the effects of climate change

USGS Publications Warehouse

Miller, Brian W.; Frid, Leonardo; Chang, Tony; Piekielek, N. B.; Hansen, Andrew J.; Morisette, Jeffrey T.

2015-01-01

State-and-transition simulation models (STSMs) are known for their ability to explore the combined effects of multiple disturbances, ecological dynamics, and management actions on vegetation. However, integrating the additional impacts of climate change into STSMs remains a challenge. We address this challenge by combining an STSM with species distribution modeling (SDM). SDMs estimate the probability of occurrence of a given species based on observed presence and absence locations as well as environmental and climatic covariates. Thus, in order to account for changes in habitat suitability due to climate change, we used SDM to generate continuous surfaces of species occurrence probabilities. These data were imported into ST-Sim, an STSM platform, where they dictated the probability of each cell transitioning between alternate potential vegetation types at each time step. The STSM was parameterized to capture additional processes of vegetation growth and disturbance that are relevant to a keystone species in the Greater Yellowstone Ecosystem—whitebark pine (Pinus albicaulis). We compared historical model runs against historical observations of whitebark pine and a key disturbance agent (mountain pine beetle, Dendroctonus ponderosae), and then projected the simulation into the future. Using this combination of correlative and stochastic simulation models, we were able to reproduce historical observations and identify key data gaps. Results indicated that SDMs and STSMs are complementary tools, and combining them is an effective way to account for the anticipated impacts of climate change, biotic interactions, and disturbances, while also allowing for the exploration of management options.

High-Fidelity Dynamic Modeling of Spacecraft in the Continuum--Rarefied Transition Regime

NASA Astrophysics Data System (ADS)

Turansky, Craig P.

The state of the art of spacecraft rarefied aerodynamics seldom accounts for detailed rigid-body dynamics. In part because of computational constraints, simpler models based upon the ballistic and drag coefficients are employed. Of particular interest is the continuum-rarefied transition regime of Earth's thermosphere where gas dynamic simulation is difficult yet wherein many spacecraft operate. The feasibility of increasing the fidelity of modeling spacecraft dynamics is explored by coupling rarefied aerodynamics with rigid-body dynamics modeling similar to that traditionally used for aircraft in atmospheric flight. Presented is a framework of analysis and guiding principles which capitalize on the availability of increasing computational methods and resources. Aerodynamic force inputs for modeling spacecraft in two dimensions in a rarefied flow are provided by analytical equations in the free-molecular regime, and the direct simulation Monte Carlo method in the transition regime. The application of the direct simulation Monte Carlo method to this class of problems is examined in detail with a new code specifically designed for engineering-level rarefied aerodynamic analysis. Time-accurate simulations of two distinct geometries in low thermospheric flight and atmospheric entry are performed, demonstrating non-linear dynamics that cannot be predicted using simpler approaches. The results of this straightforward approach to the aero-orbital coupled-field problem highlight the possibilities for future improvements in drag prediction, control system design, and atmospheric science. Furthermore, a number of challenges for future work are identified in the hope of stimulating the development of a new subfield of spacecraft dynamics.

Finite-temperature behavior of a classical spin-orbit-coupled model for YbMgGaO4 with and without bond disorder

NASA Astrophysics Data System (ADS)

Parker, Edward; Balents, Leon

2018-05-01

We present the results of finite-temperature classical Monte Carlo simulations of a strongly spin-orbit-coupled nearest-neighbor triangular-lattice model for the candidate U (1 ) quantum spin liquid YbMgGaO4 at large system sizes. We find a single continuous finite-temperature stripe-ordering transition with slowly diverging heat capacity that completely breaks the sixfold ground-state degeneracy, despite the absence of a known conformal field theory describing such a transition. We also simulate the effect of random-bond disorder in the model, and find that even weak bond disorder destroys the transition by fragmenting the system into very large domains—possibly explaining the lack of observed ordering in the real material. The Imry-Ma argument only partially explains this fragility to disorder, and we extend the argument with a physical explanation for the preservation of our system's time-reversal symmetry even under a disorder model that preserves the same symmetry.

Characteristics of traffic flow at a non-signalized intersection in the framework of game theory

NASA Astrophysics Data System (ADS)

Fan, Hongqiang; Jia, Bin; Tian, Junfang; Yun, Lifen

2014-12-01

At a non-signalized intersection, some vehicles violate the traffic rules to pass the intersection as soon as possible. These behaviors may cause many traffic conflicts even traffic accidents. In this paper, a simulation model is proposed to research the effects of these behaviors at a non-signalized intersection. Vehicle’s movement is simulated by the cellular automaton (CA) model. The game theory is introduced for simulating the intersection dynamics. Two types of driver participate the game process: cooperator (C) and defector (D). The cooperator obey the traffic rules, but the defector does not. A transition process may occur when the cooperator is waiting before the intersection. The critical value of waiting time follows the Weibull distribution. One transition regime is found in the phase diagram. The simulation results illustrate the applicability of the proposed model and reveal a number of interesting insights into the intersection management, including that the existence of defectors is benefit for the capacity of intersection, but also reduce the safety of intersection.

Downscaling global land-use/land-cover projections for use in region-level state-and-transition simulation modeling

USGS Publications Warehouse

Sherba, Jason T.; Sleeter, Benjamin M.; Davis, Adam W.; Parker, Owen P.

2015-01-01

Global land-use/land-cover (LULC) change projections and historical datasets are typically available at coarse grid resolutions and are often incompatible with modeling applications at local to regional scales. The difficulty of downscaling and reapportioning global gridded LULC change projections to regional boundaries is a barrier to the use of these datasets in a state-and-transition simulation model (STSM) framework. Here we compare three downscaling techniques to transform gridded LULC transitions into spatial scales and thematic LULC classes appropriate for use in a regional STSM. For each downscaling approach, Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathway (RCP) LULC projections, at the 0.5 × 0.5 cell resolution, were downscaled to seven Level III ecoregions in the Pacific Northwest, United States. RCP transition values at each cell were downscaled based on the proportional distribution between ecoregions of (1) cell area, (2) land-cover composition derived from remotely-sensed imagery, and (3) historic LULC transition values from a LULC history database. Resulting downscaled LULC transition values were aggregated according to their bounding ecoregion and “cross-walked” to relevant LULC classes. Ecoregion-level LULC transition values were applied in a STSM projecting LULC change between 2005 and 2100. While each downscaling methods had advantages and disadvantages, downscaling using the historical land-use history dataset consistently apportioned RCP LULC transitions in agreement with historical observations. Regardless of the downscaling method, some LULC projections remain improbable and require further investigation.

UTM: Universal Transit Modeller

NASA Astrophysics Data System (ADS)

Deeg, Hans J.

2014-12-01

The Universal Transit Modeller (UTM) is a light-curve simulator for all kinds of transiting or eclipsing configurations between arbitrary numbers of several types of objects, which may be stars, planets, planetary moons, and planetary rings. A separate fitting program, UFIT (Universal Fitter) is part of the UTM distribution and may be used to derive best fits to light-curves for any set of continuously variable parameters. UTM/UFIT is written in IDL code and its source is released in the public domain under the GNU General Public License.

Three-dimensional Mesoscale Simulations of Detonation Initiation in Energetic Materials with Density-based Kinetics

NASA Astrophysics Data System (ADS)

Jackson, Thomas; Jost, A. M.; Zhang, Ju; Sridharan, P.; Amadio, G.

2017-06-01

In this work we present three-dimensional mesoscale simulations of detonation initiation in energetic materials. We solve the reactive Euler equations, with the energy equation augmented by a power deposition term. The reaction rate at the mesoscale is modelled using a density-based kinetics scheme, adapted from standard Ignition and Growth models. The deposition term is based on previous results of simulations of pore collapse at the microscale, modelled at the mesoscale as hot-spots. We carry out three-dimensional mesoscale simulations of random packs of HMX crystals in a binder, and show that the transition between no-detonation and detonation depends on the number density of the hot-spots, the initial radius of the hot-spot, the post-shock pressure of an imposed shock, and the amplitude of the power deposition term. The trends of transition at lower pressure of the imposed shock for larger number density of pore observed in experiments is reproduced. Initial attempts to improve the agreement between the simulation and experiments through calibration of various parameters will also be made.

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation.

PubMed

Lee, Juyong; Kim, Yang-Gyun; Kim, Kyeong Kyu; Seok, Chaok

2010-08-05

Canonical, right-handed B-DNA can be transformed into noncanonical, left-handed Z-DNA in vitro at high salt concentrations or in vivo under physiological conditions. The molecular mechanism of this drastic conformational transition is still unknown despite numerous studies. Inspired by the crystal structure of a B-Z junction and the previous zipper model, we show here, with the aid of molecular dynamics simulations, that a stepwise propagation of a B-Z junction is a highly probable pathway for the B-Z transition. In this paper, the movement of a B-Z junction by a two-base-pair step in a double-strand nonamer, [d(GpCpGpCpGpCpGpCpG)](2), is considered. Targeted molecular dynamics simulations and umbrella sampling for this transition resulted in a transition pathway with a free energy barrier of 13 kcal/mol. This barrier is much more favorable than those obtained from previous atomistic simulations that lead to concerted transitions of the whole strands. The free energy difference between B-DNA and Z-DNA evaluated from our simulation is 0.9 kcal/mol per dinucleotide unit, which is consistent with previous experiments. The current computation thus strongly supports the proposal that the B-Z transition involves a relatively fast extension of B-DNA or Z-DNA by sequential propagation of B-Z junctions once nucleation of junctions is established.

Two-Equation Low-Reynolds-Number Turbulence Modeling of Transitional Boundary Layer Flows Characteristic of Gas Turbine Blades. Ph.D. Thesis. Final Contractor Report

NASA Technical Reports Server (NTRS)

Schmidt, Rodney C.; Patankar, Suhas V.

1988-01-01

The use of low Reynolds number (LRN) forms of the k-epsilon turbulence model in predicting transitional boundary layer flow characteristic of gas turbine blades is developed. The research presented consists of: (1) an evaluation of two existing models; (2) the development of a modification to current LRN models; and (3) the extensive testing of the proposed model against experimental data. The prediction characteristics and capabilities of the Jones-Launder (1972) and Lam-Bremhorst (1981) LRN k-epsilon models are evaluated with respect to the prediction of transition on flat plates. Next, the mechanism by which the models simulate transition is considered and the need for additional constraints is discussed. Finally, the transition predictions of a new model are compared with a wide range of different experiments, including transitional flows with free-stream turbulence under conditions of flat plate constant velocity, flat plate constant acceleration, flat plate but strongly variable acceleration, and flow around turbine blade test cascades. In general, calculational procedure yields good agreement with most of the experiments.

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

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

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

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

Methodology for modeling the microbial contamination of air filters.

PubMed

Joe, Yun Haeng; Yoon, Ki Young; Hwang, Jungho

2014-01-01

In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter.

Exploration of government policy structure which support and block energy transition process in indonesia using system dynamics model

NASA Astrophysics Data System (ADS)

Destyanto, A. R.; Silalahi, T. D.; Hidayatno, A.

2017-11-01

System dynamic modeling is widely used to predict and simulate the energy system in several countries. One of the applications of system dynamics is to evaluate national energy policy alternatives, and energy efficiency analysis. Using system dynamic modeling, this research aims to evaluate the energy transition policy that has been implemented in Indonesia on the past conversion program of kerosene to LPG for household cook fuel consumption, which considered as successful energy transition program implemented since 2007. This research is important since Indonesia considered not yet succeeded to execute another energy transition program on conversion program of oil fuel to gas fuel for transportation that has started since 1989. The aim of this research is to explore which policy intervention that has significant contribution to support or even block the conversion program. Findings in this simulation show that policy intervention to withdraw the kerosene supply and government push to increase production capacity of the support equipment industries (gas stove, regulator, and LPG Cylinder) is the main influence on the success of the program conversion program.

A Network of Conformational Transitions in the Apo Form of NDM-1 Enzyme Revealed by MD Simulation and a Markov State Model.

PubMed

Gao, Kaifu; Zhao, Yunjie

2017-04-13

New Delhi metallo-β-lactamase-1 (NDM-1) is a novel β-lactamase enzyme that confers enteric bacteria with nearly complete resistance to all β-lactam antibiotics, so it raises a formidable and global threat to human health. However, the binding mechanism between apo-NDM-1 and antibiotics as well as related conformational changes remains poorly understood, which largely hinders the overcoming of its antibiotic resistance. In our study, long-time conventional molecular dynamics simulation and Markov state models were applied to reveal both the dynamical and conformational landscape of apo-NDM-1: the MD simulation demonstrates that loop L3, which is responsible for antibiotic binding, is the most flexible and undergoes dramatic conformational changes; moreover, the Markov state model built from the simulation maps four metastable states including open, semiopen, and closed conformations of loop L3 as well as frequent transitions between the states. Our findings propose a possible conformational selection model for the binding mechanism between apo-NDM-1 and antibiotics, which facilitates the design of novel inhibitors and antibiotics.

Correlation-based Transition Modeling for External Aerodynamic Flows

NASA Astrophysics Data System (ADS)

Medida, Shivaji

Conventional turbulence models calibrated for fully turbulent boundary layers often over-predict drag and heat transfer on aerodynamic surfaces with partially laminar boundary layers. A robust correlation-based model is developed for use in Reynolds-Averaged Navier-Stokes simulations to predict laminar-to-turbulent transition onset of boundary layers on external aerodynamic surfaces. The new model is derived from an existing transition model for the two-equation k-omega Shear Stress Transport (SST) turbulence model, and is coupled with the one-equation Spalart-Allmaras (SA) turbulence model. The transition model solves two transport equations for intermittency and transition momentum thickness Reynolds number. Experimental correlations and local mean flow quantities are used in the model to account for effects of freestream turbulence level and pressure gradients on transition onset location. Transition onset is triggered by activating intermittency production using a vorticity Reynolds number criterion. In the new model, production and destruction terms of the intermittency equation are modified to improve consistency in the fully turbulent boundary layer post-transition onset, as well as ensure insensitivity to freestream eddy viscosity value specified in the SA model. In the original model, intermittency was used to control production and destruction of turbulent kinetic energy. Whereas, in the new model, only the production of eddy viscosity in SA model is controlled, and the destruction term is not altered. Unlike the original model, the new model does not use an additional correction to intermittency for separation-induced transition. Accuracy of drag predictions are improved significantly with the use of the transition model for several two-dimensional single- and multi-element airfoil cases over a wide range of Reynolds numbers. The new model is able to predict the formation of stable and long laminar separation bubbles on low-Reynolds number airfoils that is not captured with conventional turbulence models. The validated transition model is successfully applied to rotating blade configurations in axial flow conditions to study the effects of transitional boundary layers on rotor thrust and torque. In helicopter rotors, inclusion of transition effects increased thrust prediction by 2% and decreased torque by as much as 8% at lower collective angles, due to reduced airfoil profile drag. In wind turbine rotors, transition model predicted a 7%--70% increase in generated shaft torque at lower wind speeds, due to lower viscous drag. This has important implications for CFD analysis of small wind turbines operating at low values of rated power. Transition onset locations along upper and lower surfaces of rotor blades are analyzed in detail. A new crossflow transition onset criterion is developed to account for crossflow instability effects in three-dimensional boundary layers. Preliminary results for swept wing and rotating blade flows demonstrate the need to account for crossflow transition in three-dimensional simulations of wings, rotating blades, and airframes. Inclusion of crossflow effects resulted in accelerated transition in the presence of favorable pressure gradients and yawed flow. Finally, a new correction to the wall damping function in the Spalart-Allmaras turbulence model is proposed to improve sensitivity of the model to strong adverse pressure gradients (APG). The correction reduces turbulence production in the boundary layer when the ratio of magnitudes of local turbulent stress to the wall shear stress exceeds a threshold value, therefore enabling earlier separation of boundary layer. Improved prediction of static and dynamic stall on two-dimensional airfoils is demonstrated with the APG correction.

Large eddy simulation of transitional flow in an idealized stenotic blood vessel: evaluation of subgrid scale models.

PubMed

Pal, Abhro; Anupindi, Kameswararao; Delorme, Yann; Ghaisas, Niranjan; Shetty, Dinesh A; Frankel, Steven H

2014-07-01

In the present study, we performed large eddy simulation (LES) of axisymmetric, and 75% stenosed, eccentric arterial models with steady inflow conditions at a Reynolds number of 1000. The results obtained are compared with the direct numerical simulation (DNS) data (Varghese et al., 2007, "Direct Numerical Simulation of Stenotic Flows. Part 1. Steady Flow," J. Fluid Mech., 582, pp. 253-280). An inhouse code (WenoHemo) employing high-order numerical methods for spatial and temporal terms, along with a 2nd order accurate ghost point immersed boundary method (IBM) (Mark, and Vanwachem, 2008, "Derivation and Validation of a Novel Implicit Second-Order Accurate Immersed Boundary Method," J. Comput. Phys., 227(13), pp. 6660-6680) for enforcing boundary conditions on curved geometries is used for simulations. Three subgrid scale (SGS) models, namely, the classical Smagorinsky model (Smagorinsky, 1963, "General Circulation Experiments With the Primitive Equations," Mon. Weather Rev., 91(10), pp. 99-164), recently developed Vreman model (Vreman, 2004, "An Eddy-Viscosity Subgrid-Scale Model for Turbulent Shear Flow: Algebraic Theory and Applications," Phys. Fluids, 16(10), pp. 3670-3681), and the Sigma model (Nicoud et al., 2011, "Using Singular Values to Build a Subgrid-Scale Model for Large Eddy Simulations," Phys. Fluids, 23(8), 085106) are evaluated in the present study. Evaluation of SGS models suggests that the classical constant coefficient Smagorinsky model gives best agreement with the DNS data, whereas the Vreman and Sigma models predict an early transition to turbulence in the poststenotic region. Supplementary simulations are performed using Open source field operation and manipulation (OpenFOAM) ("OpenFOAM," http://www.openfoam.org/) solver and the results are inline with those obtained with WenoHemo.

Simulation of ridesourcing using agent-based demand and supply regional models : potential market demand for first-mile transit travel and reduction in vehicle miles traveled in the San Francisco Bay Area.

DOT National Transportation Integrated Search

2016-01-01

In this study, we use existing modeling tools and data from the San Francisco Bay Area : (California) to understand the potential market demand for a first mile transit access service : and possible reductions in vehicle miles traveled (VMT) (a...

Application of the algebraic RNG model for transition simulation. [renormalization group theory

NASA Technical Reports Server (NTRS)

Lund, Thomas S.

1990-01-01

The algebraic form of the RNG model of Yakhot and Orszag (1986) is investigated as a transition model for the Reynolds averaged boundary layer equations. It is found that the cubic equation for the eddy viscosity contains both a jump discontinuity and one spurious root. A yet unpublished transformation to a quartic equation is shown to remove the numerical difficulties associated with the discontinuity, but only at the expense of merging both the physical and spurious root of the cubic. Jumps between the branches of the resulting multiple-valued solution are found to lead to oscillations in flat plate transition calculations. Aside from the oscillations, the transition behavior is qualitatively correct.

Rapid freezing of water under dynamic compression

NASA Astrophysics Data System (ADS)

Myint, Philip C.; Belof, Jonathan L.

2018-06-01

Understanding the behavior of materials at extreme pressures is a central issue in fields like aerodynamics, astronomy, and geology, as well as for advancing technological grand challenges such as inertial confinement fusion. Dynamic compression experiments to probe high-pressure states often encounter rapid phase transitions that may cause the materials to behave in unexpected ways, and understanding the kinetics of these phase transitions remains an area of great interest. In this review, we examine experimental and theoretical/computational efforts to study the freezing kinetics of water to a high-pressure solid phase known as ice VII. We first present a detailed analysis of dynamic compression experiments in which water has been observed to freeze on sub-microsecond time scales to ice VII. This is followed by a discussion of the limitations of currently available molecular and continuum simulation methods in modeling these experiments. We then describe how our phase transition kinetics models, which are based on classical nucleation theory, provide a more physics-based framework that overcomes some of these limitations. Finally, we give suggestions on future experimental and modeling work on the liquid–ice VII transition, including an outline of the development of a predictive multiscale model in which molecular and continuum simulations are intimately coupled.

Rapid freezing of water under dynamic compression.

PubMed

Myint, Philip C; Belof, Jonathan L

2018-06-13

Understanding the behavior of materials at extreme pressures is a central issue in fields like aerodynamics, astronomy, and geology, as well as for advancing technological grand challenges such as inertial confinement fusion. Dynamic compression experiments to probe high-pressure states often encounter rapid phase transitions that may cause the materials to behave in unexpected ways, and understanding the kinetics of these phase transitions remains an area of great interest. In this review, we examine experimental and theoretical/computational efforts to study the freezing kinetics of water to a high-pressure solid phase known as ice VII. We first present a detailed analysis of dynamic compression experiments in which water has been observed to freeze on sub-microsecond time scales to ice VII. This is followed by a discussion of the limitations of currently available molecular and continuum simulation methods in modeling these experiments. We then describe how our phase transition kinetics models, which are based on classical nucleation theory, provide a more physics-based framework that overcomes some of these limitations. Finally, we give suggestions on future experimental and modeling work on the liquid-ice VII transition, including an outline of the development of a predictive multiscale model in which molecular and continuum simulations are intimately coupled.

Dipole saturated absorption modeling in gas phase: Dealing with a Gaussian beam

NASA Astrophysics Data System (ADS)

Dupré, Patrick

2018-01-01

With the advent of new accurate and sensitive spectrometers, cf. combining optical cavities (for absorption enhancement), the requirement for reliable molecular transition modeling is becoming more pressing. Unfortunately, there is no trivial approach which can provide a definitive formalism allowing us to solve the coupled systems of equations associated with nonlinear absorption. Here, we propose a general approach to deal with any spectral shape of the electromagnetic field interacting with a molecular species under saturation conditions. The development is specifically applied to Gaussian-shaped beams. To make the analytical expressions tractable, approximations are proposed. Finally, two or three numerical integrations are required for describing the Lamb-dip profile. The implemented model allows us to describe the saturated absorption under low pressure conditions where the broadening by the transit-time may dominate the collision rates. The model is applied to two specific overtone transitions of the molecular acetylene. The simulated line shapes are discussed versus the collision and the transit-time rates. The specific collisional and collision-free regimes are illustrated, while the Rabi frequency controls the intermediate regime. We illustrate how to recover the input parameters by fitting the simulated profiles.

Continuous Easy-Plane Deconfined Phase Transition on the Kagome Lattice

NASA Astrophysics Data System (ADS)

Zhang, Xue-Feng; He, Yin-Chen; Eggert, Sebastian; Moessner, Roderich; Pollmann, Frank

2018-03-01

We use large scale quantum Monte Carlo simulations to study an extended Hubbard model of hard core bosons on the kagome lattice. In the limit of strong nearest-neighbor interactions at 1 /3 filling, the interplay between frustration and quantum fluctuations leads to a valence bond solid ground state. The system undergoes a quantum phase transition to a superfluid phase as the interaction strength is decreased. It is still under debate whether the transition is weakly first order or represents an unconventional continuous phase transition. We present a theory in terms of an easy plane noncompact C P1 gauge theory describing the phase transition at 1 /3 filling. Utilizing large scale quantum Monte Carlo simulations with parallel tempering in the canonical ensemble up to 15552 spins, we provide evidence that the phase transition is continuous at exactly 1 /3 filling. A careful finite size scaling analysis reveals an unconventional scaling behavior hinting at deconfined quantum criticality.

Experimental Investigation of Roughness Effects on Transition Onset and Turbulent Heating Augmentation on a Hemisphere at Mach 6 and Mach 10

NASA Technical Reports Server (NTRS)

Hollis, Brian R.

2017-01-01

An experimental investigation of the effects of distributed surface roughness on boundary-layer transition and turbulent heating has been conducted. Hypersonic wind tunnel testing was performed using hemispherical models with surface roughness patterns simulating those produced by heat shield ablation. Global aeroheating and transition onset data were obtained using phosphor thermography at Mach 6 and Mach 10 over a range of roughness heights and free stream Reynolds numbers sufficient to produce laminar, transitional and turbulent flow. Upstream movement of the transition onset location and increasing heating augmentation over predicted smooth-wall levels were observed with both increasing roughness heights and increasing free stream Reynolds numbers. The experimental heating data are presented herein, as are comparisons to smooth-wall heat transfer distributions from computational flow-field simulations. The transition onset data are also tabulated, and correlations of these data are presented.

Systems Operations Studies for Automated Guideway Transit Systems : Discrete Event Simulation Model User's Manual.

DOT National Transportation Integrated Search

1982-06-01

In order to examine specific Automated Guideway Transit (AGT) developments and concepts, and to build a better knowledge base for future decision-making, the Urban Mass Transportation Administration (UMTA) undertook a new program of studies and techn...

Evaluating synoptic systems in the CMIP5 climate models over the Australian region

NASA Astrophysics Data System (ADS)

Gibson, Peter B.; Uotila, Petteri; Perkins-Kirkpatrick, Sarah E.; Alexander, Lisa V.; Pitman, Andrew J.

2016-10-01

Climate models are our principal tool for generating the projections used to inform climate change policy. Our confidence in projections depends, in part, on how realistically they simulate present day climate and associated variability over a range of time scales. Traditionally, climate models are less commonly assessed at time scales relevant to daily weather systems. Here we explore the utility of a self-organizing maps (SOMs) procedure for evaluating the frequency, persistence and transitions of daily synoptic systems in the Australian region simulated by state-of-the-art global climate models. In terms of skill in simulating the climatological frequency of synoptic systems, large spread was observed between models. A positive association between all metrics was found, implying that relative skill in simulating the persistence and transitions of systems is related to skill in simulating the climatological frequency. Considering all models and metrics collectively, model performance was found to be related to model horizontal resolution but unrelated to vertical resolution or representation of the stratosphere. In terms of the SOM procedure, the timespan over which evaluation was performed had some influence on model performance skill measures, as did the number of circulation types examined. These findings have implications for selecting models most useful for future projections over the Australian region, particularly for projections related to synoptic scale processes and phenomena. More broadly, this study has demonstrated the utility of the SOMs procedure in providing a process-based evaluation of climate models.

Using state-and-transition modeling to account for imperfect detection in invasive species management

USGS Publications Warehouse

Frid, Leonardo; Holcombe, Tracy; Morisette, Jeffrey T.; Olsson, Aaryn D.; Brigham, Lindy; Bean, Travis M.; Betancourt, Julio L.; Bryan, Katherine

2013-01-01

Buffelgrass, a highly competitive and flammable African bunchgrass, is spreading rapidly across both urban and natural areas in the Sonoran Desert of southern and central Arizona. Damages include increased fire risk, losses in biodiversity, and diminished revenues and quality of life. Feasibility of sustained and successful mitigation will depend heavily on rates of spread, treatment capacity, and cost–benefit analysis. We created a decision support model for the wildland–urban interface north of Tucson, AZ, using a spatial state-and-transition simulation modeling framework, the Tool for Exploratory Landscape Scenario Analyses. We addressed the issues of undetected invasions, identifying potentially suitable habitat and calibrating spread rates, while answering questions about how to allocate resources among inventory, treatment, and maintenance. Inputs to the model include a state-and-transition simulation model to describe the succession and control of buffelgrass, a habitat suitability model, management planning zones, spread vectors, estimated dispersal kernels for buffelgrass, and maps of current distribution. Our spatial simulations showed that without treatment, buffelgrass infestations that started with as little as 80 ha (198 ac) could grow to more than 6,000 ha by the year 2060. In contrast, applying unlimited management resources could limit 2060 infestation levels to approximately 50 ha. The application of sufficient resources toward inventory is important because undetected patches of buffelgrass will tend to grow exponentially. In our simulations, areas affected by buffelgrass may increase substantially over the next 50 yr, but a large, upfront investment in buffelgrass control could reduce the infested area and overall management costs.

Simulation of groundwater flow pathlines and freshwater/saltwater transition zone movement, Manhasset Neck, Nassau County, New York

USGS Publications Warehouse

Misut, Paul; Aphale, Omkar

2014-01-01

A density-dependent groundwater flow and solute transport model of Manhasset Neck, Long Island, New York, was used to analyze (1) the effects of seasonal stress on the position of the freshwater/saltwater transition zone and (2) groundwater flowpaths. The following were used in the simulation: 182 transient stress periods, representing the historical record from 1920 to 2011, and 44 transient stress periods, representing future hypothetical conditions from 2011 to 2030. Simulated water-level and salinity (chloride concentration) values are compared with values from a previously developed two-stress-period (1905–1944 and 1945–2005) model. The 182-stress-period model produced salinity (chloride concentration) values that more accurately matched the observed salinity (chloride concentration) values in response to hydrologic stress than did the two-stress-period model, and salinity ranged from zero to about 3 parts per thousand (equivalent to zero to 1,660 milligrams per liter chloride). The 182-stress-period model produced improved calibration statistics of water-level measurements made throughout the study area than did the two-stress-period model, reducing the Lloyd aquifer root mean square error from 7.0 to 5.2 feet. Decreasing horizontal and vertical hydraulic conductivities (fixed anisotropy ratio) of the Lloyd and North Shore aquifers by 20 percent resulted in nearly doubling the simulated salinity(chloride concentration) increase at Port Washington observation well N12508. Groundwater flowpath analysis was completed for 24 production wells to delineate water source areas. The freshwater/saltwater transition zone moved toward and(or) away from wells during future hypothetical scenarios.

Mathematical simulation of forced expiration.

PubMed

Elad, D; Kamm, R D; Shapiro, A H

1988-07-01

Flow limitation during forced expiration is simulated by a mathematical model. This model draws on the pressure-area law obtained in the accompanying paper, and the methods of analysis for one-dimensional flow in collapsible tubes developed by Shapiro (Trans. ASME J. Biomech. Eng. 99: 126-147, 1977). These methods represent an improvement over previous models in that 1) the effects of changing lung volume and of parenchymal-bronchial interdependence are simulated; 2) a more realistic representation of collapsed airways is employed; 3) a solution is obtained mouthward of the flow-limiting site by allowing for a smooth transition from sub- to supercritical flow speeds, then matching mouth pressure by imposing an elastic jump (an abrupt transition from super- to subcritical flow speeds) at the appropriate location; and 4) the effects of levels of effort (or vacuum pressure) in excess of those required to produce incipient flow limitation are examined, including the effects of potential physiological limitation.

Stabilization of Model Membrane Systems by Disaccharides. Quasielastic Neutron Scattering Experiments and Atomistic Simulations

NASA Astrophysics Data System (ADS)

Doxastakis, Emmanouil; Garcia Sakai, Victoria; Ohtake, Satoshi; Maranas, Janna K.; de Pablo, Juan J.

2006-03-01

Trehalose, a disaccharide of glucose, is often used for the stabilization of cell membranes in the absence of water. This work studies the effects of trehalose on model membrane systems as they undergo a melting transition using a combination of experimental methods and atomistic molecular simulations. Quasielastic neutron scattering experiments on selectively deuterated samples provide the incoherent dynamic structure over a wide time range. Elastic scans probing the lipid tail dynamics display clear evidence of a main melting transition that is significantly lowered in the presence of trehalose. Lipid headgroup mobility is considerably restricted at high temperatures and directly associated with the dynamics of the sugar in the mixture. Molecular simulations provide a detailed overview of the dynamics and their spatial and time dependence. The combined simulation and experimental methodology offers a unique, molecular view of the physics of systems commonly employed in cryopreservation and lyophilization processes.

Large Eddy Simulations of Continental Boundary Layer Clouds Observed during the RACORO Field Campaign

NASA Astrophysics Data System (ADS)

Endo, S.; Fridlind, A. M.; Lin, W.; Vogelmann, A. M.; Toto, T.; Liu, Y.

2013-12-01

Three cases of boundary layer clouds are analyzed in the FAst-physics System TEstbed and Research (FASTER) project, based on continental boundary-layer-cloud observations during the RACORO Campaign [Routine Atmospheric Radiation Measurement (ARM) Aerial Facility (AAF) Clouds with Low Optical Water Depths (CLOWD) Optical Radiative Observations] at the ARM Climate Research Facility's Southern Great Plains (SGP) site. The three 60-hour case study periods are selected to capture the temporal evolution of cumulus, stratiform, and drizzling boundary-layer cloud systems under a range of conditions, intentionally including those that are relatively more mixed or transitional in nature versus being of a purely canonical type. Multi-modal and temporally varying aerosol number size distribution profiles are derived from aircraft observations. Large eddy simulations (LESs) are performed for the three case study periods using the GISS Distributed Hydrodynamic Aerosol and Radiative Modeling Application (DHARMA) model and the WRF-FASTER model, which is the Weather Research and Forecasting (WRF) model implemented with forcing ingestion and other functions to constitute a flexible LES. The two LES models commonly capture the significant transitions of cloud-topped boundary layers in the three periods: diurnal evolution of cumulus layers repeating over multiple days, nighttime evolution/daytime diminution of thick stratus, and daytime breakup of stratus and stratocumulus clouds. Simulated transitions of thermodynamic structures of the cloud-topped boundary layers are examined by balloon-borne soundings and ground-based remote sensors. Aircraft observations are then used to statistically evaluate the predicted cloud droplet number size distributions under varying aerosol and cloud conditions. An ensemble approach is used to refine the model configuration for the combined use of observations with parallel LES and single-column model simulations. See Lin et al. poster for single-column model investigation.

Toward large eddy simulation of turbulent flow over an airfoil

NASA Technical Reports Server (NTRS)

Choi, Haecheon

1993-01-01

The flow field over an airfoil contains several distinct flow characteristics, e.g. laminar, transitional, turbulent boundary layer flow, flow separation, unstable free shear layers, and a wake. This diversity of flow regimes taxes the presently available Reynolds averaged turbulence models. Such models are generally tuned to predict a particular flow regime, and adjustments are necessary for the prediction of a different flow regime. Similar difficulties are likely to emerge when the large eddy simulation technique is applied with the widely used Smagorinsky model. This model has not been successful in correctly representing different turbulent flow fields with a single universal constant and has an incorrect near-wall behavior. Germano et al. (1991) and Ghosal, Lund & Moin have developed a new subgrid-scale model, the dynamic model, which is very promising in alleviating many of the persistent inadequacies of the Smagorinsky model: the model coefficient is computed dynamically as the calculation progresses rather than input a priori. The model has been remarkably successful in prediction of several turbulent and transitional flows. We plan to simulate turbulent flow over a '2D' airfoil using the large eddy simulation technique. Our primary objective is to assess the performance of the newly developed dynamic subgrid-scale model for computation of complex flows about aircraft components and to compare the results with those obtained using the Reynolds average approach and experiments. The present computation represents the first application of large eddy simulation to a flow of aeronautical interest and a key demonstration of the capabilities of the large eddy simulation technique.

Influence of vertical and lateral heat transfer on permafrost thaw, peatland landscape transition, and groundwater flow

USGS Publications Warehouse

Kurylyk, Barret L.; Masaki, Masaki; Quinton, William L.; McKenzie, Jeffrey M.; Voss, Clifford I.

2016-01-01

Recent climate change has reduced the spatial extent and thickness of permafrost in many discontinuous permafrost regions. Rapid permafrost thaw is producing distinct landscape changes in the Taiga Plains of the Northwest Territories, Canada. As permafrost bodies underlying forested peat plateaus shrink, the landscape slowly transitions into unforested wetlands. The expansion of wetlands has enhanced the hydrologic connectivity of many watersheds via new surface and near-surface flow paths, and increased streamflow has been observed. Furthermore, the decrease in forested peat plateaus results in a net loss of boreal forest and associated ecosystems. This study investigates fundamental processes that contribute to permafrost thaw by comparing observed and simulated thaw development and landscape transition of a peat plateau-wetland complex in the Northwest Territories, Canada from 1970 to 2012. Measured climate data are first used to drive surface energy balance simulations for the wetland and peat plateau. Near-surface soil temperatures simulated in the surface energy balance model are then applied as the upper boundary condition to a three-dimensional model of subsurface water flow and coupled energy transport with freeze-thaw. Simulation results demonstrate that lateral heat transfer, which is not considered in many permafrost models, can influence permafrost thaw rates. Furthermore, the simulations indicate that landscape evolution arising from permafrost thaw acts as a positive feedback mechanism that increases the energy absorbed at the land surface and produces additional permafrost thaw. The modeling results also demonstrate that flow rates in local groundwater flow systems may be enhanced by the degradation of isolated permafrost bodies.

Transitional flow in thin tubes for space station freedom radiator

NASA Technical Reports Server (NTRS)

Loney, Patrick; Ibrahim, Mounir

1995-01-01

A two dimensional finite volume method is used to predict the film coefficients in the transitional flow region (laminar or turbulent) for the radiator panel tubes. The code used to perform this analysis is CAST (Computer Aided Simulation of Turbulent Flows). The information gathered from this code is then used to augment a Sinda85 model that predicts overall performance of the radiator. A final comparison is drawn between the results generated with a Sinda85 model using the Sinda85 provided transition region heat transfer correlations and the Sinda85 model using the CAST generated data.

Large Eddy Simulation of Gravitational Effects on Transitional and Turbulent Gas-Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Givi, Peyman; Jaberi, Farhad A.

2001-01-01

The basic objective of this work is to assess the influence of gravity on "the compositional and the spatial structures" of transitional and turbulent diffusion flames via large eddy simulation (LES), and direct numerical simulation (DNS). The DNS is conducted for appraisal of the various closures employed in LES, and to study the effect of buoyancy on the small scale flow features. The LES is based on our "filtered mass density function"' (FMDF) model. The novelty of the methodology is that it allows for reliable simulations with inclusion of "realistic physics." It also allows for detailed analysis of the unsteady large scale flow evolution and compositional flame structure which is not usually possible via Reynolds averaged simulations.

Conceptualization and Simulation of the Alaskan Arctic Tundra Landscape Evolution Using the Alaska Thermokarst Model

NASA Astrophysics Data System (ADS)

Bolton, W. R.; Lara, M. J.; Genet, H.; Romanovsky, V. E.; McGuire, A. D.

2016-12-01

The Arctic, including Alaska, is currently undergoing a change in climate, with observed increases in both mean surface temperature and precipitation. The combination of these increases in precipitation and temperature has resulted in a permafrost condition that is susceptible to thermokarst. Changes in the landscape due to thermokarst takes place whenever ice-rich permafrost thaws and the land surface subsides due to the volume loss when ground-ice transitions to water. The important processes associated with thermokarst include surface ponding, changes in topography, vegetation distribution, soil moisture conditions, drainage patterns, and related erosion. The Alaska Thermokarst Model (ATM) is a large-scale, state-and-transition model designed to simulate transitions between landscape units affected by thermokarst disturbance. The ATM using a frame-based methodology to track cohorts transitions and their respective proportions within each model grid cell. In the arctic tundra environment, the ATM tracks thermokarst related transitions among wetland tundra, graminoid tundra,shrub tundra and lakes. The transition from one cohort to another due to thermokarst processes can take place if thaw reaches ice-rich ground layers either due to pulse disturbance or due to gradual active layer deepening that eventually results in penetration of the protective layer. The protective layer buffers the ice-rich soils from the land surface and is critical to determine how susceptible an area is to thermokarst degradation. The initial landcover distribution is based upon analysis of compiled remote sensing data sets at 30-m resolution. Remote sensing analysis and field measurements from previous and ongoing studies are used to determine the ice-content of the soil, the drainage efficiency (or the ability of the landscape to store or transport water), the cumulative probability of thermokarst initiation, distance from rivers, lake dynamics (increasing, decreasing, or stable), and other factors which help determine landscape transition rates. Tundra types are allowed to transition from one type to another (for example, wetland tundra to graminoid tundra) under favorable climatic conditions. In this study, we present our conceptualization and initial simulation results from in the arctic regions of Alaska.

Tempo: A Toolkit for the Timed Input/Output Automata Formalism

DTIC Science & Technology

2008-01-30

generation of distributed code from specifications. F .4.3 [Formal Languages]: Tempo;, D.3 [Programming Many distributed systems involve a combination of...and require The chek (i) transition is enabled when process i’s program the simulator to check the assertions after every single step counter is set to...output foo (n:Int) The Tempo simulator addresses this issue by putting the states x: Int : = 10;transitions modeler in charge of resolving the non

Multiscale analysis of structure development in expanded starch snacks

NASA Astrophysics Data System (ADS)

van der Sman, R. G. M.; Broeze, J.

2014-11-01

In this paper we perform a multiscale analysis of the food structuring process of the expansion of starchy snack foods like keropok, which obtains a solid foam structure. In particular, we want to investigate the validity of the hypothesis of Kokini and coworkers, that expansion is optimal at the moisture content, where the glass transition and the boiling line intersect. In our analysis we make use of several tools, (1) time scale analysis from the field of physical transport phenomena, (2) the scale separation map (SSM) developed within a multiscale simulation framework of complex automata, (3) the supplemented state diagram (SSD), depicting phase transition and glass transition lines, and (4) a multiscale simulation model for the bubble expansion. Results of the time scale analysis are plotted in the SSD, and give insight into the dominant physical processes involved in expansion. Furthermore, the results of the time scale analysis are used to construct the SSM, which has aided us in the construction of the multiscale simulation model. Simulation results are plotted in the SSD. This clearly shows that the hypothesis of Kokini is qualitatively true, but has to be refined. Our results show that bubble expansion is optimal for moisture content, where the boiling line for gas pressure of 4 bars intersects the isoviscosity line of the critical viscosity 106 Pa.s, which runs parallel to the glass transition line.

Flex Fuel Optimized SI and HCCI Engine

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

Zhu, Guoming; Schock, Harold; Yang, Xiaojian

The central objective of the proposed work is to demonstrate an HCCI (homogeneous charge compression ignition) capable SI (spark ignited) engine that is capable of fast and smooth mode transition between SI and HCCI combustion modes. The model-based control technique was used to develop and validate the proposed control strategy for the fast and smooth combustion mode transition based upon the developed control-oriented engine; and an HCCI capable SI engine was designed and constructed using production ready two-step valve-train with electrical variable valve timing actuating system. Finally, smooth combustion mode transition was demonstrated on a metal engine within eight enginemore » cycles. The Chrysler turbocharged 2.0L I4 direct injection engine was selected as the base engine for the project and the engine was modified to fit the two-step valve with electrical variable valve timing actuating system. To develop the model-based control strategy for stable HCCI combustion and smooth combustion mode transition between SI and HCCI combustion, a control-oriented real-time engine model was developed and implemented into the MSU HIL (hardware-in-the-loop) simulation environment. The developed model was used to study the engine actuating system requirement for the smooth and fast combustion mode transition and to develop the proposed mode transition control strategy. Finally, a single cylinder optical engine was designed and fabricated for studying the HCCI combustion characteristics. Optical engine combustion tests were conducted in both SI and HCCI combustion modes and the test results were used to calibrate the developed control-oriented engine model. Intensive GT-Power simulations were conducted to determine the optimal valve lift (high and low) and the cam phasing range. Delphi was selected to be the supplier for the two-step valve-train and Denso to be the electrical variable valve timing system supplier. A test bench was constructed to develop control strategies for the electrical variable valve timing (VVT) actuating system and satisfactory electrical VVT responses were obtained. Target engine control system was designed and fabricated at MSU for both single-cylinder optical and multi-cylinder metal engines. Finally, the developed control-oriented engine model was successfully implemented into the HIL simulation environment. The Chrysler 2.0L I4 DI engine was modified to fit the two-step vale with electrical variable valve timing actuating system. A used prototype engine was used as the base engine and the cylinder head was modified for the two-step valve with electrical VVT actuating system. Engine validation tests indicated that cylinder #3 has very high blow-by and it cannot be reduced with new pistons and rings. Due to the time constraint, it was decided to convert the four-cylinder engine into a single cylinder engine by blocking both intake and exhaust ports of the unused cylinders. The model-based combustion mode transition control algorithm was developed in the MSU HIL simulation environment and the Simulink based control strategy was implemented into the target engine controller. With both single-cylinder metal engine and control strategy ready, stable HCCI combustion was achived with COV of 2.1% Motoring tests were conducted to validate the actuator transient operations including valve lift, electrical variable valve timing, electronic throttle, multiple spark and injection controls. After the actuator operations were confirmed, 15-cycle smooth combustion mode transition from SI to HCCI combustion was achieved; and fast 8-cycle smooth combustion mode transition followed. With a fast electrical variable valve timing actuator, the number of engine cycles required for mode transition can be reduced down to five. It was also found that the combustion mode transition is sensitive to the charge air and engine coolant temperatures and regulating the corresponding temperatures to the target levels during the combustion mode transition is the key for a smooth combustion mode transition. As a summary, the proposed combustion mode transition strategy using the hybrid combustion mode that starts with the SI combustion and ends with the HCCI combustion was experimentally validated on a metal engine. The proposed model-based control approach made it possible to complete the SI-HCCI combustion mode transition within eight engine cycles utilizing the well controlled hybrid combustion mode. Without intensive control-oriented engine modeling and HIL simulation study of using the hybrid combustion mode during the mode transition, it would be impossible to validate the proposed combustion mode transition strategy in a very short period.« less

Measurement and reactive burn modeling of the shock to detonation transition for the HMX based explosive LX-14

NASA Astrophysics Data System (ADS)

Jones, J. D.; Ma, Xia; Clements, B. E.; Gibson, L. L.; Gustavsen, R. L.

2017-06-01

Gas-gun driven plate-impact techniques were used to study the shock to detonation transition in LX-14 (95.5 weight % HMX, 4.5 weight % estane binder). The transition was recorded using embedded electromagnetic particle velocity gauges. Initial shock pressures, P, ranged from 2.5 to 8 GPa and the resulting distances to detonation, xD, were in the range 1.9 to 14 mm. Numerical simulations using the SURF reactive burn scheme coupled with a linear US -up / Mie-Grueneisen equation of state for the reactant and a JWL equation of state for the products, match the experimental data well. Comparison of simulation with experiment as well as the ``best fit'' parameter set for the simulations is presented.

Initial conditions and modeling for simulations of shock driven turbulent material mixing

DOE PAGES

Grinstein, Fernando F.

2016-11-17

Here, we focus on the simulation of shock-driven material mixing driven by flow instabilities and initial conditions (IC). Beyond complex multi-scale resolution issues of shocks and variable density turbulence, me must address the equally difficult problem of predicting flow transition promoted by energy deposited at the material interfacial layer during the shock interface interactions. Transition involves unsteady large-scale coherent-structure dynamics capturable by a large eddy simulation (LES) strategy, but not by an unsteady Reynolds-Averaged Navier–Stokes (URANS) approach based on developed equilibrium turbulence assumptions and single-point-closure modeling. On the engineering end of computations, such URANS with reduced 1D/2D dimensionality and coarsermore » grids, tend to be preferred for faster turnaround in full-scale configurations.« less

Velocity statistics of the Nagel-Schreckenberg model

NASA Astrophysics Data System (ADS)

Bain, Nicolas; Emig, Thorsten; Ulm, Franz-Josef; Schreckenberg, Michael

2016-02-01

The statistics of velocities in the cellular automaton model of Nagel and Schreckenberg for traffic are studied. From numerical simulations, we obtain the probability distribution function (PDF) for vehicle velocities and the velocity-velocity (vv) covariance function. We identify the probability to find a standing vehicle as a potential order parameter that signals nicely the transition between free congested flow for a sufficiently large number of velocity states. Our results for the vv covariance function resemble features of a second-order phase transition. We develop a 3-body approximation that allows us to relate the PDFs for velocities and headways. Using this relation, an approximation to the velocity PDF is obtained from the headway PDF observed in simulations. We find a remarkable agreement between this approximation and the velocity PDF obtained from simulations.

Velocity statistics of the Nagel-Schreckenberg model.

PubMed

Bain, Nicolas; Emig, Thorsten; Ulm, Franz-Josef; Schreckenberg, Michael

2016-02-01

The statistics of velocities in the cellular automaton model of Nagel and Schreckenberg for traffic are studied. From numerical simulations, we obtain the probability distribution function (PDF) for vehicle velocities and the velocity-velocity (vv) covariance function. We identify the probability to find a standing vehicle as a potential order parameter that signals nicely the transition between free congested flow for a sufficiently large number of velocity states. Our results for the vv covariance function resemble features of a second-order phase transition. We develop a 3-body approximation that allows us to relate the PDFs for velocities and headways. Using this relation, an approximation to the velocity PDF is obtained from the headway PDF observed in simulations. We find a remarkable agreement between this approximation and the velocity PDF obtained from simulations.

Simulations of Cold Electroweak Baryogenesis: quench from portal coupling to new singlet field

NASA Astrophysics Data System (ADS)

Mou, Zong-Gang; Saffin, Paul M.; Tranberg, Anders

2018-01-01

We compute the baryon asymmetry generated from Cold Electroweak Baryogenesis, when a dynamical Beyond-the-Standard-Model scalar singlet field triggers the spinodal transition. Using a simple potential for this additional field, we match the speed of the quench to earlier simulations with a "by-hand" mass flip. We find that for the parameter subspace most similar to a by-hand transition, the final baryon asymmetry shows a similar dependence on quench time and is of the same magnitude. For more general parameter choices the Higgs-singlet dynamics can be very complicated, resulting in an enhancement of the final baryon asymmetry. Our results validate and generalise results of simulations in the literature and open up the Cold Electroweak Baryogenesis scenario to further model building.

TRANSIT MODEL OF PLANETS WITH MOON AND RING SYSTEMS

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

Tusnski, Luis Ricardo M.; Valio, Adriana, E-mail: lrtusnski@das.inpe.br, E-mail: avalio@craam.mackenzie.br

2011-12-10

Since the discovery of the first exoplanets, those most adequate for life to begin and evolve have been sought. Due to observational bias, however, most of the discovered planets so far are gas giants, precluding their habitability. However, if these hot Jupiters are located in the habitable zones of their host stars, and if rocky moons orbit them, then these moons may be habitable. In this work, we present a model for planetary transit simulation considering the presence of moons and planetary rings around a planet. The moon's orbit is considered to be circular and coplanar with the planetary orbit.more » The other physical and orbital parameters of the star, planet, moon, and rings can be adjusted in each simulation. It is possible to simulate as many successive transits as desired. Since the presence of spots on the surface of the star may produce a signal similar to that of the presence of a moon, our model also allows for the inclusion of starspots. The result of the simulation is a light curve with a planetary transit. White noise may also be added to the light curves to produce curves similar to those obtained by the CoRoT and Kepler space telescopes. The goal is to determine the criteria for detectability of moons and/or ring systems using photometry. The results show that it is possible to detect moons with radii as little as 1.3 R{sub Circled-Plus} with CoRoT and 0.3 R{sub Circled-Plus} with Kepler.« less

Machine learning of frustrated classical spin models. I. Principal component analysis

NASA Astrophysics Data System (ADS)

Wang, Ce; Zhai, Hui

2017-10-01

This work aims at determining whether artificial intelligence can recognize a phase transition without prior human knowledge. If this were successful, it could be applied to, for instance, analyzing data from the quantum simulation of unsolved physical models. Toward this goal, we first need to apply the machine learning algorithm to well-understood models and see whether the outputs are consistent with our prior knowledge, which serves as the benchmark for this approach. In this work, we feed the computer data generated by the classical Monte Carlo simulation for the X Y model in frustrated triangular and union jack lattices, which has two order parameters and exhibits two phase transitions. We show that the outputs of the principal component analysis agree very well with our understanding of different orders in different phases, and the temperature dependences of the major components detect the nature and the locations of the phase transitions. Our work offers promise for using machine learning techniques to study sophisticated statistical models, and our results can be further improved by using principal component analysis with kernel tricks and the neural network method.

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

NASA Astrophysics Data System (ADS)

Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

2016-04-01

Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

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

Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao; Huang, Xuhui, E-mail: xuhuihuang@ust.hk

2016-04-21

Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kineticsmore » are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.« less

Simulating the Thermal Response of High Explosives on Time Scales of Days to Microseconds

NASA Astrophysics Data System (ADS)

Yoh, Jack J.; McClelland, Matthew A.

2004-07-01

We present an overview of computational techniques for simulating the thermal cookoff of high explosives using a multi-physics hydrodynamics code, ALE3D. Recent improvements to the code have aided our computational capability in modeling the response of energetic materials systems exposed to extreme thermal environments, such as fires. We consider an idealized model process for a confined explosive involving the transition from slow heating to rapid deflagration in which the time scale changes from days to hundreds of microseconds. The heating stage involves thermal expansion and decomposition according to an Arrhenius kinetics model while a pressure-dependent burn model is employed during the explosive phase. We describe and demonstrate the numerical strategies employed to make the transition from slow to fast dynamics.

Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

2016-11-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume. This work is funded by NSF under Grant DMS-1222550.

Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.

Transition index maps for urban growth simulation: application of artificial neural networks, weight of evidence and fuzzy multi-criteria evaluation.

PubMed

Shafizadeh-Moghadam, Hossein; Tayyebi, Amin; Helbich, Marco

2017-06-01

Transition index maps (TIMs) are key products in urban growth simulation models. However, their operationalization is still conflicting. Our aim was to compare the prediction accuracy of three TIM-based spatially explicit land cover change (LCC) models in the mega city of Mumbai, India. These LCC models include two data-driven approaches, namely artificial neural networks (ANNs) and weight of evidence (WOE), and one knowledge-based approach which integrates an analytical hierarchical process with fuzzy membership functions (FAHP). Using the relative operating characteristics (ROC), the performance of these three LCC models were evaluated. The results showed 85%, 75%, and 73% accuracy for the ANN, FAHP, and WOE. The ANN was clearly superior compared to the other LCC models when simulating urban growth for the year 2010; hence, ANN was used to predict urban growth for 2020 and 2030. Projected urban growth maps were assessed using statistical measures, including figure of merit, average spatial distance deviation, producer accuracy, and overall accuracy. Based on our findings, we recomend ANNs as an and accurate method for simulating future patterns of urban growth.

Phase transition of traveling waves in bacterial colony pattern

NASA Astrophysics Data System (ADS)

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

2004-05-01

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

Phase transition in a spatial Lotka-Volterra model

NASA Astrophysics Data System (ADS)

Szabó, György; Czárán, Tamás

2001-06-01

Spatial evolution is investigated in a simulated system of nine competing and mutating bacterium strains, which mimics the biochemical war among bacteria capable of producing two different bacteriocins (toxins) at most. Random sequential dynamics on a square lattice is governed by very symmetrical transition rules for neighborhood invasions of sensitive strains by killers, killers by resistants, and resistants by sensitives. The community of the nine possible toxicity/resistance types undergoes a critical phase transition as the uniform transmutation rates between the types decreases below a critical value Pc above that all the nine types of strains coexist with equal frequencies. Passing the critical mutation rate from above, the system collapses into one of three topologically identical (degenerated) states, each consisting of three strain types. Of the three possible final states each accrues with equal probability and all three maintain themselves in a self-organizing polydomain structure via cyclic invasions. Our Monte Carlo simulations support that this symmetry-breaking transition belongs to the universality class of the three-state Potts model.

Mesoscopic simulations of shock-to-detonation transition in reactive liquid high explosive

NASA Astrophysics Data System (ADS)

Maillet, J. B.; Bourasseau, E.; Desbiens, N.; Vallverdu, G.; Stoltz, G.

2011-12-01

An extension of the model described in a previous work (see Maillet J. B. et al., EPL, 78 (2007) 68001) based on Dissipative Particle Dynamics is presented and applied to a liquid high explosive (HE), with thermodynamic properties mimicking those of liquid nitromethane. Large scale nonequilibrium simulations of reacting liquid HE with model kinetic under sustained shock conditions allow a better understanding of the shock-to-detonation transition in homogeneous explosives. Moreover, the propagation of the reactive wave appears discontinuous since ignition points in the shocked material can be activated by the compressive waves emitted from the onset of chemical reactions.

The impact of individual-level heterogeneity on estimated infectious disease burden: a simulation study.

PubMed

McDonald, Scott A; Devleesschauwer, Brecht; Wallinga, Jacco

2016-12-08

Disease burden is not evenly distributed within a population; this uneven distribution can be due to individual heterogeneity in progression rates between disease stages. Composite measures of disease burden that are based on disease progression models, such as the disability-adjusted life year (DALY), are widely used to quantify the current and future burden of infectious diseases. Our goal was to investigate to what extent ignoring the presence of heterogeneity could bias DALY computation. Simulations using individual-based models for hypothetical infectious diseases with short and long natural histories were run assuming either "population-averaged" progression probabilities between disease stages, or progression probabilities that were influenced by an a priori defined individual-level frailty (i.e., heterogeneity in disease risk) distribution, and DALYs were calculated. Under the assumption of heterogeneity in transition rates and increasing frailty with age, the short natural history disease model predicted 14% fewer DALYs compared with the homogenous population assumption. Simulations of a long natural history disease indicated that assuming homogeneity in transition rates when heterogeneity was present could overestimate total DALYs, in the present case by 4% (95% quantile interval: 1-8%). The consequences of ignoring population heterogeneity should be considered when defining transition parameters for natural history models and when interpreting the resulting disease burden estimates.

TESSIM: a simulator for the Athena-X-IFU

NASA Astrophysics Data System (ADS)

Wilms, J.; Smith, S. J.; Peille, P.; Ceballos, M. T.; Cobo, B.; Dauser, T.; Brand, T.; den Hartog, R. H.; Bandler, S. R.; de Plaa, J.; den Herder, J.-W. A.

2016-07-01

We present the design of tessim, a simulator for the physics of transition edge sensors developed in the framework of the Athena end to end simulation effort. Designed to represent the general behavior of transition edge sensors and to provide input for engineering and science studies for Athena, tessim implements a numerical solution of the linearized equations describing these devices. The simulation includes a model for the relevant noise sources and several implementations of possible trigger algorithms. Input and output of the software are standard FITS- files which can be visualized and processed using standard X-ray astronomical tool packages. Tessim is freely available as part of the SIXTE package (http://www.sternwarte.uni-erlangen.de/research/sixte/).

TESSIM: A Simulator for the Athena-X-IFU

NASA Technical Reports Server (NTRS)

Wilms, J.; Smith, S. J.; Peille, P.; Ceballos, M. T.; Cobo, B.; Dauser, T.; Brand, T.; Den Hartog, R. H.; Bandler, S. R.; De Plaa, J.;

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning

PubMed Central

Matsunaga, Yasuhiro

2018-01-01

Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide time-series data, such as donor-acceptor distances, whereas the latter give atomistic information, although this information is often biased by model parameters. Here, we devise a machine-learning method to combine the complementary information from the two approaches and construct a consistent model of conformational dynamics. It is applied to the folding dynamics of the formin-binding protein WW domain. MD simulations over 400 μs led to an initial Markov state model (MSM), which was then "refined" using single-molecule Förster resonance energy transfer (FRET) data through hidden Markov modeling. The refined or data-assimilated MSM reproduces the FRET data and features hairpin one in the transition-state ensemble, consistent with mutation experiments. The folding pathway in the data-assimilated MSM suggests interplay between hydrophobic contacts and turn formation. Our method provides a general framework for investigating conformational transitions in other proteins. PMID:29723137

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning.

PubMed

Matsunaga, Yasuhiro; Sugita, Yuji

2018-05-03

Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide time-series data, such as donor-acceptor distances, whereas the latter give atomistic information, although this information is often biased by model parameters. Here, we devise a machine-learning method to combine the complementary information from the two approaches and construct a consistent model of conformational dynamics. It is applied to the folding dynamics of the formin-binding protein WW domain. MD simulations over 400 μs led to an initial Markov state model (MSM), which was then "refined" using single-molecule Förster resonance energy transfer (FRET) data through hidden Markov modeling. The refined or data-assimilated MSM reproduces the FRET data and features hairpin one in the transition-state ensemble, consistent with mutation experiments. The folding pathway in the data-assimilated MSM suggests interplay between hydrophobic contacts and turn formation. Our method provides a general framework for investigating conformational transitions in other proteins. © 2018, Matsunaga et al.

Influence of climate variability, fire and phosphorus limitation on vegetation structure and dynamics of the Amazon-Cerrado border

NASA Astrophysics Data System (ADS)

Ane Dionizio, Emily; Heil Costa, Marcos; de Almeida Castanho, Andrea D.; Ferreira Pires, Gabrielle; Schwantes Marimon, Beatriz; Hur Marimon-Junior, Ben; Lenza, Eddie; Martins Pimenta, Fernando; Yang, Xiaojuan; Jain, Atul K.

2018-02-01

Climate, fire and soil nutrient limitation are important elements that affect vegetation dynamics in areas of the forest-savanna transition. In this paper, we use the dynamic vegetation model INLAND to evaluate the influence of interannual climate variability, fire and phosphorus (P) limitation on Amazon-Cerrado transitional vegetation structure and dynamics. We assess how each environmental factor affects net primary production, leaf area index and aboveground biomass (AGB), and compare the AGB simulations to an observed AGB map. We used two climate data sets (monthly average climate for 1961-1990 and interannual climate variability for 1948-2008), two data sets of total soil P content (one based on regional field measurements and one based on global data), and the INLAND fire module. Our results show that the inclusion of interannual climate variability, P limitation and fire occurrence each contribute to simulating vegetation types that more closely match observations. These effects are spatially heterogeneous and synergistic. In terms of magnitude, the effect of fire is strongest and is the main driver of vegetation changes along the transition. Phosphorus limitation, in turn, has a stronger effect on transitional ecosystem dynamics than interannual climate variability does. Overall, INLAND typically simulates more than 80 % of the AGB variability in the transition zone. However, the AGB in many places is clearly not well simulated, indicating that important soil and physiological factors in the Amazon-Cerrado border region, such as lithology, water table depth, carbon allocation strategies and mortality rates, still need to be included in the model.

Three-dimensional instabilities of mantle convection with multiple phase transitions

NASA Technical Reports Server (NTRS)

Honda, S.; Yuen, D. A.; Balachandar, S.; Reuteler, D.

1993-01-01

The effects of multiple phase transitions on mantle convection are investigated by numerical simulations that are based on three-dimensional models. These simulations show that cold sheets of mantle material collide at junctions, merge, and form a strong downflow that is stopped temporarily by the transition zone. The accumulated cold material gives rise to a strong gravitational instability that causes the cold mass to sink rapidly into the lower mantle. This process promotes a massive exchange between the lower and upper mantles and triggers a global instability in the adjacent plume system. This mechanism may be cyclic in nature and may be linked to the generation of superplumes.

Búsqueda de exoplanetas: ?`Cuán confiables son las observaciones obtenidas mediante telescopios terrestres?

NASA Astrophysics Data System (ADS)

von Essen, C.; Páez, R. I.; Schmitt, J. H. M. M.

The main goal of this work is to present a model that generates synthetic light curves of primary transits, comparable to real observations, to study transit timing variations (TTV). Considering that we can observe the sky from different virtual observatories, we simulated observations of primary transits caused by a hot-Jupiter. We artificially added a perturbation caused by an Earth-like exoplanet in a 3:2 mean motion resonance. These simulations would allow to analyze the degree of distorsion that the light curves admit, in order to recover back the induced signal by the exoplanet. FULL TEXT IN SPANISH

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

A Micromechanics-Based Elastoplastic Damage Model for Rocks with a Brittle-Ductile Transition in Mechanical Response

NASA Astrophysics Data System (ADS)

Hu, Kun; Zhu, Qi-zhi; Chen, Liang; Shao, Jian-fu; Liu, Jian

2018-06-01

As confining pressure increases, crystalline rocks of moderate porosity usually undergo a transition in failure mode from localized brittle fracture to diffused damage and ductile failure. This transition has been widely reported experimentally for several decades; however, satisfactory modeling is still lacking. The present paper aims at modeling the brittle-ductile transition process of rocks under conventional triaxial compression. Based on quantitative analyses of experimental results, it is found that there is a quite satisfactory linearity between the axial inelastic strain at failure and the confining pressure prescribed. A micromechanics-based frictional damage model is then formulated using an associated plastic flow rule and a strain energy release rate-based damage criterion. The analytical solution to the strong plasticity-damage coupling problem is provided and applied to simulate the nonlinear mechanical behaviors of Tennessee marble, Indiana limestone and Jinping marble, each presenting a brittle-ductile transition in stress-strain curves.

Comparison of Quantum and Classical Monte Carlo on a Simple Model Phase Transition

NASA Astrophysics Data System (ADS)

Cohen, D. E.; Cohen, R. E.

2005-12-01

Most simulations of phase transitions in minerals use classical molecular dynamics or classical Monte Carlo. However, it is known that in some cases, quantum effects are quite large, even for perovskite oxides [1]. We have studied the simplest model of a phase transition where this can be tested, that of interacting of double wells with an infinite- range interaction. The energy is E = ∑i (-A xi2 + B xi4 + ξ xi) . We used the same parameters used in a study of vibrational spectra and soft- mode behavior [4], A=0.01902, B=0.14294, ξ=0.025 in Hartree atomic units. This gives Tc of about 400 K. We varied the oscillator mass from 18 to 100. Classical Monte Carlo and path integral Monte Carlo (PIMC) were performed on this model. The maximum effect was for the lightest mass, in which PIMC gave a 75K lower Tc than the classical simulation. This is similar to the reduction in Tc observed in PIMC simulations for BaTiO3 at zero pressure [1]. We will explore the effects of varying the well depths. Shallower wells would show a greater quantum effect, as was seen in the high pressure BaTiO3 simulations, since pressure reduces the double well depths [5]. [1] Iniguez, J. & Vanderbilt, D. First-principles study of the temperature-pressure phase diagram of BaTiO3. Phys. Rev. Lett. 89, 115503 (2002). [2] Gillis, N. S. & Koehler, T. R. Phase transitions in a simple model ferroelectric-- -comparison of exact and variational treatments of a molecular-field Hamiltonian. Phys. Rev. B 9, 3806 (1974). [3] Koehler, T. R. & Gillis, N. S. Phase Transitions in a Model of Interacting Anharmonic Oscillators. Phys. Rev. B 7, 4980 (1973). [4] Flocken, J. W., Guenther, R. A., Hardy, J. R. & Boyer, L. L. Dielectric response spectrum of a damped one-dimensional double-well oscillator. Phys. Rev. B 40, 11496-11501 (1989). [5] Cohen, R. E. Origin of ferroelectricity in oxide ferroelectrics and the difference in ferroelectric behavior of BaTiO3 and PbTiO3. Nature 358, 136-138 (1992).

Research activities at the Center for Modeling of Turbulence and Transition

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing

1993-01-01

The main research activities at the Center for Modeling of Turbulence and Transition (CMOTT) are described. The research objective of CMOTT is to improve and/or develop turbulence and transition models for propulsion systems. The flows of interest in propulsion systems can be both compressible and incompressible, three dimensional, bounded by complex wall geometries, chemically reacting, and involve 'bypass' transition. The most relevant turbulence and transition models for the above flows are one- and two-equation eddy viscosity models, Reynolds stress algebraic- and transport-equation models, pdf models, and multiple-scale models. All these models are classified as one-point closure schemes since only one-point (in time and space) turbulent correlations, such as second moments (Reynolds stresses and turbulent heat fluxes) and third moments, are involved. In computational fluid dynamics, all turbulent quantities are one-point correlations. Therefore, the study of one-point turbulent closure schemes is the focus of our turbulence research. However, other research, such as the renormalization group theory, the direct interaction approximation method, and numerical simulations are also pursued to support the development of turbulence modeling.

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.

Chapter 5: Application of state-and-transition models to evaluate wildlife habitat

Treesearch

Anita T. Morzillo; Pamela Comeleo; Blair Csuti; Stephanie Lee

2014-01-01

Wildlife habitat analysis often is a central focus of natural resources management and policy. State-and-transition models (STMs) allow for simulation of landscape level ecological processes, and for managers to test “what if” scenarios of how those processes may affect wildlife habitat. This chapter describes the methods used to link STM output to wildlife habitat to...

Multiplicative Modeling of Children's Growth and Its Statistical Properties

NASA Astrophysics Data System (ADS)

Kuninaka, Hiroto; Matsushita, Mitsugu

2014-03-01

We develop a numerical growth model that can predict the statistical properties of the height distribution of Japanese children. Our previous studies have clarified that the height distribution of schoolchildren shows a transition from the lognormal distribution to the normal distribution during puberty. In this study, we demonstrate by simulation that the transition occurs owing to the variability of the onset of puberty.

Dynamical modeling and analysis of large cellular regulatory networks

NASA Astrophysics Data System (ADS)

Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.

2013-06-01

The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.

Single-Column Model Simulations of Subtropical Marine Boundary-Layer Cloud Transitions Under Weakening Inversions

NASA Astrophysics Data System (ADS)

Neggers, R. A. J.; Ackerman, A. S.; Angevine, W. M.; Bazile, E.; Beau, I.; Blossey, P. N.; Boutle, I. A.; de Bruijn, C.; Cheng, A.; van der Dussen, J.; Fletcher, J.; Dal Gesso, S.; Jam, A.; Kawai, H.; Cheedela, S. K.; Larson, V. E.; Lefebvre, M.-P.; Lock, A. P.; Meyer, N. R.; de Roode, S. R.; de Rooy, W.; Sandu, I.; Xiao, H.; Xu, K.-M.

2017-10-01

Results are presented of the GASS/EUCLIPSE single-column model intercomparison study on the subtropical marine low-level cloud transition. A central goal is to establish the performance of state-of-the-art boundary-layer schemes for weather and climate models for this cloud regime, using large-eddy simulations of the same scenes as a reference. A novelty is that the comparison covers four different cases instead of one, in order to broaden the covered parameter space. Three cases are situated in the North-Eastern Pacific, while one reflects conditions in the North-Eastern Atlantic. A set of variables is considered that reflects key aspects of the transition process, making use of simple metrics to establish the model performance. Using this method, some longstanding problems in low-level cloud representation are identified. Considerable spread exists among models concerning the cloud amount, its vertical structure, and the associated impact on radiative transfer. The sign and amplitude of these biases differ somewhat per case, depending on how far the transition has progressed. After cloud breakup the ensemble median exhibits the well-known "too few too bright" problem. The boundary-layer deepening rate and its state of decoupling are both underestimated, while the representation of the thin capping cloud layer appears complicated by a lack of vertical resolution. Encouragingly, some models are successful in representing the full set of variables, in particular, the vertical structure and diurnal cycle of the cloud layer in transition. An intriguing result is that the median of the model ensemble performs best, inspiring a new approach in subgrid parameterization.

Reynolds-averaged Navier-Stokes investigation of high-lift low-pressure turbine blade aerodynamics at low Reynolds number

NASA Astrophysics Data System (ADS)

Arko, Bryan M.

Design trends for the low-pressure turbine (LPT) section of modern gas turbine engines include increasing the loading per airfoil, which promises a decreased airfoil count resulting in reduced manufacturing and operating costs. Accurate Reynolds-Averaged Navier-Stokes predictions of separated boundary layers and transition to turbulence are needed, as the lack of an economical and reliable computational model has contributed to this high-lift concept not reaching its full potential. Presented here for what is believed to be the first time applied to low-Re computations of high-lift linear cascade simulations is the Abe-Kondoh-Nagano (AKN) linear low-Re two-equation turbulence model which utilizes the Kolmogorov velocity scale for improved predictions of separated boundary layers. A second turbulence model investigated is the Kato-Launder modified version of the AKN, denoted MPAKN, which damps turbulent production in highly strained regions of flow. Fully Laminar solutions have also been calculated in an effort to elucidate the transitional quality of the turbulence model solutions. Time accurate simulations of three modern high-lift blades at a Reynolds number of 25,000 are compared to experimental data and higher-order computations in order to judge the accuracy of the results, where it is shown that the RANS simulations with highly refined grids can produce both quantitatively and qualitatively similar separation behavior as found in experiments. In particular, the MPAKN model is shown to predict the correct boundary layer behavior for all three blades, and evidence of transition is found through inspection of the components of the Reynolds Stress Tensor, spectral analysis, and the turbulence production parameter. Unfortunately, definitively stating that transition is occurring becomes an uncertain task, as similar evidence of the transition process is found in the Laminar predictions. This reveals that boundary layer reattachment may be a result of laminar vortex shedding interaction with the blade surface, or that application of Laminar solvers with highly refined grids may be valid for investigations of transitional flow. It is recommended that this be studied in the future along with further studies of the turbulence models presented, which have proved to be worthy of additional study in the present application.

Longitudinal train dynamics model for a rail transit simulation system

DOE PAGES

Wang, Jinghui; Rakha, Hesham A.

2018-01-01

The paper develops a longitudinal train dynamics model in support of microscopic railway transportation simulation. The model can be calibrated without any mechanical data making it ideal for implementation in transportation simulators. The calibration and validation work is based on data collected from the Portland light rail train fleet. The calibration procedure is mathematically formulated as a constrained non-linear optimization problem. The validity of the model is assessed by comparing instantaneous model predictions against field observations, and also evaluated in the domains of acceleration/deceleration versus speed and acceleration/deceleration versus distance. A test is conducted to investigate the adequacy of themore » model in simulation implementation. The results demonstrate that the proposed model can adequately capture instantaneous train dynamics, and provides good performance in the simulation test. Thus, the model provides a simple theoretical foundation for microscopic simulators and will significantly support the planning, management and control of railway transportation systems.« less

Longitudinal train dynamics model for a rail transit simulation system

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

Wang, Jinghui; Rakha, Hesham A.

The paper develops a longitudinal train dynamics model in support of microscopic railway transportation simulation. The model can be calibrated without any mechanical data making it ideal for implementation in transportation simulators. The calibration and validation work is based on data collected from the Portland light rail train fleet. The calibration procedure is mathematically formulated as a constrained non-linear optimization problem. The validity of the model is assessed by comparing instantaneous model predictions against field observations, and also evaluated in the domains of acceleration/deceleration versus speed and acceleration/deceleration versus distance. A test is conducted to investigate the adequacy of themore » model in simulation implementation. The results demonstrate that the proposed model can adequately capture instantaneous train dynamics, and provides good performance in the simulation test. Thus, the model provides a simple theoretical foundation for microscopic simulators and will significantly support the planning, management and control of railway transportation systems.« less

Constraints on Cumulus Parameterization from Simulations of Observed MJO Events

NASA Technical Reports Server (NTRS)

Del Genio, Anthony; Wu, Jingbo; Wolf, Audrey B.; Chen, Yonghua; Yao, Mao-Sung; Kim, Daehyun

2015-01-01

Two recent activities offer an opportunity to test general circulation model (GCM) convection and its interaction with large-scale dynamics for observed Madden-Julian oscillation (MJO) events. This study evaluates the sensitivity of the Goddard Institute for Space Studies (GISS) GCM to entrainment, rain evaporation, downdrafts, and cold pools. Single Column Model versions that restrict weakly entraining convection produce the most realistic dependence of convection depth on column water vapor (CWV) during the Atmospheric Radiation Measurement MJO Investigation Experiment at Gan Island. Differences among models are primarily at intermediate CWV where the transition from shallow to deeper convection occurs. GCM 20-day hindcasts during the Year of Tropical Convection that best capture the shallow–deep transition also produce strong MJOs, with significant predictability compared to Tropical Rainfall Measuring Mission data. The dry anomaly east of the disturbance on hindcast day 1 is a good predictor of MJO onset and evolution. Initial CWV there is near the shallow–deep transition point, implicating premature onset of deep convection as a predictor of a poor MJO simulation. Convection weakly moistens the dry region in good MJO simulations in the first week; weakening of large-scale subsidence over this time may also affect MJO onset. Longwave radiation anomalies are weakest in the worst model version, consistent with previous analyses of cloud/moisture greenhouse enhancement as the primary MJO energy source. The authors’ results suggest that both cloud-/moisture-radiative interactions and convection–moisture sensitivity are required to produce a successful MJO simulation.

A stress-induced phase transition model for semi-crystallize shape memory polymer

NASA Astrophysics Data System (ADS)

Guo, Xiaogang; Zhou, Bo; Liu, Liwu; Liu, Yanju; Leng, Jinsong

2014-03-01

The developments of constitutive models for shape memory polymer (SMP) have been motivated by its increasing applications. During cooling or heating process, the phase transition which is a continuous time-dependent process happens in semi-crystallize SMP and the various individual phases form at different temperature and in different configuration. Then, the transformation between these phases occurred and shape memory effect will emerge. In addition, stress applied on SMP is an important factor for crystal melting during phase transition. In this theory, an ideal phase transition model considering stress or pre-strain is the key to describe the behaviors of shape memory effect. So a normal distributed model was established in this research to characterize the volume fraction of each phase in SMP during phase transition. Generally, the experiment results are partly backward (in heating process) or forward (in cooling process) compared with the ideal situation considering delay effect during phase transition. So, a correction on the normal distributed model is needed. Furthermore, a nonlinear relationship between stress and phase transition temperature Tg is also taken into account for establishing an accurately normal distributed phase transition model. Finally, the constitutive model which taking the stress as an influence factor on phase transition was also established. Compared with the other expressions, this new-type model possesses less parameter and is more accurate. For the sake of verifying the rationality and accuracy of new phase transition and constitutive model, the comparisons between the simulated and experimental results were carried out.

Numerical simulation of transitional flow on a wind turbine airfoil with RANS-based transition model

NASA Astrophysics Data System (ADS)

Zhang, Ye; Sun, Zhengzhong; van Zuijlen, Alexander; van Bussel, Gerard

2017-09-01

This paper presents a numerical investigation of transitional flow on the wind turbine airfoil DU91-W2-250 with chord-based Reynolds number Rec = 1.0 × 106. The Reynolds-averaged Navier-Stokes based transition model using laminar kinetic energy concept, namely the k - kL - ω model, is employed to resolve the boundary layer transition. Some ambiguities for this model are discussed and it is further implemented into OpenFOAM-2.1.1. The k - kL - ω model is first validated through the chosen wind turbine airfoil at the angle of attack (AoA) of 6.24° against wind tunnel measurement, where lift and drag coefficients, surface pressure distribution and transition location are compared. In order to reveal the transitional flow on the airfoil, the mean boundary layer profiles in three zones, namely the laminar, transitional and fully turbulent regimes, are investigated. Observation of flow at the transition location identifies the laminar separation bubble. The AoA effect on boundary layer transition over wind turbine airfoil is also studied. Increasing the AoA from -3° to 10°, the laminar separation bubble moves upstream and reduces in size, which is in close agreement with wind tunnel measurement.

Polymorphic phase transitions: Macroscopic theory and molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2017-08-01

Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation. To address these issues and to advance technology, there is an urgent need for significant insights that can only come from a detailed molecular level understanding of the involved processes. Whilst experimental approaches at best yield time- and space-averaged structural information, molecular simulation offers unprecedented, time-resolved molecular-level resolution of the processes taking place. This review aims to provide a comprehensive and critical account of state-of-the-art methods for modelling polymorph stability and transitions between solid phases. This is flanked by revisiting the associated macroscopic theoretical framework for phase transitions, including their classification, proposed molecular mechanisms, and kinetics. The simulation methods are presented in tutorial form, focusing on their application to phase transition phenomena. We describe molecular simulation studies for crystal structure prediction and polymorph screening, phase coexistence and phase diagrams, simulations of crystal-crystal transitions of various types (displacive/martensitic, reconstructive and diffusive), effects of defects, and phase stability and transitions at the nanoscale. Our selection of literature is intended to illustrate significant insights, concepts and understanding, as well as the current scope of using molecular simulations for understanding polymorphic transitions in an accessible way, rather than claiming completeness. With exciting prospects in both simulation methods development and enhancements in computer hardware, we are on the verge of accessing an unprecedented capability for designing and developing dosage forms and drug delivery systems in silico, including tackling challenges in polymorph control on a rational basis. Copyright © 2017 Elsevier B.V. All rights reserved.

A multiscale modeling framework model (superparameterized CAM5) with a higher-order turbulence closure: Model description and low-cloud simulations

DOE PAGES

Wang, Minghuai; Larson, Vincent E.; Ghan, Steven; ...

2015-04-18

In this study, a higher-order turbulence closure scheme, called Cloud Layers Unified by Binormals (CLUBB), is implemented into a Multi-scale Modeling Framework (MMF) model to improve low cloud simulations. The performance of CLUBB in MMF simulations with two different microphysics configurations (one-moment cloud microphysics without aerosol treatment and two-moment cloud microphysics coupled with aerosol treatment) is evaluated against observations and further compared with results from the Community Atmosphere Model, Version 5 (CAM5) with conventional cloud parameterizations. CLUBB is found to improve low cloud simulations in the MMF, and the improvement is particularly evident in the stratocumulus-to-cumulus transition regions. Compared tomore » the single-moment cloud microphysics, CLUBB with two-moment microphysics produces clouds that are closer to the coast, and agrees better with observations. In the stratocumulus-to cumulus transition regions, CLUBB with two-moment cloud microphysics produces shortwave cloud forcing in better agreement with observations, while CLUBB with single moment cloud microphysics overestimates shortwave cloud forcing. CLUBB is further found to produce quantitatively similar improvements in the MMF and CAM5, with slightly better performance in the MMF simulations (e.g., MMF with CLUBB generally produces low clouds that are closer to the coast than CAM5 with CLUBB). As a result, improved low cloud simulations in MMF make it an even more attractive tool for studying aerosol-cloud-precipitation interactions.« less

Experimental testing of a new integrated model of the budding yeast Start transition.

PubMed

Adames, Neil R; Schuck, P Logan; Chen, Katherine C; Murali, T M; Tyson, John J; Peccoud, Jean

2015-11-05

The cell cycle is composed of bistable molecular switches that govern the transitions between gap phases (G1 and G2) and the phases in which DNA is replicated (S) and partitioned between daughter cells (M). Many molecular details of the budding yeast G1-S transition (Start) have been elucidated in recent years, especially with regard to its switch-like behavior due to positive feedback mechanisms. These results led us to reevaluate and expand a previous mathematical model of the yeast cell cycle. The new model incorporates Whi3 inhibition of Cln3 activity, Whi5 inhibition of SBF and MBF transcription factors, and feedback inhibition of Whi5 by G1-S cyclins. We tested the accuracy of the model by simulating various mutants not described in the literature. We then constructed these novel mutant strains and compared their observed phenotypes to the model's simulations. The experimental results reported here led to further changes of the model, which will be fully described in a later article. Our study demonstrates the advantages of combining model design, simulation, and testing in a coordinated effort to better understand a complex biological network. © 2015 Adames et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Uncertainties in the Modelled CO2 Threshold for Antarctic Glaciation

NASA Technical Reports Server (NTRS)

Gasson, E.; Lunt, D. J.; DeConto, R.; Goldner, A.; Heinemann, M.; Huber, M.; LeGrande, A. N.; Pollard, D.; Sagoo, N.; Siddall, M.;

Rarefied flow past a flat plate at incidence

NASA Technical Reports Server (NTRS)

Dogra, Virendra K.; Moss, James N.; Price, Joseph M.

1988-01-01

Results of a numerical study using the direct simulation Monte Carlo (DSMC) method are presented for the transitional flow about a flat plate at 40 deg incidence. The plate has zero thickness and a length of 1.0 m. The flow conditions simulated are those experienced by the Shuttle Orbiter during reentry at 7.5 km/s. The range of freestream conditions are such that the freestream Knudsen number values are between 0.02 and 8.4, i.e., conditions that encompass most of the transitional flow regime. The DSMC simulations show that transitional effects are evident when compared with free molecule results for all cases considered. The calculated results demonstrate clearly the necessity of having a means of identifying the effects of transitional flow when making aerodynamic flight measurements as are currently being made with the Space Shuttle Orbiter vehicles. Previous flight data analyses have relied exclusively on adjustments in the gas-surface interaction models without accounting for the transitional effect which can be comparable in magnitude. The present calculations show that the transitional effect at 175 km would increase the Space Shuttle Orbiter lift-drag ratio by 90 percent over the free molecule value.

On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

PubMed

Wu, Chun; Shea, Joan-Emma

2010-11-18

FSD-1, a designed small ultrafast folder with a ββα fold, has been actively studied in the last few years as a model system for studying protein folding mechanisms and for testing of the accuracy of computational models. The suitability of this protein to describe the folding of naturally occurring α/β proteins has recently been challenged based on the observation that the melting transition is very broad, with ill-resolved baselines. Using molecular dynamics simulations with the AMBER protein force field (ff96) coupled with the implicit solvent model (IGB = 5), we shed new light into the nature of this transition and resolve the experimental controversies. We show that the melting transition corresponds to the melting of the protein as a whole, and not solely to the helix-coil transition. The breadth of the folding transition arises from the spread in the melting temperatures (from ∼325 K to ∼302 K) of the individual transitions: formation of the hydrophobic core, β-hairpin and tertiary fold, with the helix formed earlier. Our simulations initiated from an extended chain accurately predict the native structure, provide a reasonable estimate of the transition barrier height, and explicitly demonstrate the existence of multiple pathways and multiple transition states for folding. Our exhaustive sampling enables us to assess the quality of the Amber ff96/igb5 combination and reveals that while this force field can predict the correct native fold, it nonetheless overstabilizes the α-helix portion of the protein (Tm = ∼387K) as well as the denatured structures.

Simple model of sickle hemogloblin

NASA Astrophysics Data System (ADS)

Shiryayev, Andrey; Li, Xiaofei; Gunton, J. D.

2006-07-01

A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A solution of this model, however, requires accurate estimates of the interaction parameters which are currently unavailable. Therefore, as a first step toward a molecular understanding of the nucleation mechanisms in sickle hemoglobin, a Monte Carlo simulation of a simplified two patch model is carried out. A gradual transition from monomers to one dimensional chains is observed as one varies the density of molecules at fixed temperature, somewhat similar to the transition from monomers to polymer fibers in sickle hemoglobin molecules in solution. An observed competition between chain formation and crystallization for the model is also discussed. The results of the simulation of the equation of state are shown to be in excellent agreement with a theory for a model of globular proteins, for the case of two interacting sites.

Simulation of glioblastoma multiforme (GBM) tumor cells using ising model on the Creutz Cellular Automaton

NASA Astrophysics Data System (ADS)

Züleyha, Artuç; Ziya, Merdan; Selçuk, Yeşiltaş; Kemal, Öztürk M.; Mesut, Tez

2017-11-01

Computational models for tumors have difficulties due to complexity of tumor nature and capacities of computational tools, however, these models provide visions to understand interactions between tumor and its micro environment. Moreover computational models have potential to develop strategies for individualized treatments for cancer. To observe a solid brain tumor, glioblastoma multiforme (GBM), we present a two dimensional Ising Model applied on Creutz cellular automaton (CCA). The aim of this study is to analyze avascular spherical solid tumor growth, considering transitions between non tumor cells and cancer cells are like phase transitions in physical system. Ising model on CCA algorithm provides a deterministic approach with discrete time steps and local interactions in position space to view tumor growth as a function of time. Our simulation results are given for fixed tumor radius and they are compatible with theoretical and clinic data.

Gap Filler Induced Transition on the Mars Science Laboratory Heatshield

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan; Barnhardt, Michael D.; Tang, Chun Y.; Sozer, Emre; Candler, Graham

2012-01-01

Detached Eddy Simulations have been performed to investigate the effects of high-fidelity turbulence modeling on roughness-induced transition to turbulence during Mars entry. Chemically reacting flow solutions will be obtained for a gap filler of Mars Science Laboratory at the peak heating condition.

Gravitational waves from a first-order electroweak phase transition: a brief review

NASA Astrophysics Data System (ADS)

Weir, David J.

2018-01-01

We review the production of gravitational waves by an electroweak first-order phase transition. The resulting signal is a good candidate for detection at next-generation gravitational wave detectors, such as LISA. Detection of such a source of gravitational waves could yield information about physics beyond the Standard Model that is complementary to that accessible to current and near-future collider experiments. We summarize efforts to simulate and model the phase transition and the resulting production of gravitational waves. This article is part of the Theo Murphy meeting issue `Higgs cosmology'.

Transit Bus Fuel Economy and Performance Simulation

DOT National Transportation Integrated Search

1984-01-01

This report presents the results of bus simulation studies to determine the effects of various design and operating parameters on bus fuel economy and performance. The bus components are first described in terms of how they are modeled. Then a variat...

Mean field study of a propagation-turnover lattice model for the dynamics of histone marking

NASA Astrophysics Data System (ADS)

Yao, Fan; Li, FangTing; Li, TieJun

2017-02-01

We present a mean field study of a propagation-turnover lattice model, which was proposed by Hodges and Crabtree [Proc. Nat. Acad. Sci. 109, 13296 (2012)] for understanding how posttranslational histone marks modulate gene expression in mammalian cells. The kinetics of the lattice model consists of nucleation, propagation and turnover mechanisms, and exhibits second-order phase transition for the histone marking domain. We showed rigorously that the dynamics essentially depends on a non-dimensional parameter κ = k +/ k -, the ratio between the propagation and turnover rates, which has been observed in the simulations. We then studied the lowest order mean field approximation, and observed the phase transition with an analytically obtained critical parameter. The boundary layer analysis was utilized to investigate the structure of the decay profile of the mark density. We also studied the higher order mean field approximation to achieve sharper estimate of the critical transition parameter and more detailed features. The comparison between the simulation and theoretical results shows the validity of our theory.

Freezing Transition Studies Through Constrained Cell Model Simulation

NASA Astrophysics Data System (ADS)

Nayhouse, Michael; Kwon, Joseph Sang-Il; Heng, Vincent R.; Amlani, Ankur M.; Orkoulas, G.

2014-10-01

In the present work, a simulation method based on cell models is used to deduce the fluid-solid transition of a system of particles that interact via a pair potential, , which is of the form with . The simulations are implemented under constant-pressure conditions on a generalized version of the constrained cell model. The constrained cell model is constructed by dividing the volume into Wigner-Seitz cells and confining each particle in a single cell. This model is a special case of a more general cell model which is formed by introducing an additional field variable that controls the number of particles per cell and, thus, the relative stability of the solid against the fluid phase. High field values force configurations with one particle per cell and thus favor the solid phase. Fluid-solid coexistence on the isotherm that corresponds to a reduced temperature of 2 is determined from constant-pressure simulations of the generalized cell model using tempering and histogram reweighting techniques. The entire fluid-solid phase boundary is determined through a thermodynamic integration technique based on histogram reweighting, using the previous coexistence point as a reference point. The vapor-liquid phase diagram is obtained from constant-pressure simulations of the unconstrained system using tempering and histogram reweighting. The phase diagram of the system is found to contain a stable critical point and a triple point. The phase diagram of the corresponding constrained cell model is also found to contain both a stable critical point and a triple point.

Transition Induced by Fence Geometrics on Shuttle Orbiter at Mach 10

NASA Technical Reports Server (NTRS)

Everhart, Joel L.

2010-01-01

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

Ising model for collective decision making during group motion

NASA Astrophysics Data System (ADS)

Pinkoviezky, Itai; Gov, Nir; Couzin, Iain

Collective decision making is a key feature during natural motion of animal groups and is also crucial for human groups. This phenomenon can be exemplified by the scenario of two subgroups that hold conflicting preferred directions of motion. The constraint of group cohesion drives the motion either towards a compromise or towards one of the preferred targets. The transition between compromise and decision has been found in simulations of flock models, but the nature of this transition is not well understood. We present a minimal spin model for this system where we interpret the spin-spin interaction as a social force. This model exhibits both first and second order transitions. The group motion changes from size-dependent diffusion at high temperatures to run-and-tumble motion below the critical temperature. In the presence of minority and majority subgroups, we find that there is a trade-off between the speed of reaching a target and the accuracy. We then compare the results of the spin model to detailed simulations of a flock model, and find overall very similar dynamics, with the role of the temperature taken by the inverse of the number of uninformed individuals.

Free energies from dynamic weighted histogram analysis using unbiased Markov state model.

PubMed

Rosta, Edina; Hummer, Gerhard

2015-01-13

The weighted histogram analysis method (WHAM) is widely used to obtain accurate free energies from biased molecular simulations. However, WHAM free energies can exhibit significant errors if some of the biasing windows are not fully equilibrated. To account for the lack of full equilibration, we develop the dynamic histogram analysis method (DHAM). DHAM uses a global Markov state model to obtain the free energy along the reaction coordinate. A maximum likelihood estimate of the Markov transition matrix is constructed by joint unbiasing of the transition counts from multiple umbrella-sampling simulations along discretized reaction coordinates. The free energy profile is the stationary distribution of the resulting Markov matrix. For this matrix, we derive an explicit approximation that does not require the usual iterative solution of WHAM. We apply DHAM to model systems, a chemical reaction in water treated using quantum-mechanics/molecular-mechanics (QM/MM) simulations, and the Na(+) ion passage through the membrane-embedded ion channel GLIC. We find that DHAM gives accurate free energies even in cases where WHAM fails. In addition, DHAM provides kinetic information, which we here use to assess the extent of convergence in each of the simulation windows. DHAM may also prove useful in the construction of Markov state models from biased simulations in phase-space regions with otherwise low population.

Static and Dynamic Properties of Ferroelectric Thin Film Memories.

NASA Astrophysics Data System (ADS)

Duiker, Hendrik Matthew

Several properties of ferroelectric thin-film memories have been modeled. First, it has been observed experimentally that the bulk phase KNO_3 has a first-order phase transition, and that the transition temperature of KNO_3 thin-films increases as the thickness of the film is decreased. A Landau theory of first-order phase transitions in bulk systems has been generalized by adding surface terms to the free energy expansion to account for these transition properties. The model successfully describes the observed transition properties and predicts the existence of films in which the surfaces are ordered at temperatures higher than the bulk transition temperature. Second, the Avrami model of polarization-reversal kinetics has been modified to describe the following cases: ferroelectrics composed of a large number of small grains; ferroelectric thin-films in which nucleation occurs at the surfaces, not in the bulk; ferroelectrics in which long-range dipolar interactions significantly affect the nucleation rate; and non-square wave switching pulses. The models were verified by applying them to the results of two-dimensional Ising model simulations. It was shown that the models allow the possibility of directly obtaining microscopic parameters, such as the nucleation rate and domain wall velocity, from bulk measurements. Finally, a model describing the fatigue of ferroelectric memories has been developed. As a ferroelectric memory fatigues the spontaneous polarization per unit volume decreases, the switching time decreases, and eventually the memory "shorts out" and becomes conducting. The model assumes the following: during each polarization reversal the film undergoes, every unit cell in the film has a chance of "degrading" and thus losing an ion. Degraded cells no longer contribute to the polarization. The ions are allowed to diffuse to the surfaces of the film and form, with other ions, conducting dendrites which grow into the bulk of the film. Computer simulations performed on a two dimensional lattice with the above model successfully described the phenomena observed during the fatigue of PZT and other types of ferroelectric thin-film memories films.

Development and validation of rear impact computer simulation model of an adult manual transit wheelchair with a seated occupant.

PubMed

Salipur, Zdravko; Bertocci, Gina

2010-01-01

It has been shown that ANSI WC19 transit wheelchairs that are crashworthy in frontal impact exhibit catastrophic failures in rear impact and may not be able to provide stable seating support and thus occupant protection for the wheelchair occupant. Thus far only limited sled test and computer simulation data have been available to study rear impact wheelchair safety. Computer modeling can be used as an economic and comprehensive tool to gain critical knowledge regarding wheelchair integrity and occupant safety. This study describes the development and validation of a computer model simulating an adult wheelchair-seated occupant subjected to a rear impact event. The model was developed in MADYMO and validated rigorously using the results of three similar sled tests conducted to specifications provided in the draft ISO/TC 173 standard. Outcomes from the model can provide critical wheelchair loading information to wheelchair and tiedown manufacturers, resulting in safer wheelchair designs for rear impact conditions. (c) 2009 IPEM. Published by Elsevier Ltd. All rights reserved.

Unidirectional Transition Waves in Bistable Lattices

NASA Astrophysics Data System (ADS)

Nadkarni, Neel; Arrieta, Andres F.; Chong, Christopher; Kochmann, Dennis M.; Daraio, Chiara

2016-06-01

We present a model system for strongly nonlinear transition waves generated in a periodic lattice of bistable members connected by magnetic links. The asymmetry of the on-site energy wells created by the bistable members produces a mechanical diode that supports only unidirectional transition wave propagation with constant wave velocity. We theoretically justify the cause of the unidirectionality of the transition wave and confirm these predictions by experiments and simulations. We further identify how the wave velocity and profile are uniquely linked to the double-well energy landscape, which serves as a blueprint for transition wave control.

Analysis of a semiclassical model for rotational transition probabilities. [in highly nonequilibrium flow of diatomic molecules

NASA Technical Reports Server (NTRS)

Deiwert, G. S.; Yoshikawa, K. K.

1975-01-01

A semiclassical model proposed by Pearson and Hansen (1974) for computing collision-induced transition probabilities in diatomic molecules is tested by the direct-simulation Monte Carlo method. Specifically, this model is described by point centers of repulsion for collision dynamics, and the resulting classical trajectories are used in conjunction with the Schroedinger equation for a rigid-rotator harmonic oscillator to compute the rotational energy transition probabilities necessary to evaluate the rotation-translation exchange phenomena. It is assumed that a single, average energy spacing exists between the initial state and possible final states for a given collision.

Increased Rail Transit Vehicle Crashworthiness in Head-On Collisions. Volume I. Initial Impact.

DOT National Transportation Integrated Search

1980-06-01

A specific goal of safety is to reduce the number of injuries that may result from the collision of two trains. In Volume I, a two-dimensional analytic simulation model of the leading cars of two impacting transit car consists is formulated. This mod...

Simulation of Glacial Cycles Before and After the Mid-Pleistocene Transition

NASA Astrophysics Data System (ADS)

Ganopolski, A.; Willeit, M.; Calov, R.

2017-12-01

In spite of significant progress achieved in understanding of glacial cycles, the cause of Mid-Pleistocene transition (MPT) is still not fully understood. To study possible mechanisms of the MPT we used the Earth system model of intermediate complexity CLIMBER-2 which incorporates all major components of the Earth system - atmosphere, ocean, land surface, northern hemisphere ice sheets, terrestrial biota and soil carbon, aeolian dust and marine biogeochemistry. We run the model through the entire Quaternary. The only prescribed forcing in these simulations is variations in Earth orbital parameters. In addition we prescribed gradually evolving in time terrestrial sediment cover and global volcanic outgassing. We found that gradual removal of terrestrial sediment from the Northern Hemisphere continent by glacial processes is sufficient to explain transition from 40-ka to 100-ka worlds around 1 million years ago. By starting the model at different times and using the same initial conditions we found that modeling results converge to the same solution which depends only on the orbital forcing and lower boundary conditions. Our results thus strongly suggest that Quaternary glacial cycles are externally forced and nearly deterministic.

Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Cho, Minhaeng

2013-05-01

The Hessian matrix reconstruction method initially developed to extract the basis mode frequencies, vibrational coupling constants, and transition dipoles of the delocalized amide I, II, and III vibrations of polypeptides and proteins from quantum chemistry calculation results is used to obtain those properties of delocalized O-H stretch modes in liquid water. Considering the water symmetric and asymmetric O-H stretch modes as basis modes, we here develop theoretical models relating vibrational frequencies, transition dipoles, and coupling constants of basis modes to local water configuration and solvent electric potential. Molecular dynamics simulation was performed to generate an ensemble of water configurations that was in turn used to construct vibrational Hamiltonian matrices. Obtaining the eigenvalues and eigenvectors of the matrices and using the time-averaging approximation method, which was developed by the Skinner group, to calculating the vibrational spectra of coupled oscillator systems, we could numerically simulate the O-H stretch IR spectrum of liquid water. The asymmetric line shape and weak shoulder bands were quantitatively reproduced by the present computational procedure based on vibrational exciton model, where the polarization effects on basis mode transition dipoles and inter-mode coupling constants were found to be crucial in quantitatively simulating the vibrational spectra of hydrogen-bond networking liquid water.

Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A

PubMed Central

Shea, Joan-Emma; Onuchic, José N.; Brooks, Charles L.

1999-01-01

Topological frustration in an energetically unfrustrated off-lattice model of the helical protein fragment B of protein A from Staphylococcus aureus was investigated. This Gō-type model exhibited thermodynamic and kinetic signatures of a well-designed two-state folder with concurrent collapse and folding transitions and single exponential kinetics at the transition temperature. Topological frustration is determined in the absence of energetic frustration by the distribution of Fersht φ values. Topologically unfrustrated systems present a unimodal distribution sharply peaked at intermediate φ, whereas highly frustrated systems display a bimodal distribution peaked at low and high φ values. The distribution of φ values in protein A was determined both thermodynamically and kinetically. Both methods yielded a unimodal distribution centered at φ = 0.3 with tails extending to low and high φ values, indicating the presence of a small amount of topological frustration. The contacts with high φ values were located in the turn regions between helices I and II and II and III, intimating that these hairpins are in large part required in the transition state. Our results are in good agreement with all-atom simulations of protein A, as well as lattice simulations of a three- letter code 27-mer (which can be compared with a 60-residue helical protein). The relatively broad unimodal distribution of φ values obtained from the all-atom simulations and that from the minimalist model for the same native fold suggest that the structure of the transition state ensemble is determined mostly by the protein topology and not energetic frustration. PMID:10535953

Microscopic modeling of gas-surface scattering. I. A combined molecular dynamics-rate equation approach

NASA Astrophysics Data System (ADS)

Filinov, A.; Bonitz, M.; Loffhagen, D.

2018-06-01

A combination of first principle molecular dynamics (MD) simulations with a rate equation model (MD-RE approach) is presented to study the trapping and the scattering of rare gas atoms from metal surfaces. The temporal evolution of the atom fractions that are either adsorbed or scattered into the continuum is investigated in detail. We demonstrate that for this description one has to consider trapped, quasi-trapped and scattering states, and present an energetic definition of these states. The rate equations contain the transition probabilities between the states. We demonstrate how these rate equations can be derived from kinetic theory. Moreover, we present a rigorous way to determine the transition probabilities from a microscopic analysis of the particle trajectories generated by MD simulations. Once the system reaches quasi-equilibrium, the rates converge to stationary values, and the subsequent thermal adsorption/desorption dynamics is completely described by the rate equations without the need to perform further time-consuming MD simulations. As a proof of concept of our approach, MD simulations for argon atoms interacting with a platinum (111) surface are presented. A detailed deterministic trajectory analysis is performed, and the transition rates are constructed. The dependence of the rates on the incidence conditions and the lattice temperature is analyzed. Based on this example, we analyze the time scale of the gas-surface system to approach the quasi-stationary state. The MD-RE model has great relevance for the plasma-surface modeling as it makes an extension of accurate simulations to long, experimentally relevant time scales possible. Its application to the computation of atomic sticking probabilities is given in the second part (paper II).

The Challenge of Identifying Controls on Cloud Properties and Precipitation Onset for Cumulus Congestus Sampled During MC3E

DOE PAGES

Mechem, David B.; Giangrande, Scott E.

2018-03-01

Here, the controls on precipitation onset and the transition from shallow cumulus to congestus are explored using a suite of 16 large–eddy simulations based on the 25 May 2011 event from the Midlatitude Continental Convective Clouds Experiment (MC3E). The thermodynamic variables in the model are relaxed at various timescales to observationally constrained temperature and moisture profiles in order to better reproduce the observed behavior of precipitation onset and total precipitation. Three of the simulations stand out as best matching the precipitation observations and also perform well for independent comparisons of cloud fraction, precipitation area fraction, and evolution of cloud topmore » occurrence. All three simulations exhibit a destabilization over time, which leads to a transition to deeper clouds, but the evolution of traditional stability metrics by themselves is not able to explain differences in the simulations. Conditionally sampled cloud properties (in particular, mean cloud buoyancy), however, do elicit differences among the simulations. The inability of environmental profiles alone to discern subtle differences among the simulations and the usefulness of conditionally sampled model quantities argue for hybrid observational/modeling approaches. These combined approaches enable a more complete physical understanding of cloud systems by combining observational sampling of time–varying three–dimensional meteorological quantities and cloud properties, along with detailed representation of cloud microphysical and dynamical processes from numerical models.« less

The Challenge of Identifying Controls on Cloud Properties and Precipitation Onset for Cumulus Congestus Sampled During MC3E

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

Mechem, David B.; Giangrande, Scott E.

Here, the controls on precipitation onset and the transition from shallow cumulus to congestus are explored using a suite of 16 large–eddy simulations based on the 25 May 2011 event from the Midlatitude Continental Convective Clouds Experiment (MC3E). The thermodynamic variables in the model are relaxed at various timescales to observationally constrained temperature and moisture profiles in order to better reproduce the observed behavior of precipitation onset and total precipitation. Three of the simulations stand out as best matching the precipitation observations and also perform well for independent comparisons of cloud fraction, precipitation area fraction, and evolution of cloud topmore » occurrence. All three simulations exhibit a destabilization over time, which leads to a transition to deeper clouds, but the evolution of traditional stability metrics by themselves is not able to explain differences in the simulations. Conditionally sampled cloud properties (in particular, mean cloud buoyancy), however, do elicit differences among the simulations. The inability of environmental profiles alone to discern subtle differences among the simulations and the usefulness of conditionally sampled model quantities argue for hybrid observational/modeling approaches. These combined approaches enable a more complete physical understanding of cloud systems by combining observational sampling of time–varying three–dimensional meteorological quantities and cloud properties, along with detailed representation of cloud microphysical and dynamical processes from numerical models.« less

The Challenge of Identifying Controls on Cloud Properties and Precipitation Onset for Cumulus Congestus Sampled During MC3E

NASA Astrophysics Data System (ADS)

Mechem, David B.; Giangrande, Scott E.

2018-03-01

Controls on precipitation onset and the transition from shallow cumulus to congestus are explored using a suite of 16 large-eddy simulations based on the 25 May 2011 event from the Midlatitude Continental Convective Clouds Experiment (MC3E). The thermodynamic variables in the model are relaxed at various timescales to observationally constrained temperature and moisture profiles in order to better reproduce the observed behavior of precipitation onset and total precipitation. Three of the simulations stand out as best matching the precipitation observations and also perform well for independent comparisons of cloud fraction, precipitation area fraction, and evolution of cloud top occurrence. All three simulations exhibit a destabilization over time, which leads to a transition to deeper clouds, but the evolution of traditional stability metrics by themselves is not able to explain differences in the simulations. Conditionally sampled cloud properties (in particular, mean cloud buoyancy), however, do elicit differences among the simulations. The inability of environmental profiles alone to discern subtle differences among the simulations and the usefulness of conditionally sampled model quantities argue for hybrid observational/modeling approaches. These combined approaches enable a more complete physical understanding of cloud systems by combining observational sampling of time-varying three-dimensional meteorological quantities and cloud properties, along with detailed representation of cloud microphysical and dynamical processes from numerical models.

Methodology for Modeling the Microbial Contamination of Air Filters

PubMed Central

Joe, Yun Haeng; Yoon, Ki Young; Hwang, Jungho

2014-01-01

In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter. PMID:24523908

Introduction to MOVES2010, October 2010 Webinar Slides

EPA Pesticide Factsheets

This presentation provides a general overview of MOVES (MOtor Vehicle Emission Simulator) for non-modelers who need to understand the transition from MOBILE to MOVES, and background information on MOVES for modelers.

Dynamics of social contagions with local trend imitation.

PubMed

Zhu, Xuzhen; Wang, Wei; Cai, Shimin; Stanley, H Eugene

2018-05-09

Research on social contagion dynamics has not yet included a theoretical analysis of the ubiquitous local trend imitation (LTI) characteristic. We propose a social contagion model with a tent-like adoption probability to investigate the effect of this LTI characteristic on behavior spreading. We also propose a generalized edge-based compartmental theory to describe the proposed model. Through extensive numerical simulations and theoretical analyses, we find a crossover in the phase transition: when the LTI capacity is strong, the growth of the final adoption size exhibits a second-order phase transition. When the LTI capacity is weak, we see a first-order phase transition. For a given behavioral information transmission probability, there is an optimal LTI capacity that maximizes the final adoption size. Finally we find that the above phenomena are not qualitatively affected by the heterogeneous degree distribution. Our suggested theoretical predictions agree with the simulation results.

Numerical simulation of hot-melt extrusion processes for amorphous solid dispersions using model-based melt viscosity.

PubMed

Bochmann, Esther S; Steffens, Kristina E; Gryczke, Andreas; Wagner, Karl G

2018-03-01

Simulation of HME processes is a valuable tool for increased process understanding and ease of scale-up. However, the experimental determination of all required input parameters is tedious, namely the melt rheology of the amorphous solid dispersion (ASD) in question. Hence, a procedure to simplify the application of hot-melt extrusion (HME) simulation for forming amorphous solid dispersions (ASD) is presented. The commercial 1D simulation software Ludovic ® was used to conduct (i) simulations using a full experimental data set of all input variables including melt rheology and (ii) simulations using model-based melt viscosity data based on the ASDs glass transition and the physical properties of polymeric matrix only. Both types of HME computation were further compared to experimental HME results. Variation in physical properties (e.g. heat capacity, density) and several process characteristics of HME (residence time distribution, energy consumption) among the simulations and experiments were evaluated. The model-based melt viscosity was calculated by using the glass transition temperature (T g ) of the investigated blend and the melt viscosity of the polymeric matrix by means of a T g -viscosity correlation. The results of measured melt viscosity and model-based melt viscosity were similar with only few exceptions, leading to similar HME simulation outcomes. At the end, the experimental effort prior to HME simulation could be minimized and the procedure enables a good starting point for rational development of ASDs by means of HME. As model excipients, Vinylpyrrolidone-vinyl acetate copolymer (COP) in combination with various APIs (carbamazepine, dipyridamole, indomethacin, and ibuprofen) or polyethylene glycol (PEG 1500) as plasticizer were used to form the ASDs. Copyright © 2017 Elsevier B.V. All rights reserved.

Discretely Integrated Condition Event (DICE) Simulation for Pharmacoeconomics.

PubMed

Caro, J Jaime

2016-07-01

Several decision-analytic modeling techniques are in use for pharmacoeconomic analyses. Discretely integrated condition event (DICE) simulation is proposed as a unifying approach that has been deliberately designed to meet the modeling requirements in a straightforward transparent way, without forcing assumptions (e.g., only one transition per cycle) or unnecessary complexity. At the core of DICE are conditions that represent aspects that persist over time. They have levels that can change and many may coexist. Events reflect instantaneous occurrences that may modify some conditions or the timing of other events. The conditions are discretely integrated with events by updating their levels at those times. Profiles of determinant values allow for differences among patients in the predictors of the disease course. Any number of valuations (e.g., utility, cost, willingness-to-pay) of conditions and events can be applied concurrently in a single run. A DICE model is conveniently specified in a series of tables that follow a consistent format and the simulation can be implemented fully in MS Excel, facilitating review and validation. DICE incorporates both state-transition (Markov) models and non-resource-constrained discrete event simulation in a single formulation; it can be executed as a cohort or a microsimulation; and deterministically or stochastically.

Gas heating dynamics during leader inception in long air gaps at atmospheric pressure

NASA Astrophysics Data System (ADS)

Liu, Lipeng; Becerra, Marley

2017-08-01

The inception of leader discharges in long air gaps at atmospheric pressure is simulated with a thermo-hydrodynamic model and a detailed kinetic scheme for N2/O2/H2O mixtures. In order to investigate the effect of humidity, the kinetic scheme includes the most important reactions with the H2O molecule and its derivatives, resulting in a scheme with 45 species and 192 chemical reactions. The heating of a thin plasma channel in front of an anode electrode during the streamer to leader transition is evaluated with a detailed 1D radial model. The analysis includes the simulation of the corresponding streamer bursts, dark periods and aborted leaders that may occur prior to the inception of a propagating leader discharge. The simulations are performed using the time-varying discharge current in two laboratory discharge events of positive polarity reported in the literature as input. Excellent agreement between the simulated and the experimental time variation of the thermal radius for a 1 m rod-plate air gap discharge event reported in the literature has been found. The role of different energy transfer and loss mechanisms prior to the inception of a stable leader is also discussed. It is found that although a small percentage of water molecules can accelerate the vibrational-translational relaxation to some extent, this effect leads to a negligible temperature increase during the streamer-to-leader transition. It is also found that the gas temperature should significantly exceed 2000 K for the transition to lead to the inception of a propagating leader. Otherwise, the strong convection loss produced by the gas expansion during the transition causes a drop in the translational temperature below 2000 K, aborting the incepted leader. Furthermore, it is shown that the assumptions used by the widely-used model of Gallimberti do not hold when evaluating the streamer-to-leader transition.

Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation: Report of an FDA Public Workshop

PubMed Central

Duan, J; Kesisoglou, F; Novakovic, J; Amidon, GL; Jamei, M; Lukacova, V; Eissing, T; Tsakalozou, E; Zhao, L; Lionberger, R

2017-01-01

On May 19, 2016, the US Food and Drug Administration (FDA) hosted a public workshop, entitled “Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation.”1 The topic of mechanistic oral absorption modeling, which is one of the major applications of physiologically based pharmacokinetic (PBPK) modeling and simulation, focuses on predicting oral absorption by mechanistically integrating gastrointestinal transit, dissolution, and permeation processes, incorporating systems, active pharmaceutical ingredient (API), and the drug product information, into a systemic mathematical whole‐body framework.2 PMID:28571121

Cooperative Allosteric Ligand Binding in Calmodulin

NASA Astrophysics Data System (ADS)

Nandigrami, Prithviraj

Conformational dynamics is often essential for a protein's function. For example, proteins are able to communicate the effect of binding at one site to a distal region of the molecule through changes in its conformational dynamics. This so called allosteric coupling fine tunes the sensitivity of ligand binding to changes in concentration. A conformational change between a "closed" (apo) and an "open" (holo) conformation upon ligation often produces this coupling between binding sites. Enhanced sensitivity between the unbound and bound ensembles leads to a sharper binding curve. There are two basic conceptual frameworks that guide our visualization about ligand binding mechanisms. First, a ligand can stabilize the unstable "open" state from a dynamic ensemble of conformations within the unbound basin. This binding mechanism is called conformational selection. Second, a ligand can weakly bind to the low-affinity "closed" state followed by a conformational transition to the "open" state. In this dissertation, I focus on molecular dynamics simulations to understand microscopic origins of ligand binding cooperativity. A minimal model of allosteric binding transitions must include ligand binding/unbinding events, while capturing the transition mechanism between two distinct meta-stable free energy basins. Due in part to computational timescales limitations, work in this dissertation describes large-scale conformational transitions through a simplified, coarse-grained model based on the energy basins defined by the open and closed conformations of the protein Calmodulin (CaM). CaM is a ubiquitous calcium-binding protein consisting of two structurally similar globular domains connected by a flexible linker. The two domains of CaM, N-terminal domain (nCaM) and C-terminal domain (cCaM) consists of two helix-loop-helix motifs (the EF-hands) connected by a flexible linker. Each domain of CaM consists of two binding loops and binds 2 calcium ions each. The intact domain binds up to 4 calcium ions. The simulations use a coupled molecular dynamics/monte carlo scheme where the protein dynamics is simulated explicitly, while ligand binding/unbinding are treated implicitly. In the model, ligand binding/unbinding events coupled with a conformational change of the protein within the grand canonical ensemble. Here, ligand concentration is controlled through the chemical potential (micro). This allows us to use a simple thermodynamic model to analyze the simulated data and quantify binding cooperativity. Simulated binding titration curves are calculated through equilibrium simulations at different values of micro. First, I study domain opening transitions of isolated nCaM and cCaM in the absence of calcium. This work is motivated by results from a recent analytic variational model that predicts distinct domain opening transition mechanism for the domains of CaM. This is a surprising result because the domains have the same folded state topology. In the simulations, I find the two domains of CaM have distinct transition mechanism over a broad range of temperature, in harmony with the analytic predictions. In particular, the simulated transition mechanism of nCaM follows a two-state behavior, while domain opening in cCaM involves global unfolding and refolding of the tertiary structure. The unfolded intermediate also appears in the landscape of nCaM, but at a higher temperature than it appears in cCaM's energy landscape. This is consistent with nCaM's higher thermal stability. Under approximate physiological conditions, majority of the sampled transitions in cCaM involves unfolding and refolding during conformational change. Kinetically, the transient unfolding and refolding in cCaM significantly slows the domain opening and closing rates in cCaM. Second, I investigate the structural origins of binding affinity and allosteric cooperativity of binding 2 calcium-ions to each domain of CaM. In my work, I predict the order of binding strength of CaM's loops. I analyze simulated binding curves within the framework of the classic Monod-Wyman-Changeux (MWC) model of allostery to extract the binding free energies to the closed and open ensembles. The simulations predict that cCaM binds calcium with higher affinity and greater cooperativity than nCaM. Where it is possible to compare, these predictions are in good agreement with experimental results. The analysis of the simulations offers a rationale for why the two domains differ in cooperativity: the higher cooperativity of cCaM is due to larger difference in affinity of its binding loops. Third, I extend the work to investigate structural origins of binding cooperativity of 4 calcium-ions to intact CaM. I characterize the microscopic cooperativities of each ligation state and provide a kinetic description of the binding mechanism. Due to the heterogeneous nature of CaM's loops, as predicted in our simulations of isolated domains, I focus on investigating the influence of this heterogeneity on the kinetic flux of binding pathways as a function of concentration. The formalism developed for Network Models of protein folding kinetics, is used to evaluate the directed flux of all possible pathways between unligated and fully loaded CaM. (Abstract shortened by ProQuest.).

Free energy and phase equilibria for the restricted primitive model of ionic fluids from Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Orkoulas, Gerassimos; Panagiotopoulos, Athanassios Z.

1994-07-01

In this work, we investigate the liquid-vapor phase transition of the restricted primitive model of ionic fluids. We show that at the low temperatures where the phase transition occurs, the system cannot be studied by conventional molecular simulation methods because convergence to equilibrium is slow. To accelerate convergence, we propose cluster Monte Carlo moves capable of moving more than one particle at a time. We then address the issue of charged particle transfers in grand canonical and Gibbs ensemble Monte Carlo simulations, for which we propose a biased particle insertion/destruction scheme capable of sampling short interparticle distances. We compute the chemical potential for the restricted primitive model as a function of temperature and density from grand canonical Monte Carlo simulations and the phase envelope from Gibbs Monte Carlo simulations. Our calculated phase coexistence curve is in agreement with recent results of Caillol obtained on the four-dimensional hypersphere and our own earlier Gibbs ensemble simulations with single-ion transfers, with the exception of the critical temperature, which is lower in the current calculations. Our best estimates for the critical parameters are T*c=0.053, ρ*c=0.025. We conclude with possible future applications of the biased techniques developed here for phase equilibrium calculations for ionic fluids.

Data-driven RANS for simulations of large wind farms

NASA Astrophysics Data System (ADS)

Iungo, G. V.; Viola, F.; Ciri, U.; Rotea, M. A.; Leonardi, S.

2015-06-01

In the wind energy industry there is a growing need for real-time predictions of wind turbine wake flows in order to optimize power plant control and inhibit detrimental wake interactions. To this aim, a data-driven RANS approach is proposed in order to achieve very low computational costs and adequate accuracy through the data assimilation procedure. The RANS simulations are implemented with a classical Boussinesq hypothesis and a mixing length turbulence closure model, which is calibrated through the available data. High-fidelity LES simulations of a utility-scale wind turbine operating with different tip speed ratios are used as database. It is shown that the mixing length model for the RANS simulations can be calibrated accurately through the Reynolds stress of the axial and radial velocity components, and the gradient of the axial velocity in the radial direction. It is found that the mixing length is roughly invariant in the very near wake, then it increases linearly with the downstream distance in the diffusive region. The variation rate of the mixing length in the downstream direction is proposed as a criterion to detect the transition between near wake and transition region of a wind turbine wake. Finally, RANS simulations were performed with the calibrated mixing length model, and a good agreement with the LES simulations is observed.

Intra-Urban Human Mobility and Activity Transition: Evidence from Social Media Check-In Data

PubMed Central

Wu, Lun; Zhi, Ye; Sui, Zhengwei; Liu, Yu

2014-01-01

Most existing human mobility literature focuses on exterior characteristics of movements but neglects activities, the driving force that underlies human movements. In this research, we combine activity-based analysis with a movement-based approach to model the intra-urban human mobility observed from about 15 million check-in records during a yearlong period in Shanghai, China. The proposed model is activity-based and includes two parts: the transition of travel demands during a specific time period and the movement between locations. For the first part, we find the transition probability between activities varies over time, and then we construct a temporal transition probability matrix to represent the transition probability of travel demands during a time interval. For the second part, we suggest that the travel demands can be divided into two classes, locationally mandatory activity (LMA) and locationally stochastic activity (LSA), according to whether the demand is associated with fixed location or not. By judging the combination of predecessor activity type and successor activity type we determine three trip patterns, each associated with a different decay parameter. To validate the model, we adopt the mechanism of an agent-based model and compare the simulated results with the observed pattern from the displacement distance distribution, the spatio-temporal distribution of activities, and the temporal distribution of travel demand transitions. The results show that the simulated patterns fit the observed data well, indicating that these findings open new directions for combining activity-based analysis with a movement-based approach using social media check-in data. PMID:24824892

Exploration of Force Transition in Stability Operations Using Multi-Agent Simulation

DTIC Science & Technology

2006-09-01

risk, mission failure risk, and time in the context of the operational threat environment. The Pythagoras Multi-Agent Simulation and Data Farming...NUMBER OF PAGES 173 14. SUBJECT TERMS Stability Operations, Peace Operations, Data Farming, Pythagoras , Agent- Based Model, Multi-Agent Simulation...the operational threat environment. The Pythagoras Multi-Agent Simulation and Data Farming techniques are used to investigate force-level

Modeling the Dynamics of the Atmospheric Boundary Layer Over the Antarctic Plateau With a General Circulation Model

NASA Astrophysics Data System (ADS)

Vignon, Etienne; Hourdin, Frédéric; Genthon, Christophe; Van de Wiel, Bas J. H.; Gallée, Hubert; Madeleine, Jean-Baptiste; Beaumet, Julien

2018-01-01

Observations evidence extremely stable boundary layers (SBL) over the Antarctic Plateau and sharp regime transitions between weakly and very stable conditions. Representing such features is a challenge for climate models. This study assesses the modeling of the dynamics of the boundary layer over the Antarctic Plateau in the LMDZ general circulation model. It uses 1 year simulations with a stretched-grid over Dome C. The model is nudged with reanalyses outside of the Dome C region such as simulations can be directly compared to in situ observations. We underline the critical role of the downward longwave radiation for modeling the surface temperature. LMDZ reasonably represents the near-surface seasonal profiles of wind and temperature but strong temperature inversions are degraded by enhanced turbulent mixing formulations. Unlike ERA-Interim reanalyses, LMDZ reproduces two SBL regimes and the regime transition, with a sudden increase in the near-surface inversion with decreasing wind speed. The sharpness of the transition depends on the stability function used for calculating the surface drag coefficient. Moreover, using a refined vertical grid leads to a better reversed "S-shaped" relationship between the inversion and the wind. Sudden warming events associated to synoptic advections of warm and moist air are also well reproduced. Near-surface supersaturation with respect to ice is not allowed in LMDZ but the impact on the SBL structure is moderate. Finally, climate simulations with the free model show that the recommended configuration leads to stronger inversions and winds over the ice-sheet. However, the near-surface wind remains underestimated over the slopes of East-Antarctica.

Glassiness versus Order in Densely Frustrated Josephson Arrays

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

Gupta, P.; Teitel, S.; Gingras, M.J.

1998-01-01

We carry out extensive Monte Carlo simulations of the Coulomb gas dual to the uniformly frustrated two-dimensional XY model, for a sequence of frustrations f converging to the irrational (3{minus}{radical}(5))/ 2. We find in these systems a sharp first order equilibrium phase transition to an ordered vortex structure at a T{sub c} which varies only slightly with f . This ordered vortex structure remains, in general, phase incoherent until a lower vortex pinning transition T{sub p}(f) that varies with f. We argue that the glassy behaviors reported for this model in earlier simulations are dynamic effects. {copyright} {ital 1997} {italmore » The American Physical Society}« less

Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations

PubMed Central

Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-01-01

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. PMID:23663843

Mapping conformational dynamics of proteins using torsional dynamics simulations.

PubMed

Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-05-07

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Elastic Model Transitions: A Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

NASA Technical Reports Server (NTRS)

Hannan, Mike R.; Jurenko, Robert J.; Bush, Jason; Ottander, John

2014-01-01

A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes a hybrid approach for determining physical displacements by augmenting the original quadratically constrained least squares (LSQI) algorithm with Direct Shape Mapping (DSM) and modifying the energy constraints. The approach presented is applicable to simulation of the elastic behavior of launch vehicles and other structures that utilize discrete LTI finite element model (FEM) derived mode sets (eigenvalues and eigenvectors) that are propagated throughout time. The time invariant nature of the elastic data presents a problem of how to properly transition elastic states from the prior to the new model while preserving motion across the transition and ensuring there is no truncation or excitation of the system. A previous approach utilizes a LSQI algorithm with an energy constraint to effect smooth transitions between eigenvector sets with no requirement that the models be of similar dimension or have any correlation. This approach assumes energy is conserved across the transition, which results in significant non-physical transients due to changing quasi-steady state energy between mode sets, a phenomenon seen when utilizing a truncated mode set. The computational burden of simulating a full mode set is significant so a subset of modes is often selected to reduce run time. As a result of this truncation, energy between mode sets may not be constant and solutions across transitions could produce non-physical transients. In an effort to abate these transients an improved methodology was developed based on the aforementioned approach, but this new approach can handle significant changes in energy across mode set transitions. It is proposed that physical velocities due to elastic behavior be solved for using the LSQI algorithm, but solve for displacements using a two-step process that independently addresses the quasi-steady-state and non-steady-state contributions to the elastic displacement. For structures subject to large external forces, such as thrust or atmospheric drag, it is imperative to capture these forces when solving for elastic displacement. To simplify the mathematical formulation, assumptions are made regarding mass matrix normalization, constant external forcing, and constant viscous damping. These simplifications allow for direct solutions to the quasi-steady-state displacements through a process titled Direct Shape Mapping. DSM solves for the displacements using the eigenvalues of the elastic modes and the external forcing and returns a set of elastic displacements dictated by the eigenvectors of the post-transition mode set. For the non-steady-state contributions to displacement we formulate a LSQI problem that is constrained by energy of the non-steady state terms. The contributions from the quasi-steady-state and non-steady state solutions are then combined to obtain the physical displacements associated with the new set of eigenvectors. Results for the LSQI-DSM approach show significant reduction/complete removal of transients across mode set transitions while maintaining elastic motion from the prior state. For time propagation applications employing discrete elastic models that need to be transitioned in time and where running with full a full mode set is not feasible, the method developed offers a practical solution to simulating vehicle elasticity.

Impact of Basal Hydrology Near Grounding Lines: Results from the MISMIP-3D and MISMIP+ Experiments Using the Community Ice Sheet Model

NASA Astrophysics Data System (ADS)

Leguy, G.; Lipscomb, W. H.; Asay-Davis, X.

2017-12-01

Ice sheets and ice shelves are linked by the transition zone, the region where the grounded ice lifts off the bedrock and begins to float. Adequate resolution of the transition zone is necessary for numerically accurate ice sheet-ice shelf simulations. In previous work we have shown that by using a simple parameterization of the basal hydrology, a smoother transition in basal water pressure between floating and grounded ice improves the numerical accuracy of a one-dimensional vertically integrated fixed-grid model. We used a set of experiments based on the Marine Ice Sheet Model Intercomparison Project (MISMIP) to show that reliable grounding-line dynamics at resolutions 1 km is achievable. In this presentation we use the Community Ice Sheet Model (CISM) to demonstrate how the representation of basal lubrication impacts three-dimensional models using the MISMIP-3D and MISMIP+ experiments. To this end we will compare three different Stokes approximations: the Shallow Shelf Approximation (SSA), a depth-integrated higher-order approximation, and the Blatter-Pattyn model. The results from our one-dimensional model carry over to the 3-D models; a resolution of 1 km (and in some cases 2 km) remains sufficient to accurately simulate grounding-line dynamics.

Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification

NASA Astrophysics Data System (ADS)

Swinburne, Thomas D.; Perez, Danny

2018-05-01

A massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.

Direct calculation of liquid-vapor phase equilibria from transition matrix Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Errington, Jeffrey R.

2003-06-01

An approach for directly determining the liquid-vapor phase equilibrium of a model system at any temperature along the coexistence line is described. The method relies on transition matrix Monte Carlo ideas developed by Fitzgerald, Picard, and Silver [Europhys. Lett. 46, 282 (1999)]. During a Monte Carlo simulation attempted transitions between states along the Markov chain are monitored as opposed to tracking the number of times the chain visits a given state as is done in conventional simulations. Data collection is highly efficient and very precise results are obtained. The method is implemented in both the grand canonical and isothermal-isobaric ensemble. The main result from a simulation conducted at a given temperature is a density probability distribution for a range of densities that includes both liquid and vapor states. Vapor pressures and coexisting densities are calculated in a straightforward manner from the probability distribution. The approach is demonstrated with the Lennard-Jones fluid. Coexistence properties are directly calculated at temperatures spanning from the triple point to the critical point.

Simulation Studies of LCST-like Phase Transitions in Elastin-like Polypeptides (ELPs) and Conjugates of ELP with Rigid Macromolecules

NASA Astrophysics Data System (ADS)

Condon, Joshua; Martin, Tyler; Jayaraman, Arthi

We use atomistic (AA) and coarse-grained (CG) molecular dynamics simulations to elucidate the thermodynamic driving forces governing lower critical solution temperature (LCST)-like phase transition exhibited by elastin-like peptides (ELPs) and conjugates of ELP with other macromolecules. In the AA simulations, we study ELP oligomers in explicit water, and mark the transition as the temperature at which they undergo a change in ``hydration'' state. While AA simulations are restricted to small systems of short ELPs and do not capture the chain aggregation observed in experiments of ELPs, they guide the phenomenological CG model development by highlighting the solvent induced polymer-polymer effective interactions with changing temperature. In the CG simulations, we capture the LCST polymer aggregation by increasing polymer-polymer effective attractive interactions in an implicit solvent. We examine the impact of conjugating a block of LCST polymer to another rigid unresponsive macromolecular block on the LCST-like transition. We find that when multiple LCST polymers are conjugated to a rigid polymer block, increased crowding of the LCST polymers shifts the onset of chain aggregation to smaller effective polymer-polymer attraction compared to the free LCST polymers. These simulation results provide guidance on the design of conjugated bio-mimetic thermoresponsive materials, and shape the fundamental understanding of the impact of polymer crowding on phase behavior in thermoresponsive LCST polymer systems.

ONE ATMOSPHERE MODELING FOR AIR QUALITY: BUILDING PARTNERSHIPS THAT TRANSITION RESEARCH INTO APPLICATIONS

EPA Science Inventory

The Community Miultiscale Air Quality (CMAQ) modeling system is a "one atmosphere" chemical transport model that simulates the transport and fate of air pollutants from urban to continental scales and from daily to annual time intervals.

Systems Operation Studies for Automated Guideway Transit Systems : System Availability Model User's Manual

DOT National Transportation Integrated Search

1981-01-01

The System Availability Model (SAM) is a system-level model which provides measures of vehicle and passenger availability. The SAM operates in conjunction with the AGT discrete Event Simulation Model (DESM). The DESM output is the normal source of th...

Computer Simulation of the Forces Acting on the Polystyrene Probe Submerged into the Succinonitrile Near Phase Transition

NASA Technical Reports Server (NTRS)

Bune, Andris V.; Kaukler, William F.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. At mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. The model of cantilever oscillations is applicable to both non-contact and "tapping" AFM. This model can be farther enhanced to describe nanoparticle manipulation by cantilever. At microscopic level tip contamination and details of tip-surface interaction can be simulated using molecular dynamics approach. Integration of mesoscale model with molecular dynamic model is discussed.

Stochastic dynamics for reinfection by transmitted diseases

NASA Astrophysics Data System (ADS)

Barros, Alessandro S.; Pinho, Suani T. R.

2017-06-01

The use of stochastic models to study the dynamics of infectious diseases is an important tool to understand the epidemiological process. For several directly transmitted diseases, reinfection is a relevant process, which can be expressed by endogenous reactivation of the pathogen or by exogenous reinfection due to direct contact with an infected individual (with smaller reinfection rate σ β than infection rate β ). In this paper, we examine the stochastic susceptible, infected, recovered, infected (SIRI) model simulating the endogenous reactivation by a spontaneous reaction, while exogenous reinfection by a catalytic reaction. Analyzing the mean-field approximations of a site and pairs of sites, and Monte Carlo (MC) simulations for the particular case of exogenous reinfection, we obtained continuous phase transitions involving endemic, epidemic, and no transmission phases for the simple approach; the approach of pairs is better to describe the phase transition from endemic phase (susceptible, infected, susceptible (SIS)-like model) to epidemic phase (susceptible, infected, and removed or recovered (SIR)-like model) considering the comparison with MC results; the reinfection increases the peaks of outbreaks until the system reaches endemic phase. For the particular case of endogenous reactivation, the approach of pairs leads to a continuous phase transition from endemic phase (SIS-like model) to no transmission phase. Finally, there is no phase transition when both effects are taken into account. We hope the results of this study can be generalized for the susceptible, exposed, infected, and removed or recovered (SEIRIE) model, for which the state exposed (infected but not infectious), describing more realistically transmitted diseases such as tuberculosis. In future work, we also intend to investigate the effect of network topology on phase transitions when the SIRI model describes both transmitted diseases (σ <1 ) and social contagions (σ >1 ).

Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding.

PubMed

Tamura, Koichi; Hayashi, Shigehiko

2015-07-14

Molecular functions of proteins are often fulfilled by global conformational changes that couple with local events such as the binding of ligand molecules. High molecular complexity of proteins has, however, been an obstacle to obtain an atomistic view of the global conformational transitions, imposing a limitation on the mechanistic understanding of the functional processes. In this study, we developed a new method of molecular dynamics (MD) simulation called the linear response path following (LRPF) to simulate a protein's global conformational changes upon ligand binding. The method introduces a biasing force based on a linear response theory, which determines a local reaction coordinate in the configuration space that represents linear coupling between local events of ligand binding and global conformational changes and thus provides one with fully atomistic models undergoing large conformational changes without knowledge of a target structure. The overall transition process involving nonlinear conformational changes is simulated through iterative cycles consisting of a biased MD simulation with an updated linear response force and a following unbiased MD simulation for relaxation. We applied the method to the simulation of global conformational changes of the yeast calmodulin N-terminal domain and successfully searched out the end conformation. The atomistically detailed trajectories revealed a sequence of molecular events that properly lead to the global conformational changes and identified key steps of local-global coupling that induce the conformational transitions. The LRPF method provides one with a powerful means to model conformational changes of proteins such as motors and transporters where local-global coupling plays a pivotal role in their functional processes.

Simulating the minimum core for hydrophobic collapse in globular proteins.

PubMed Central

Tsai, J.; Gerstein, M.; Levitt, M.

1997-01-01

To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling of the cluster formation observed by simulation indicates that this aggregation is cooperative and that the simulations favor the formation of a single cluster midway through the transition stage. This defines a minimum solute hydrophobic core volume. We compare this with protein hydrophobic core volumes determined from solved crystal structures. Our analysis shows that the solute core volume roughly estimates the minimum core size required for independent hydrophobic stabilization of a protein and defines a limiting concentration of nonpolar residues that can cause hydrophobic collapse. These results suggest that the physical forces driving aggregation of hydrophobic molecules in water is indeed responsible for protein folding. PMID:9416609

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

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

Microphysical characteristics of squall-line stratiform precipitation and transition zones inferred using an ice particle property-evolving model

NASA Astrophysics Data System (ADS)

Jensen, A. A.; Harrington, J. Y.; Morrison, H.

2017-12-01

A quasi-idealized 3D squall line (based on a June 2007 Oklahoma case) is simulated using a novel bulk microphysics scheme called the Ice-Spheroids Habit Model with Aspect-ratio Evolution (ISHMAEL). In ISHMAEL, the evolution of ice particle properties, such as mass, shape, maximum diameter, density, and fall speed, are tracked as these properties evolve from vapor growth, sublimation, riming, and melting. Thus, ice properties evolve from various microphysical processes without needing separate unrimed and rimed ice categories. Simulation results show that ISHMAEL produces both a squall-line transition zone and an enhanced stratiform precipitation region. The ice particle properties produced in this simulation are analyzed and compared to observations to determine the characteristics of ice that lead to the development of these squall-line features. It is shown that rimed particles advected rearward from the convective region produce the enhanced stratiform precipitation region. The development of the transition zone results from hydrometer sorting: the evolution of ice particle properties in the convective region produces specific fall speeds that favor significant ice advecting rearward of the transition zone before reaching the melting level, causing a local minimum in precipitation rate and reflectivity there. Microphysical sensitivity studies, for example turning rime splintering off, that lead to changes in ice particle properties reveal that the fall speed of ice particles largely determines both the location of the enhanced stratiform precipitation region and whether or not a transition zone forms.

Phase transitions in the q -voter model with noise on a duplex clique

NASA Astrophysics Data System (ADS)

Chmiel, Anna; Sznajd-Weron, Katarzyna

2015-11-01

We study a nonlinear q -voter model with stochastic noise, interpreted in the social context as independence, on a duplex network. To study the role of the multilevelness in this model we propose three methods of transferring the model from a mono- to a multiplex network. They take into account two criteria: one related to the status of independence (LOCAL vs GLOBAL) and one related to peer pressure (AND vs OR). In order to examine the influence of the presence of more than one level in the social network, we perform simulations on a particularly simple multiplex: a duplex clique, which consists of two fully overlapped complete graphs (cliques). Solving numerically the rate equation and simultaneously conducting Monte Carlo simulations, we provide evidence that even a simple rearrangement into a duplex topology may lead to significant changes in the observed behavior. However, qualitative changes in the phase transitions can be observed for only one of the considered rules: LOCAL&AND. For this rule the phase transition becomes discontinuous for q =5 , whereas for a monoplex such behavior is observed for q =6 . Interestingly, only this rule admits construction of realistic variants of the model, in line with recent social experiments.

Simulation model for port shunting yards

NASA Astrophysics Data System (ADS)

Rusca, A.; Popa, M.; Rosca, E.; Rosca, M.; Dragu, V.; Rusca, F.

2016-08-01

Sea ports are important nodes in the supply chain, joining two high capacity transport modes: rail and maritime transport. The huge cargo flows transiting port requires high capacity construction and installation such as berths, large capacity cranes, respectively shunting yards. However, the port shunting yards specificity raises several problems such as: limited access since these are terminus stations for rail network, the in-output of large transit flows of cargo relatively to the scarcity of the departure/arrival of a ship, as well as limited land availability for implementing solutions to serve these flows. It is necessary to identify technological solutions that lead to an answer to these problems. The paper proposed a simulation model developed with ARENA computer simulation software suitable for shunting yards which serve sea ports with access to the rail network. Are investigates the principal aspects of shunting yards and adequate measures to increase their transit capacity. The operation capacity for shunting yards sub-system is assessed taking in consideration the required operating standards and the measure of performance (e.g. waiting time for freight wagons, number of railway line in station, storage area, etc.) of the railway station are computed. The conclusion and results, drawn from simulation, help transports and logistics specialists to test the proposals for improving the port management.

Mott transition in the π -flux S U (4 ) Hubbard model on a square lattice

NASA Astrophysics Data System (ADS)

Zhou, Zhichao; Wu, Congjun; Wang, Yu

2018-05-01

With increasing repulsive interaction, we show that a Mott transition occurs from the semimetal to the valence bond solid, accompanied by the Z4 discrete symmetry breaking. Our simulations demonstrate the existence of a second-order phase transition, which confirms the Ginzburg-Landau analysis. The phase transition point and the critical exponent η are also estimated. To account for the effect of a π flux on the ordering in the strong-coupling regime, we analytically derive by the perturbation theory the ring-exchange term, which is the leading-order term that can reflect the difference between the π -flux and zero-flux S U (4 ) Hubbard models.

Mechanical Metamaterials with Negative Compressibility Transitions

NASA Astrophysics Data System (ADS)

Motter, Adilson

2015-03-01

When tensioned, ordinary materials expand along the direction of the applied force. In this presentation, I will explore network concepts to design metamaterials exhibiting negative compressibility transitions, during which the material undergoes contraction when tensioned (or expansion when pressured). Such transitions, which are forbidden in thermodynamic equilibrium, are possible during the decay of metastable, super-strained states. I will introduce a statistical physics theory for negative compressibility transitions, derive a first-principles model to predict these transitions, and present a validation of the model using molecular dynamics simulations. Aside from its immediate mechanical implications, our theory points to a wealth of analogous inverted responses, such as inverted susceptibility or heat-capacity transitions, allowed when considering realistic scales. This research was done in collaboration with Zachary Nicolaou, and was supported by the National Science Foundation and the Alfred P. Sloan Foundation.

Anomalous critical slowdown at a first order phase transition in single polymer chains.

PubMed

Zhang, Shuangshuang; Qi, Shuanhu; Klushin, Leonid I; Skvortsov, Alexander M; Yan, Dadong; Schmid, Friederike

2017-08-14

Using Brownian dynamics, we study the dynamical behavior of a polymer grafted onto an adhesive surface close to the mechanically induced adsorption-stretching transition. Even though the transition is first order (in the infinite chain length limit, the stretching degree of the chain jumps discontinuously), the characteristic relaxation time is found to grow according to a power law as the transition point is approached. We present a dynamic effective interface model which reproduces these observations and provides an excellent quantitative description of the simulation data. The generic nature of the theoretical model suggests that the unconventional mixing of features that are characteristic for first-order transitions (a jump in an order parameter) and features that are characteristic of critical points (an anomalous slowdown) may be a common phenomenon in force-driven phase transitions of macromolecules.

Ashkin-Teller criticality and weak first-order behavior of the phase transition to a fourfold degenerate state in two-dimensional frustrated Ising antiferromagnets

NASA Astrophysics Data System (ADS)

Liu, R. M.; Zhuo, W. Z.; Chen, J.; Qin, M. H.; Zeng, M.; Lu, X. B.; Gao, X. S.; Liu, J.-M.

2017-07-01

We study the thermal phase transition of the fourfold degenerate phases (the plaquette and single-stripe states) in the two-dimensional frustrated Ising model on the Shastry-Sutherland lattice using Monte Carlo simulations. The critical Ashkin-Teller-like behavior is identified both in the plaquette phase region and the single-stripe phase region. The four-state Potts critical end points differentiating the continuous transitions from the first-order ones are estimated based on finite-size-scaling analyses. Furthermore, a similar behavior of the transition to the fourfold single-stripe phase is also observed in the anisotropic triangular Ising model. Thus, this work clearly demonstrates that the transitions to the fourfold degenerate states of two-dimensional Ising antiferromagnets exhibit similar transition behavior.

Large Eddy Simulation of Transitional Flow in an Idealized Stenotic Blood Vessel: Evaluation of Subgrid Scale Models

PubMed Central

Pal, Abhro; Anupindi, Kameswararao; Delorme, Yann; Ghaisas, Niranjan; Shetty, Dinesh A.; Frankel, Steven H.

2014-01-01

In the present study, we performed large eddy simulation (LES) of axisymmetric, and 75% stenosed, eccentric arterial models with steady inflow conditions at a Reynolds number of 1000. The results obtained are compared with the direct numerical simulation (DNS) data (Varghese et al., 2007, “Direct Numerical Simulation of Stenotic Flows. Part 1. Steady Flow,” J. Fluid Mech., 582, pp. 253–280). An inhouse code (WenoHemo) employing high-order numerical methods for spatial and temporal terms, along with a 2nd order accurate ghost point immersed boundary method (IBM) (Mark, and Vanwachem, 2008, “Derivation and Validation of a Novel Implicit Second-Order Accurate Immersed Boundary Method,” J. Comput. Phys., 227(13), pp. 6660–6680) for enforcing boundary conditions on curved geometries is used for simulations. Three subgrid scale (SGS) models, namely, the classical Smagorinsky model (Smagorinsky, 1963, “General Circulation Experiments With the Primitive Equations,” Mon. Weather Rev., 91(10), pp. 99–164), recently developed Vreman model (Vreman, 2004, “An Eddy-Viscosity Subgrid-Scale Model for Turbulent Shear Flow: Algebraic Theory and Applications,” Phys. Fluids, 16(10), pp. 3670–3681), and the Sigma model (Nicoud et al., 2011, “Using Singular Values to Build a Subgrid-Scale Model for Large Eddy Simulations,” Phys. Fluids, 23(8), 085106) are evaluated in the present study. Evaluation of SGS models suggests that the classical constant coefficient Smagorinsky model gives best agreement with the DNS data, whereas the Vreman and Sigma models predict an early transition to turbulence in the poststenotic region. Supplementary simulations are performed using Open source field operation and manipulation (OpenFOAM) (“OpenFOAM,” http://www.openfoam.org/) solver and the results are inline with those obtained with WenoHemo. PMID:24801556

Hybrid Global Model Simulations of He/N2 and He/H2O Atmospheric Pressure Capacitive Discharges

NASA Astrophysics Data System (ADS)

Lieberman, M. A.; Kawamura, E.; Ke, Ding; Lichtenberg, A. J.; Chabert, P.; Lazzaroni, C.

2014-10-01

We used 1D particle-in-cell (PIC) simulations of an atmospheric He/0.1%N2 discharge with simplified chemistry to guide the development of a hybrid analytical/numerical global model that includes electron multiplication and two classes of electrons: ``hot'' electrons associated with the sheaths, and ``warm'' electrons associated with the bulk. The model and PIC results show reasonable agreement and indicate a transition from a low power α-mode with a relatively high bulk electron temperature Te to a high power γ-mode with a low Te. The transition is accompanied by an increase in density and a decrease in sheath widths. Water is a trace gas of bio-medical interest since it may arise from contact with skin. We use the hybrid global model to simulate a chemically complex, bounded He/H2O atmospheric pressure discharge, including 148 volume reactions among 43 species, and including clusters up to H19O9+.For a planar discharge with a 1 cm electrode radius and a 0.5 mm gap driven at 13.56 MHz, we determine the depletion and diffusion effects and the α to γ transition for secondary emission γse = 0.25 over a range of rf currents and external H2O concentrations. Each simulation takes about 2 minutes on a moderate laptop. This work was partially supported by the Department of Energy Office of Fusion Energy Science Contract DE-SC000193 and by the Natural Science Foundation of China Contract 11375042.

Analysis of an anisotropic coastal aquifer system using variable-density flow and solute transport simulation

USGS Publications Warehouse

Souza, W.R.; Voss, C.I.

1987-01-01

The groundwater system in southern Oahu, Hawaii consists of a thick, areally extensive freshwater lens overlying a zone of transition to a thick saltwater body. This system is analyzed in cross section with a variable-density groundwater flow and solute transport model on a regional scale. The simulation is difficult, because the coastal aquifer system has a saltwater transition zone that is broadly dispersed near the discharge area, but is very sharply defined inland. Steady-state simulation analysis of the transition zone in the layered basalt aquifer of southern Oahu indicates that a small transverse dispersivity is characteristic of horizontal regional flow. Further, in this system flow is generally parallel to isochlors and steady-state behavior is insensitive to the longitudinal dispersivity. Parameter analysis identifies that only six parameters control the complex hydraulics of the system: horizontal and vertical hydraulic conductivity of the basalt aquifer; hydraulic conductivity of the confining "caprock" layer; leakance below the caprock; specific yield; and aquifer matrix compressibility. The best-fitting models indicate the horizontal hydraulic conductivity is significantly greater than the vertical hydraulic conductivity. These models give values for specific yield and aquifer compressibility which imply a considerable degree of compressive storage in the water table aquifer. ?? 1987.

Jet Simulation in a Diesel Engine

NASA Astrophysics Data System (ADS)

Xu, Zhiliang

2005-03-01

We present a numerical study of the jet breakup and spray formation in a diesel engine by the Front Tracking method. The mechanisms of jet breakup and spray formation of a high speed diesel jet injected through a circular nozzle are the key to design a fuel efficient, nonpolluting diesel engine. We conduct the simulations for the jet breakup within a 2D axis-symmetric geometry. Our goal is to model the spray at a micro-physical level, with the creation of individual droplets. The problem is multiscale. The droplets are a few microns in size. The nozzle is about 0.2 mm in diameter and 1 mm in length. To resolve various physical patterns such as vortex, shock waves, vacuum and track droplets and spray, the Burger-Colella adaptive mesh refinement technique is used. To simulate the spray formation, we model mixed vapor-liquid region through a heterogeneous model with dynamic vapor bubble insertion. The formation of the cavitation is represented by the dynamic creation of vapor bubbles. On the liquid/vapor interface, a phase transition problem is solved numerically. The phase transition is governed by the compressible Euler equations with heat diffusion. Our solution is a new description for the Riemann problem associated with a phase transition in a fully compressible fluid.

Generalized model for k -core percolation and interdependent networks

NASA Astrophysics Data System (ADS)

Panduranga, Nagendra K.; Gao, Jianxi; Yuan, Xin; Stanley, H. Eugene; Havlin, Shlomo

2017-09-01

Cascading failures in complex systems have been studied extensively using two different models: k -core percolation and interdependent networks. We combine the two models into a general model, solve it analytically, and validate our theoretical results through extensive simulations. We also study the complete phase diagram of the percolation transition as we tune the average local k -core threshold and the coupling between networks. We find that the phase diagram of the combined processes is very rich and includes novel features that do not appear in the models studying each of the processes separately. For example, the phase diagram consists of first- and second-order transition regions separated by two tricritical lines that merge and enclose a two-stage transition region. In the two-stage transition, the size of the giant component undergoes a first-order jump at a certain occupation probability followed by a continuous second-order transition at a lower occupation probability. Furthermore, at certain fixed interdependencies, the percolation transition changes from first-order → second-order → two-stage → first-order as the k -core threshold is increased. The analytic equations describing the phase boundaries of the two-stage transition region are set up, and the critical exponents for each type of transition are derived analytically.

3D filling simulation of micro- and nanostructures in comparison to iso- and variothermal injection moulding trials

NASA Astrophysics Data System (ADS)

Rytka, C.; Lungershausen, J.; Kristiansen, P. M.; Neyer, A.

2016-06-01

Flow simulations can cut down both costs and time for the development of injection moulded polymer parts with functional surfaces used in life science and optical applications. We simulated the polymer melt flow into 3D micro- and nanostructures with Moldflow and Comsol and compared the results to real iso- and variothermal injection moulding trials below, at and above the transition temperature of the polymer. By adjusting the heat transfer coefficient and the transition temperature in the simulation it was possible to achieve good correlation with experimental findings at different processing conditions (mould temperature, injection velocity) for two polymers, namely polymethylmethacrylate and amorphous polyamide. The macroscopic model can be scaled down in volume and number of elements to save computational time for microstructure simulation and to enable first and foremost the nanostructure simulation, as long as local boundary conditions such as flow front speed are transferred correctly. The heat transfer boundary condition used in Moldflow was further evaluated in Comsol. Results showed that the heat transfer coefficient needs to be increased compared to macroscopic moulding in order to represent interfacial polymer/mould effects correctly. The transition temperature is most important in the packing phase for variothermal injection moulding.

Multimodel evaluation of cloud phase transition using satellite and reanalysis data

NASA Astrophysics Data System (ADS)

Cesana, G.; Waliser, D. E.; Jiang, X.; Li, J.-L. F.

2015-08-01

We take advantage of climate simulations from two multimodel experiments to characterize and evaluate the cloud phase partitioning in 16 general circulation models (GCMs), specifically the vertical structure of the transition between liquid and ice in clouds. We base our analysis on the ratio of ice condensates to the total condensates (phase ratio, PR). Its transition at 90% (PR90) and its links with other relevant variables are evaluated using the GCM-Oriented Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation Cloud Product climatology, reanalysis data, and other satellite observations. In 13 of 16 models, the PR90 transition height occurs too low (6 km to 8.4 km) and at temperatures too warm (-13.9°C to -32.5°C) compared to observations (8.6 km, -33.7°C); features consistent with a lack of supercooled liquid with respect to ice above 6.5 km. However, this bias would be slightly reduced by using the lidar simulator. In convective regimes (more humid air and precipitation), the observed cloud phase transition occurs at a warmer temperature than for subsidence regimes (less humid air and precipitation). Only few models manage to roughly replicate the observed correlations with humidity (5/16), vertical velocity (5/16), and precipitation (4/16); 3/16 perform well for all these parameters (MPI-ESM, NCAR-CAM5, and NCHU). Using an observation-based Clausius-Clapeyron phase diagram, we illustrate that the Bergeron-Findeisen process is a necessary condition for models to represent the observed features. Finally, the best models are those that include more complex microphysics.

Acoustic waves and the detectability of first-order phase transitions by eLISA

NASA Astrophysics Data System (ADS)

Weir, David J.

2017-05-01

In various extensions of the Standard Model it is possible that the electroweak phase transition was first order. This would have been a violent process, involving the formation of bubbles and associated shock waves. Not only would the collision of these bubbles and shock waves be a detectable source of gravitational waves, but persistent acoustic waves could enhance the signal and improve prospects of detection by eLISA. I summarise the results of a recent campaign to model such a phase transition based on large-scale hydrodynamical simulations, and its implications for the eLISA mission.

Steady-state and transitional aerodynamic characteristics of a wing in simulated heavy rain

NASA Technical Reports Server (NTRS)

Campbell, Bryan A.; Bezos, Gaudy M.

1989-01-01

The steady-state and transient effects of simulated heavy rain on the subsonic aerodynamic characteristics of a wing model were determined in the Langley 14- by 22-Foot Subsonic Tunnel. The 1.29 foot chord wing was comprised of a NACA 23015 airfoil and had an aspect ratio of 6.10. Data were obtained while test variables of liquid water content, angle of attack, and trailing edge flap angle were parametrically varied at dynamic pressures of 10, 30, and 50 psf (i.e., Reynolds numbers of .76x10(6), 1.31x10(6), and 1.69x10(6)). The experimental results showed reductions in lift and increases in drag when in the simulated rain environment. Accompanying this was a reduction of the stall angle of attack by approximately 4 deg. The transient aerodynamic performance during transition from dry to wet steady-state conditions varied between a linear and a nonlinear transition.

Molecular dynamics simulation of premelting and melting phase transitions in stoichiometric uranium dioxide

NASA Astrophysics Data System (ADS)

Yakub, Eugene; Ronchi, Claudio; Staicu, Dragos

2007-09-01

Results of molecular dynamics (MD) simulation of UO2 in a wide temperature range are presented and discussed. A new approach to the calibration of a partly ionic Busing-Ida-type model is proposed. A potential parameter set is obtained reproducing the experimental density of solid UO2 in a wide range of temperatures. A conventional simulation of the high-temperature stoichiometric UO2 on large MD cells, based on a novel fast method of computation of Coulomb forces, reveals characteristic features of a premelting λ transition at a temperature near to that experimentally observed (Tλ=2670K ). A strong deviation from the Arrhenius behavior of the oxygen self-diffusion coefficient was found in the vicinity of the transition point. Predictions for liquid UO2, based on the same potential parameter set, are in good agreement with existing experimental data and theoretical calculations.

Simulating Valence-to-Core X-ray Emission Spectroscopy of Transition Metal Complexes with Time-Dependent Density Functional Theory.

PubMed

Zhang, Yu; Mukamel, Shaul; Khalil, Munira; Govind, Niranjan

2015-12-08

Valence-to-core (VtC) X-ray emission spectroscopy (XES) has emerged as a powerful technique for the structural characterization of complex organometallic compounds in realistic environments. Since the spectrum represents electronic transitions from the ligand molecular orbitals to the core holes of the metal centers, the approach is more chemically sensitive to the metal-ligand bonding character compared with conventional X-ray absorption techniques. In this paper we study how linear-response time-dependent density functional theory (LR-TDDFT) can be harnessed to simulate K-edge VtC X-ray emission spectra reliably. LR-TDDFT allows one to go beyond the single-particle picture that has been extensively used to simulate VtC-XES. We consider seven low- and high-spin model complexes involving chromium, manganese, and iron transition metal centers. Our results are in good agreement with experiment.

Analysis of a DNA simulation model through hairpin melting experiments.

PubMed

Linak, Margaret C; Dorfman, Kevin D

2010-09-28

We compare the predictions of a two-bead Brownian dynamics simulation model to melting experiments of DNA hairpins with complementary AT or GC stems and noninteracting loops in buffer A. This system emphasizes the role of stacking and hydrogen bonding energies, which are characteristics of DNA, rather than backbone bending, stiffness, and excluded volume interactions, which are generic characteristics of semiflexible polymers. By comparing high throughput data on the open-close transition of various DNA hairpins to the corresponding simulation data, we (1) establish a suitable metric to compare the simulations to experiments, (2) find a conversion between the simulation and experimental temperatures, and (3) point out several limitations of the model, including the lack of G-quartets and cross stacking effects. Our approach and experimental data can be used to validate similar coarse-grained simulation models.

Longitudinal train dynamics: an overview

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin

2016-12-01

This paper discusses the evolution of longitudinal train dynamics (LTD) simulations, which covers numerical solvers, vehicle connection systems, air brake systems, wagon dumper systems and locomotives, resistance forces and gravitational components, vehicle in-train instabilities, and computing schemes. A number of potential research topics are suggested, such as modelling of friction, polymer, and transition characteristics for vehicle connection simulations, studies of wagon dumping operations, proper modelling of vehicle in-train instabilities, and computing schemes for LTD simulations. Evidence shows that LTD simulations have evolved with computing capabilities. Currently, advanced component models that directly describe the working principles of the operation of air brake systems, vehicle connection systems, and traction systems are available. Parallel computing is a good solution to combine and simulate all these advanced models. Parallel computing can also be used to conduct three-dimensional long train dynamics simulations.

Numerical Modeling of Footpoint-driven Magneto-acoustic Wave Propagation in a Localized Solar Flux Tube

NASA Astrophysics Data System (ADS)

Fedun, V.; Shelyag, S.; Erdélyi, R.

2011-01-01

In this paper, we present and discuss results of two-dimensional simulations of linear and nonlinear magneto-acoustic wave propagation through an open magnetic flux tube embedded in the solar atmosphere expanding from the photosphere through to the transition region and into the low corona. Our aim is to model and analyze the response of such a magnetic structure to vertical and horizontal periodic motions originating in the photosphere. To carry out the simulations, we employed our MHD code SAC (Sheffield Advanced Code). A combination of the VALIIIC and McWhirter solar atmospheres and coronal density profiles were used as the background equilibrium model in the simulations. Vertical and horizontal harmonic sources, located at the footpoint region of the open magnetic flux tube, are incorporated in the calculations, to excite oscillations in the domain of interest. To perform the analysis we have constructed a series of time-distance diagrams of the vertical and perpendicular components of the velocity with respect to the magnetic field lines at each height of the computational domain. These time-distance diagrams are subject to spatio-temporal Fourier transforms allowing us to build ω-k dispersion diagrams for all of the simulated regions in the solar atmosphere. This approach makes it possible to compute the phase speeds of waves propagating throughout the various regions of the solar atmosphere model. We demonstrate the transformation of linear slow and fast magneto-acoustic wave modes into nonlinear ones, i.e., shock waves, and also show that magneto-acoustic waves with a range of frequencies efficiently leak through the transition region into the solar corona. It is found that the waves interact with the transition region and excite horizontally propagating surface waves along the transition region for both types of drivers. Finally, we estimate the phase speed of the oscillations in the solar corona and compare it with the phase speed derived from observations.

Conditional Stochastic Models in Reduced Space: Towards Efficient Simulation of Tropical Cyclone Precipitation Patterns

NASA Astrophysics Data System (ADS)

Dodov, B.

2017-12-01

Stochastic simulation of realistic and statistically robust patterns of Tropical Cyclone (TC) induced precipitation is a challenging task. It is even more challenging in a catastrophe modeling context, where tens of thousands of typhoon seasons need to be simulated in order to provide a complete view of flood risk. Ultimately, one could run a coupled global climate model and regional Numerical Weather Prediction (NWP) model, but this approach is not feasible in the catastrophe modeling context and, most importantly, may not provide TC track patterns consistent with observations. Rather, we propose to leverage NWP output for the observed TC precipitation patterns (in terms of downscaled reanalysis 1979-2015) collected on a Lagrangian frame along the historical TC tracks and reduced to the leading spatial principal components of the data. The reduced data from all TCs is then grouped according to timing, storm evolution stage (developing, mature, dissipating, ETC transitioning) and central pressure and used to build a dictionary of stationary (within a group) and non-stationary (for transitions between groups) covariance models. Provided that the stochastic storm tracks with all the parameters describing the TC evolution are already simulated, a sequence of conditional samples from the covariance models chosen according to the TC characteristics at a given moment in time are concatenated, producing a continuous non-stationary precipitation pattern in a Lagrangian framework. The simulated precipitation for each event is finally distributed along the stochastic TC track and blended with a non-TC background precipitation using a data assimilation technique. The proposed framework provides means of efficient simulation (10000 seasons simulated in a couple of days) and robust typhoon precipitation patterns consistent with observed regional climate and visually undistinguishable from high resolution NWP output. The framework is used to simulate a catalog of 10000 typhoon seasons implemented in a flood risk model for Japan.

Study of emergency setting for urban facility using microsimulation tool

NASA Astrophysics Data System (ADS)

Campisi, Tiziana; Canale, Antonino; Tesoriere, Giovanni

2017-11-01

Today Public transport is growing not only in terms of high passenger capacity but also considering high efficiency and it has become one of the preferred alternatives to automobile travel. This is evident, as for example, in the case of airport terminal working and management. The same could be for Bus Transport station considering roadway. As a result, many railway stations experience high levels of pedestrian congestion especially during the morning and afternoon peak periods. Traditional design and evaluation procedures for pedestrian transit facilities aim to maintain a desirable Pedestrian Level-Of-Service (PLOS) for the individual pedestrian areas or sub precincts. More in general, transit facilities and their sub-precincts interact with one another so that pedestrian circulation might be better assessed from a broader systems perspective. Microsimulation packages that can model pedestrians (e.g. VISSIM-VISWALK) can be employed to assess these interactions. This research outlines a procedure for the potential implementation of pedestrian flow analysis in a bus/rail transit station using micro-simulation. Base model data requirements are identified which include static (facility layout and locations of temporary equipment) and dynamic data (pedestrian demand and public transport services). Possible model calibration criteria would be also identified. A VISSIM micro-simulation base model would be developed for one of the main Airport terminal in Sicily (Italy) for investigating proposed station operational and infrastructure changes. This case study provided a good example for the potential implementation of micro-simulation models in the analysis of pedestrian circulation.

Particle-in-cell and global simulations of α to γ transition in atmospheric pressure Penning-dominated capacitive discharges

NASA Astrophysics Data System (ADS)

Kawamura, E.; Lieberman, M. A.; Lichtenberg, A. J.; Chabert, P.; Lazzaroni, C.

2014-06-01

Atmospheric pressure radio-frequency (rf) capacitive micro-discharges are of interest due to emerging applications, especially in the bio-medical field. A previous global model did not consider high-power phenomena such as sheath multiplication, thus limiting its applicability to the lower power range. To overcome this, we use one-dimensional particle-in-cell (PIC) simulations of atmospheric He/0.1% N2 capacitive discharges over a wide range of currents and frequencies to guide the development of a more general global model which is also valid at higher powers. The new model includes sheath multiplication and two classes of electrons: the higher temperature ‘hot’ electrons associated with the sheaths, and the cooler ‘warm’ electrons associated with the bulk. The electric field and the electron power balance are solved analytically to determine the time-varying hot and warm temperatures and the effective rate coefficients. The particle balance equations are integrated numerically to determine the species densities. The model and PIC results are compared, showing reasonable agreement over the range of currents and frequencies studied. They indicate a transition from an α mode at low power characterized by relatively high electron temperature Te with a near uniform profile to a γ mode at high power with a Te profile strongly depressed in the bulk plasma. The transition is accompanied by an increase in density and a decrease in sheath widths. The current and frequency scalings of the model are confirmed by the PIC simulations.

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

NASA Astrophysics Data System (ADS)

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; Omand, Conor; Nishino, Masamichi

2016-02-01

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean-field method for a simplified model of a spin-crossover material with a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S =1 /2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley (equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shaped regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. We believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.

Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories

NASA Astrophysics Data System (ADS)

Matsunaga, Y.; Sugita, Y.

2018-06-01

A data-driven modeling scheme is proposed for conformational dynamics of biomolecules based on molecular dynamics (MD) simulations and experimental measurements. In this scheme, an initial Markov State Model (MSM) is constructed from MD simulation trajectories, and then, the MSM parameters are refined using experimental measurements through machine learning techniques. The second step can reduce the bias of MD simulation results due to inaccurate force-field parameters. Either time-series trajectories or ensemble-averaged data are available as a training data set in the scheme. Using a coarse-grained model of a dye-labeled polyproline-20, we compare the performance of machine learning estimations from the two types of training data sets. Machine learning from time-series data could provide the equilibrium populations of conformational states as well as their transition probabilities. It estimates hidden conformational states in more robust ways compared to that from ensemble-averaged data although there are limitations in estimating the transition probabilities between minor states. We discuss how to use the machine learning scheme for various experimental measurements including single-molecule time-series trajectories.

Modeling personnel turnover in the parametric organization

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1991-01-01

A model is developed for simulating the dynamics of a newly formed organization, credible during all phases of organizational development. The model development process is broken down into the activities of determining the tasks required for parametric cost analysis (PCA), determining the skills required for each PCA task, determining the skills available in the applicant marketplace, determining the structure of the model, implementing the model, and testing it. The model, parameterized by the likelihood of job function transition, has demonstrated by the capability to represent the transition of personnel across functional boundaries within a parametric organization using a linear dynamical system, and the ability to predict required staffing profiles to meet functional needs at the desired time. The model can be extended by revisions of the state and transition structure to provide refinements in functional definition for the parametric and extended organization.

An aggregate method to calibrate the reference point of cumulative prospect theory-based route choice model for urban transit network

NASA Astrophysics Data System (ADS)

Zhang, Yufeng; Long, Man; Luo, Sida; Bao, Yu; Shen, Hanxia

2015-12-01

Transit route choice model is the key technology of public transit systems planning and management. Traditional route choice models are mostly based on expected utility theory which has an evident shortcoming that it cannot accurately portray travelers' subjective route choice behavior for their risk preferences are not taken into consideration. Cumulative prospect theory (CPT), a brand new theory, can be used to describe travelers' decision-making process under the condition of uncertainty of transit supply and risk preferences of multi-type travelers. The method to calibrate the reference point, a key parameter to CPT-based transit route choice model, determines the precision of the model to a great extent. In this paper, a new method is put forward to obtain the value of reference point which combines theoretical calculation and field investigation results. Comparing the proposed method with traditional method, it shows that the new method can promote the quality of CPT-based model by improving the accuracy in simulating travelers' route choice behaviors based on transit trip investigation from Nanjing City, China. The proposed method is of great significance to logical transit planning and management, and to some extent makes up the defect that obtaining the reference point is solely based on qualitative analysis.

Simulating boundary layer transition with low-Reynolds-number k-epsilon turbulence models. I - An evaluation of prediction characteristics. II - An approach to improving the predictions

NASA Technical Reports Server (NTRS)

Schmidt, R. C.; Patankar, S. V.

1991-01-01

The capability of two k-epsilon low-Reynolds number (LRN) turbulence models, those of Jones and Launder (1972) and Lam and Bremhorst (1981), to predict transition in external boundary-layer flows subject to free-stream turbulence is analyzed. Both models correctly predict the basic qualitative aspects of boundary-layer transition with free stream turbulence, but for calculations started at low values of certain defined Reynolds numbers, the transition is generally predicted at unrealistically early locations. Also, the methods predict transition lengths significantly shorter than those found experimentally. An approach to overcoming these deficiencies without abandoning the basic LRN k-epsilon framework is developed. This approach limits the production term in the turbulent kinetic energy equation and is based on a simple stability criterion. It is correlated to the free-stream turbulence value. The modification is shown to improve the qualitative and quantitative characteristics of the transition predictions.

Critical exponents of the explosive percolation transition

NASA Astrophysics Data System (ADS)

da Costa, R. A.; Dorogovtsev, S. N.; Goltsev, A. V.; Mendes, J. F. F.

2014-04-01

In a new type of percolation phase transition, which was observed in a set of nonequilibrium models, each new connection between vertices is chosen from a number of possibilities by an Achlioptas-like algorithm. This causes preferential merging of small components and delays the emergence of the percolation cluster. First simulations led to a conclusion that a percolation cluster in this irreversible process is born discontinuously, by a discontinuous phase transition, which results in the term "explosive percolation transition." We have shown that this transition is actually continuous (second order) though with an anomalously small critical exponent of the percolation cluster. Here we propose an efficient numerical method enabling us to find the critical exponents and other characteristics of this second-order transition for a representative set of explosive percolation models with different number of choices. The method is based on gluing together the numerical solutions of evolution equations for the cluster size distribution and power-law asymptotics. For each of the models, with high precision, we obtain critical exponents and the critical point.

Advanced Shock Position Control for Mode Transition in a Turbine Based Combined Cycle Engine Inlet Model

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Stueber, Thomas J.

2013-01-01

A dual flow-path inlet system is being tested to evaluate methodologies for a Turbine Based Combined Cycle (TBCC) propulsion system to perform a controlled inlet mode transition. Prior to experimental testing, simulation models are used to test, debug, and validate potential control algorithms. One simulation package being used for testing is the High Mach Transient Engine Cycle Code simulation, known as HiTECC. This paper discusses the closed loop control system, which utilizes a shock location sensor to improve inlet performance and operability. Even though the shock location feedback has a coarse resolution, the feedback allows for a reduction in steady state error and, in some cases, better performance than with previous proposed pressure ratio based methods. This paper demonstrates the design and benefit with the implementation of a proportional-integral controller, an H-Infinity based controller, and a disturbance observer based controller.

Simulating a topological transition in a superconducting phase qubit by fast adiabatic trajectories

NASA Astrophysics Data System (ADS)

Wang, Tenghui; Zhang, Zhenxing; Xiang, Liang; Gong, Zhihao; Wu, Jianlan; Yin, Yi

2018-04-01

The significance of topological phases has been widely recognized in the community of condensed matter physics. The well controllable quantum systems provide an artificial platform to probe and engineer various topological phases. The adiabatic trajectory of a quantum state describes the change of the bulk Bloch eigenstates with the momentum, and this adiabatic simulation method is however practically limited due to quantum dissipation. Here we apply the "shortcut to adiabaticity" (STA) protocol to realize fast adiabatic evolutions in the system of a superconducting phase qubit. The resulting fast adiabatic trajectories illustrate the change of the bulk Bloch eigenstates in the Su-Schrieffer-Heeger (SSH) model. A sharp transition is experimentally determined for the topological invariant of a winding number. Our experiment helps identify the topological Chern number of a two-dimensional toy model, suggesting the applicability of the fast adiabatic simulation method for topological systems.

On the definition of a Monte Carlo model for binary crystal growth.

PubMed

Los, J H; van Enckevort, W J P; Meekes, H; Vlieg, E

2007-02-01

We show that consistency of the transition probabilities in a lattice Monte Carlo (MC) model for binary crystal growth with the thermodynamic properties of a system does not guarantee the MC simulations near equilibrium to be in agreement with the thermodynamic equilibrium phase diagram for that system. The deviations remain small for systems with small bond energies, but they can increase significantly for systems with large melting entropy, typical for molecular systems. These deviations are attributed to the surface kinetics, which is responsible for a metastable zone below the liquidus line where no growth occurs, even in the absence of a 2D nucleation barrier. Here we propose an extension of the MC model that introduces a freedom of choice in the transition probabilities while staying within the thermodynamic constraints. This freedom can be used to eliminate the discrepancy between the MC simulations and the thermodynamic equilibrium phase diagram. Agreement is achieved for that choice of the transition probabilities yielding the fastest decrease of the free energy (i.e., largest growth rate) of the system at a temperature slightly below the equilibrium temperature. An analytical model is developed, which reproduces quite well the MC results, enabling a straightforward determination of the optimal set of transition probabilities. Application of both the MC and analytical model to conditions well away from equilibrium, giving rise to kinetic phase diagrams, shows that the effect of kinetics on segregation is even stronger than that predicted by previous models.

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Extended System Operations Studies for Automated Guideway Transit Systems : Plan for Task 5--DPM Failure Management

DOT National Transportation Integrated Search

1981-06-01

The purpose of Task 5 in the Extended System Operations Studies Project, DPM Failure Management, is to enhance the capabilities of the Downtown People Mover Simulation (DPMS) and the Discrete Event Simulation Model (DESM) by increasing the failure mo...

Axelrod models of social influence with cultural repulsion

NASA Astrophysics Data System (ADS)

Radillo-Díaz, Alejandro; Pérez, Luis A.; Del Castillo-Mussot, Marcelo

2009-12-01

Since both attractive and repulsive effects among agents are important in social systems, we present simulations of two models based on Axelrod’s homogenization mechanism that includes repulsion. These models are the repulsive model, where all individuals can repel, and the partially repulsive model where only a fraction of repelling agents are considered. In these two models, attractive dynamics is implemented for agents with the ability to repel each other only if the number of features shared by them is greater than a threshold parameter. Otherwise, repelling dynamics is used. In the repulsive model, the transition from a monocultural state to a fragmented one often occurs abruptly from one cultural-variability value to the next one and a second transition emerges. For the partially repulsive model, there are also two different transitions present: the initial one being as abrupt as the one found for the repulsive model, whereas the second one follows a less abrupt behavior and resembles that of the original Axelrod model. However, the second transition for this model occurrs from a partially fragmented state and not from a monocultural one.

Study of the Transition Flow Regime using Monte Carlo Methods

NASA Technical Reports Server (NTRS)

Hassan, H. A.

1999-01-01

This NASA Cooperative Agreement presents a study of the Transition Flow Regime Using Monte Carlo Methods. The topics included in this final report are: 1) New Direct Simulation Monte Carlo (DSMC) procedures; 2) The DS3W and DS2A Programs; 3) Papers presented; 4) Miscellaneous Applications and Program Modifications; 5) Solution of Transitional Wake Flows at Mach 10; and 6) Turbulence Modeling of Shock-Dominated Fows with a k-Enstrophy Formulation.

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

Critical length scale controls adhesive wear mechanisms

PubMed Central

Aghababaei, Ramin; Warner, Derek H.; Molinari, Jean-Francois

2016-01-01

The adhesive wear process remains one of the least understood areas of mechanics. While it has long been established that adhesive wear is a direct result of contacting surface asperities, an agreed upon understanding of how contacting asperities lead to wear debris particle has remained elusive. This has restricted adhesive wear prediction to empirical models with limited transferability. Here we show that discrepant observations and predictions of two distinct adhesive wear mechanisms can be reconciled into a unified framework. Using atomistic simulations with model interatomic potentials, we reveal a transition in the asperity wear mechanism when contact junctions fall below a critical length scale. A simple analytic model is formulated to predict the transition in both the simulation results and experiments. This new understanding may help expand use of computer modelling to explore adhesive wear processes and to advance physics-based wear laws without empirical coefficients. PMID:27264270

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation

PubMed Central

Gu, Hong; Zhang, Shuming; Wong, Kin-Yiu; Radak, Brian K.; Dissanayake, Thakshila; Kellerman, Daniel L.; Dai, Qing; Miyagi, Masaru; Anderson, Vernon E.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.

2013-01-01

Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2′-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the 18O KIEs on the 2′O nucleophile, 5′O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5′O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5′O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2′-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure. PMID:23878223

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2009-01-01

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases. PMID:19714203

Self-learning Monte Carlo method

DOE PAGES

Liu, Junwei; Qi, Yang; Meng, Zi Yang; ...

2017-01-04

Monte Carlo simulation is an unbiased numerical tool for studying classical and quantum many-body systems. One of its bottlenecks is the lack of a general and efficient update algorithm for large size systems close to the phase transition, for which local updates perform badly. In this Rapid Communication, we propose a general-purpose Monte Carlo method, dubbed self-learning Monte Carlo (SLMC), in which an efficient update algorithm is first learned from the training data generated in trial simulations and then used to speed up the actual simulation. Lastly, we demonstrate the efficiency of SLMC in a spin model at the phasemore » transition point, achieving a 10–20 times speedup.« less

Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins

NASA Astrophysics Data System (ADS)

Steckmann, Timothy M.

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous alpha-helix or random-coil structure. The alpha-helices convert their structure to beta-strands that aggregate into beta-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis process from random coil to fibrils, including the molecular species that accelerate the conversions. The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process. To better understand the molecular basis of the protein structural transitions and aggregation, I report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccbeta, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow beta-hairpin proteins to straighten, and the subsequent formation of interchain hydrogen bonds during aggregation into amyloid fibrils. For my MD simulations, I found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccbeta protein experiences during the process of forming protofibrillar structures. Both the mathematical modeling of the kinetics and the MD simulations show that molecular structural heterogeneity is a major factor in the process. The MD simulations also show that intrachain and interchain hydrogen bonds breaking and forming is strongly correlated to the process of amyloid formation.

Application of nonlinear adaptive motion washout to transport ground-handling simulation

NASA Technical Reports Server (NTRS)

Parrish, R. V.; Martin, D. J., Jr.

1983-01-01

The application of a nonlinear coordinated adaptive motion washout to the transport ground-handling environment is documented. Additions to both the aircraft math model and the motion washout system are discussed. The additions to the simulated-aircraft math model provided improved modeling fidelity for braking and reverse-thrust application, and the additions to the motion-base washout system allowed transition from the desired flight parameters to the less restrictive ground parameters of the washout.

Can a simple lumped parameter model simulate complex transit time distributions? Benchmarking experiments in a virtual watershed.

NASA Astrophysics Data System (ADS)

Wilusz, D. C.; Maxwell, R. M.; Buda, A. R.; Ball, W. P.; Harman, C. J.

2016-12-01

The catchment transit-time distribution (TTD) is the time-varying, probabilistic distribution of water travel times through a watershed. The TTD is increasingly recognized as a useful descriptor of a catchment's flow and transport processes. However, TTDs are temporally complex and cannot be observed directly at watershed scale. Estimates of TTDs depend on available environmental tracers (such as stable water isotopes) and an assumed model whose parameters can be inverted from tracer data. All tracers have limitations though, such as (typically) short periods of observation or non-conservative behavior. As a result, models that faithfully simulate tracer observations may nonetheless yield TTD estimates with significant errors at certain times and water ages, conditioned on the tracer data available and the model structure. Recent advances have shown that time-varying catchment TTDs can be parsimoniously modeled by the lumped parameter rank StorAge Selection (rSAS) model, in which an rSAS function relates the distribution of water ages in outflows to the composition of age-ranked water in storage. Like other TTD models, rSAS is calibrated and evaluated against environmental tracer data, and the relative influence of tracer-dependent and model-dependent error on its TTD estimates is poorly understood. The purpose of this study is to benchmark the ability of different rSAS formulations to simulate TTDs in a complex, synthetic watershed where the lumped model can be calibrated and directly compared to a virtually "true" TTD. This experimental design allows for isolation of model-dependent error from tracer-dependent error. The integrated hydrologic model ParFlow with SLIM-FAST particle tracking code is used to simulate the watershed and its true TTD. To add field intelligence, the ParFlow model is populated with over forty years of hydrometric and physiographic data from the WE-38 subwatershed of the USDA's Mahantango Creek experimental catchment in PA, USA. The results are intended to give practical insight into tradeoffs between rSAS model structure and skill, and define a new performance benchmark to which other transit time models can be compared.

Seasonal modulation of the Asian summer monsoon between the Medieval Warm Period and Little Ice Age: a multi model study

NASA Astrophysics Data System (ADS)

Kamae, Youichi; Kawana, Toshi; Oshiro, Megumi; Ueda, Hiroaki

2017-12-01

Instrumental and proxy records indicate remarkable global climate variability over the last millennium, influenced by solar irradiance, Earth's orbital parameters, volcanic eruptions and human activities. Numerical model simulations and proxy data suggest an enhanced Asian summer monsoon during the Medieval Warm Period (MWP) compared to the Little Ice Age (LIA). Using multiple climate model simulations, we show that anomalous seasonal insolation over the Northern Hemisphere due to a long cycle of orbital parameters results in a modulation of the Asian summer monsoon transition between the MWP and LIA. Ten climate model simulations prescribing historical radiative forcing that includes orbital parameters consistently reproduce an enhanced MWP Asian monsoon in late summer and a weakened monsoon in early summer. Weakened, then enhanced Northern Hemisphere insolation before and after June leads to a seasonally asymmetric temperature response over the Eurasian continent, resulting in a seasonal reversal of the signs of MWP-LIA anomalies in land-sea thermal contrast, atmospheric circulation, and rainfall from early to late summer. This seasonal asymmetry in monsoon response is consistently found among the different climate models and is reproduced by an idealized model simulation forced solely by orbital parameters. The results of this study indicate that slow variation in the Earth's orbital parameters contributes to centennial variability in the Asian monsoon transition.[Figure not available: see fulltext.

An Investigation of a Hybrid Mixing Timescale Model for PDF Simulations of Turbulent Premixed Flames

NASA Astrophysics Data System (ADS)

Zhou, Hua; Kuron, Mike; Ren, Zhuyin; Lu, Tianfeng; Chen, Jacqueline H.

2016-11-01

Transported probability density function (TPDF) method features the generality for all combustion regimes, which is attractive for turbulent combustion simulations. However, the modeling of micromixing due to molecular diffusion is still considered to be a primary challenge for TPDF method, especially in turbulent premixed flames. Recently, a hybrid mixing rate model for TPDF simulations of turbulent premixed flames has been proposed, which recovers the correct mixing rates in the limits of flamelet regime and broken reaction zone regime while at the same time aims to properly account for the transition in between. In this work, this model is employed in TPDF simulations of turbulent premixed methane-air slot burner flames. The model performance is assessed by comparing the results from both direct numerical simulation (DNS) and conventional constant mechanical-to-scalar mixing rate model. This work is Granted by NSFC 51476087 and 91441202.

A Simulation Base Investigation of High Latency Space Systems Operations

NASA Technical Reports Server (NTRS)

Li, Zu Qun; Crues, Edwin Z.; Bielski, Paul; Moore, Michael

2017-01-01

NASA's human space program has developed considerable experience with near Earth space operations. Although NASA has experience with deep space robotic missions, NASA has little substantive experience with human deep space operations. Even in the Apollo program, the missions lasted only a few weeks and the communication latencies were on the order of seconds. Human missions beyond the relatively close confines of the Earth-Moon system will involve missions with durations measured in months and communications latencies measured in minutes. To minimize crew risk and to maximize mission success, NASA needs to develop a better understanding of the implications of these types of mission durations and communication latencies on vehicle design, mission design and flight controller interaction with the crew. To begin to address these needs, NASA performed a study using a physics-based subsystem simulation to investigate the interactions between spacecraft crew and a ground-based mission control center for vehicle subsystem operations across long communication delays. The simulation, built with a subsystem modeling tool developed at NASA's Johnson Space Center, models the life support system of a Mars transit vehicle. The simulation contains models of the cabin atmosphere and pressure control system, electrical power system, drinking and waste water systems, internal and external thermal control systems, and crew metabolic functions. The simulation has three interfaces: 1) a real-time crew interface that can be use to monitor and control the vehicle subsystems; 2) a mission control center interface with data transport delays up to 15 minutes each way; 3) a real-time simulation test conductor interface that can be use to insert subsystem malfunctions and observe the interactions between the crew, ground, and simulated vehicle. The study was conducted at the 21st NASA Extreme Environment Mission Operations (NEEMO) mission between July 18th and Aug 3rd of year 2016. The NEEMO mission provides ideal conditions for this study with crew in the loop, an active control center, and real-time flow of high latency communications and data. NEEMO crew and ground support will work through procedures including activation of the transit vehicle power system, opening the hatch between the transit vehicle and a Mars ascent vehicle, transferring simulated crewmembers between vehicles, overcoming subsystem malfunctions, sending simulated crewmember on extra-vehicular activities, and other housekeeping activities. This study is enhancing the understanding of high latency operations and the advantages and disadvantages of different communication methods. It is also providing results that will help improve the design of simulation interfaces and inform the design of Mars transit vehicles.

Applying an integrated model to the evaluation of travel demand management policies in the Sacramento Region

DOT National Transportation Integrated Search

2001-09-01

The objective of this study was to use an advanced integrated land use and transportation model to evaluate transit and supportive land use and pricing policies; the Sacramento MEPLAN model was to used to simulate these policies. The model represents...

Simulating the Interactions Among Land Use, Transportation ...

EPA Pesticide Factsheets

In most transportation studies, computer models that forecast travel behavior statistics for a future year use static projections of the spatial distribution of future population and employment growth as inputs. As a result, they are unable to account for the temporally dynamic and non-linear interactions among transportation, land use, and socioeconomic systems. System dynamics (SD) provides a common framework for modeling the complex interactions among transportation and other related systems. This study uses a SD model to simulate the cascading impacts of a proposed light rail transit (LRT) system in central North Carolina, USA. The Durham-Orange Light Rail Project (D-O LRP) SD model incorporates relationships among the land use, transportation, and economy sectors to simulate the complex feedbacks that give rise to the travel behavior changes forecasted by the region’s transportation model. This paper demonstrates the sensitivity of changes in travel behavior to the proposed LRT system and the assumptions that went into the transportation modeling, and compares those results to the impacts of an alternative fare-free transit system. SD models such as the D-O LRP SD model can complement transportation studies by providing valuable insight into the interdependent community systems that collectively contribute to travel behavior changes. Presented at the 35th International Conference of the System Dynamics Society in Cambridge, MA, July 18th, 2017

Nonlinear modeling of crystal system transition of black phosphorus using continuum-DFT model.

PubMed

Setoodeh, A R; Farahmand, H

2018-01-24

In this paper, the nonlinear behavior of black phosphorus crystals is investigated in tandem with dispersion-corrected density functional theory (DFT-D) analysis under uniaxial loadings. From the identified anisotropic behavior of black phosphorus due to its morphological anisotropy, a hyperelastic anisotropic (HA) model named continuum-DFT is established to predict the nonlinear behavior of the material. In this respect, uniaxial Cauchy stresses are employed on both the DFT-D and HA models along the zig-zag and armchair directions. Simultaneously, the transition of the crystal system is recognized at about 4.5 GPa of the applied uniaxial tensile stress along the zig-zag direction on the DFT-D simulation in the nonlinear region. In order to develop the nonlinear continuum model, unknown constants are surveyed with the optimized least square technique. In this regard, the continuum model is obtained to reproduce the Cauchy stress-stretch and density of strain-stretch results of the DFT-D simulation. Consequently, the modified HA model is introduced to characterize the nonlinear behavior of black phosphorus along the zig-zag direction. More importantly, the specific transition of the crystal system is successfully predicted in the new modified continuum-DFT model. The results reveal that the multiscale continuum-DFT model is well defined to replicate the nonlinear behavior of black phosphorus along the zig-zag and armchair directions.

Communication: phase transitions, criticality, and three-phase coexistence in constrained cell models.

PubMed

Nayhouse, Michael; Kwon, Joseph Sang-Il; Orkoulas, G

2012-05-28

In simulation studies of fluid-solid transitions, the solid phase is usually modeled as a constrained system in which each particle is confined to move in a single Wigner-Seitz cell. The constrained cell model has been used in the determination of fluid-solid coexistence via thermodynamic integration and other techniques. In the present work, the phase diagram of such a constrained system of Lennard-Jones particles is determined from constant-pressure simulations. The pressure-density isotherms exhibit inflection points which are interpreted as the mechanical stability limit of the solid phase. The phase diagram of the constrained system contains a critical and a triple point. The temperature and pressure at the critical and the triple point are both higher than those of the unconstrained system due to the reduction in the entropy caused by the single occupancy constraint.

Tipping Points towards Regional Forest or Urban Transition in Stressed Rural Areas: An Agent-based Modelling Application of Socio-Economic Shifts in Rural Vermont US

NASA Astrophysics Data System (ADS)

Tsai, Y.; Turnbull, S.; Zia, A.

2015-12-01

In rural areas where farming competes with urban development and environmental amenities, urban and forest transitions occur simultaneously at different locales with different rates due to the underlying socio-economic shifts. Here we develop an interactive land use transition agent-based model (ILUTABM) in which farmers' land use decisions are made contingent on expansion and location choices of urban businesses and urban residences, as well as farmers' perceived ecosystem services produced by their land holdings. The ILUTABM simulates heterogeneity in land use decisions at parcel levels by differentiating decision making processes for agricultural and urban landowners. Landowners are simulated to make land-use transition decisions as bounded rational agents that maximize their partial expected utility functions under different underlying socio-economic conditions given the category of a landowner and the spatial characteristics of the landowner's landholdings. The ILUTABM is parameterized by spatial data sets such as National Land Cover Database (NLCD), zoning, parcels, property prices, US census, farmers surveys, building/facility characteristics, soil, slope and elevation. We then apply the ILUTABM to the rural Vermont landscape, located in the Northeast Arm District of Lake Champlain and the downstream sub-watersheds of Missisquoi River, to generate phase transitions of rural land towards urban land near peri-urban areas and towards forest land near financially stressed farmlands during 2001-2051. Possible tipping point trajectories of rural land towards regional forest or urban transition are simulated under three socio-economic scenarios: business as usual (ILUTABM calibrated to 2011 NLCD), increased incentives for conservation easements, and increased incentives for attracting urban residences and businesses.

Influence of transitional volcanic strata on lateral diversion at Yucca Mountain, Nevada

USGS Publications Warehouse

Flint, Lorraine E.; Flint, Alan L.; Selker, John S.

2003-01-01

Natural hydraulic barriers exist at Yucca Mountain, Nevada, a potential high‐level nuclear waste repository, that have been identified as possible lateral diversions for reducing deep percolation through the waste storage area. Historical development of the conceptual model of lateral diversion has been limited by available field data, but numerical investigations presented the possibility of significant lateral diversion due to the presence of a thin, porous rock layer, the Paintbrush nonwelded tuffs. Analytical analyses of the influence of transitional changes in properties suggest that minimal lateral diversion is likely at Yucca Mountain. Numerical models, to this point, have not accounted for the gradual transition of properties or the existence of multiple layers that could inadvertently influence the simulation of lateral diversion as an artifact of numerical model discretization. Analyses were made of subsurface matric potential measurements, and comparisons were made of surface infiltration estimates with deeper percolation flux calculations using chloride‐mass‐balance calculations and simulations of measured temperature profiles. These analyses suggest that insignificant lateral diversion has occurred above the repository horizon and that water generally moves vertically through the Paintbrush nonwelded tuffs.

Study of the Z{sub 3} symmetry in QCD at finite temperature and chemical potential using a worm algorithm

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

Krein, Gastao; Leme, Rafael R.; Woitek, Marcio

Traditional Monte Carlo simulations of QCD in the presence of a baryon chemical potential are plagued by the complex phase problem and new numerical approaches are necessary for studying the phase diagram of the theory. In this work we consider a Z{sub 3} Polyakov loop model for the deconfining phase transition in QCD and discuss how a flux representation of the model in terms of dimer and monomer variable solves the complex action problem. We present results of numerical simulations using a worm algorithm for the specific heat and two-point correlation function of Polyakov loops. Evidences of a first ordermore » deconfinement phase transition are discussed.« less

General Trends of Dihedral Conformational Transitions in a Globular Protein

PubMed Central

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; McCammon, J. Andrew

2017-01-01

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and Adaptive Biasing Force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions ~2 times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the Bend, Coil and Turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein sidechains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Sidechains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. PMID:26799251

A study of electron transfer using a three-level system coupled to an ohmic bath

NASA Technical Reports Server (NTRS)

Takasu, Masako; Chandler, David

1993-01-01

Electron transfer is studied using a multi-level system coupled to a bosonic bath. Two body correlation functions are obtained using both exact enumeration of spin paths and Monte Carlo simulation. It was found that the phase boundary for the coherent-incoherent transition lies at a smaller friction in the asymmetric two-level model than in the symmetric two-level model. A similar coherent-incoherent transition is observed for three-level system.

Performance of an Automated-Mixed-Traffic-Vehicle /AMTV/ System. [urban people mover

NASA Technical Reports Server (NTRS)

Peng, T. K. C.; Chon, K.

1978-01-01

This study analyzes the operation and evaluates the expected performance of a proposed automatic guideway transit system which uses low-speed Automated Mixed Traffic Vehicles (AMTV's). Vehicle scheduling and headway control policies are evaluated with a transit system simulation model. The effect of mixed-traffic interference on the average vehicle speed is examined with a vehicle-pedestrian interface model. Control parameters regulating vehicle speed are evaluated for safe stopping and passenger comfort.

Detecting critical state before phase transition of complex systems by hidden Markov model

NASA Astrophysics Data System (ADS)

Liu, Rui; Chen, Pei; Li, Yongjun; Chen, Luonan

Identifying the critical state or pre-transition state just before the occurrence of a phase transition is a challenging task, because the state of the system may show little apparent change before this critical transition during the gradual parameter variations. Such dynamics of phase transition is generally composed of three stages, i.e., before-transition state, pre-transition state, and after-transition state, which can be considered as three different Markov processes. Thus, based on this dynamical feature, we present a novel computational method, i.e., hidden Markov model (HMM), to detect the switching point of the two Markov processes from the before-transition state (a stationary Markov process) to the pre-transition state (a time-varying Markov process), thereby identifying the pre-transition state or early-warning signals of the phase transition. To validate the effectiveness, we apply this method to detect the signals of the imminent phase transitions of complex systems based on the simulated datasets, and further identify the pre-transition states as well as their critical modules for three real datasets, i.e., the acute lung injury triggered by phosgene inhalation, MCF-7 human breast cancer caused by heregulin, and HCV-induced dysplasia and hepatocellular carcinoma.

Analysis, simulation and visualization of 1D tapping via reduced dynamical models

NASA Astrophysics Data System (ADS)

Blackmore, Denis; Rosato, Anthony; Tricoche, Xavier; Urban, Kevin; Zou, Luo

2014-04-01

A low-dimensional center-of-mass dynamical model is devised as a simplified means of approximately predicting some important aspects of the motion of a vertical column comprised of a large number of particles subjected to gravity and periodic vertical tapping. This model is investigated first as a continuous dynamical system using analytical, simulation and visualization techniques. Then, by employing an approach analogous to that used to approximate the dynamics of a bouncing ball on an oscillating flat plate, it is modeled as a discrete dynamical system and analyzed to determine bifurcations and transitions to chaotic motion along with other properties. The predictions of the analysis are then compared-primarily qualitatively-with visualization and simulation results of the reduced continuous model, and ultimately with simulations of the complete system dynamics.

Hybrid RANS-LES using high order numerical methods

NASA Astrophysics Data System (ADS)

Henry de Frahan, Marc; Yellapantula, Shashank; Vijayakumar, Ganesh; Knaus, Robert; Sprague, Michael

2017-11-01

Understanding the impact of wind turbine wake dynamics on downstream turbines is particularly important for the design of efficient wind farms. Due to their tractable computational cost, hybrid RANS/LES models are an attractive framework for simulating separation flows such as the wake dynamics behind a wind turbine. High-order numerical methods can be computationally efficient and provide increased accuracy in simulating complex flows. In the context of LES, high-order numerical methods have shown some success in predictions of turbulent flows. However, the specifics of hybrid RANS-LES models, including the transition region between both modeling frameworks, pose unique challenges for high-order numerical methods. In this work, we study the effect of increasing the order of accuracy of the numerical scheme in simulations of canonical turbulent flows using RANS, LES, and hybrid RANS-LES models. We describe the interactions between filtering, model transition, and order of accuracy and their effect on turbulence quantities such as kinetic energy spectra, boundary layer evolution, and dissipation rate. This work was funded by the U.S. Department of Energy, Exascale Computing Project, under Contract No. DE-AC36-08-GO28308 with the National Renewable Energy Laboratory.

Coordination control of flexible manufacturing systems

NASA Astrophysics Data System (ADS)

Menon, Satheesh R.

One of the first attempts was made to develop a model driven system for coordination control of Flexible Manufacturing Systems (FMS). The structure and activities of the FMS are modeled using a colored Petri Net based system. This approach has the advantage of being able to model the concurrency inherent in the system. It provides a method for encoding the system state, state transitions and the feasible transitions at any given state. Further structural analysis (for detecting conflicting actions, deadlocks which might occur during operation, etc.) can be performed. The problem is also addressed of implementing and testing the behavior of existing dynamic scheduling approaches in simulations of realistic situations. A simulation architecture was proposed and performance evaluation was carried out for establishing the correctness of the model, stability of the system from a structural (deadlocks) and temporal (boundedness of backlogs) points of view, and for collection of statistics for performance measures such as machine and robot utilizations, average wait times and idle times of resources. A real-time implementation architecture for the coordination controller was also developed and implemented in a software simulated environment. Given the current technology of FMS control, the model-driven colored Petri net-based approach promises to develop a very flexible control environment.

Particle Interactions Mediated by Dynamical Networks: Assessment of Macroscopic Descriptions

NASA Astrophysics Data System (ADS)

Barré, J.; Carrillo, J. A.; Degond, P.; Peurichard, D.; Zatorska, E.

2018-02-01

We provide a numerical study of the macroscopic model of Barré et al. (Multiscale Model Simul, 2017, to appear) derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodeling process is very fast, the macroscopic model takes the form of a single aggregation-diffusion equation for the density of particles. The theoretical study of the macroscopic model gives precise criteria for the phase transitions of the steady states, and in the one-dimensional case, we show numerically that the stationary solutions of the microscopic model undergo the same phase transitions and bifurcation types as the macroscopic model. In the two-dimensional case, we show that the numerical simulations of the macroscopic model are in excellent agreement with the predicted theoretical values. This study provides a partial validation of the formal derivation of the macroscopic model from a microscopic formulation and shows that the former is a consistent approximation of an underlying particle dynamics, making it a powerful tool for the modeling of dynamical networks at a large scale.

Particle Interactions Mediated by Dynamical Networks: Assessment of Macroscopic Descriptions.

PubMed

Barré, J; Carrillo, J A; Degond, P; Peurichard, D; Zatorska, E

2018-01-01

We provide a numerical study of the macroscopic model of Barré et al. (Multiscale Model Simul, 2017, to appear) derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodeling process is very fast, the macroscopic model takes the form of a single aggregation-diffusion equation for the density of particles. The theoretical study of the macroscopic model gives precise criteria for the phase transitions of the steady states, and in the one-dimensional case, we show numerically that the stationary solutions of the microscopic model undergo the same phase transitions and bifurcation types as the macroscopic model. In the two-dimensional case, we show that the numerical simulations of the macroscopic model are in excellent agreement with the predicted theoretical values. This study provides a partial validation of the formal derivation of the macroscopic model from a microscopic formulation and shows that the former is a consistent approximation of an underlying particle dynamics, making it a powerful tool for the modeling of dynamical networks at a large scale.

Simulation study of depositing the carbon film on nanoparticles in the magnetized methane plasma

NASA Astrophysics Data System (ADS)

Mohammadzadeh, Hosein; Pourali, Nima; Ebadi, Zahra

2018-03-01

Plasma coating of nanoparticles in low-temperature magnetized methane plasma is studied by a simulation approach. To this end, by using the global model, the electron temperature and concentration of different species considered in this plasma are determined in the center of a capacitively coupled discharge. Then, the plasma-wall transition region in the presence of an oblique magnetic field is simulated by the multi-component fluid description. Nanoparticles with different radii are injected into the transition region and surface deposition and heating models, as well as dynamics and charging models, are employed to examine the coating process. The results of the simulation show that the non-spherical growth of nanoparticles is affected by the presence of the magnetic field, as with passing time, an oscillating increase is seen in the thickness of the film deposited on nanoparticles. Also, it is shown that the uniformity of the deposited film is dependent on the rotation velocity of nanoparticles. Generally, the obtained results imply that the sphericity of nanoparticles and uniformity of the film coated on them are controllable by the magnitude and orientation of the magnetic field.

Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, S.-P.; Peng, Z.; Yuan, H.; Kfoury, R.; Young, Y.-N.

2017-01-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 ∼ 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane, such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity Yuan et al. (2010). In this work we implement such an interaction potential in LAMMPS to simulate large-scale lipid systems such as a giant unilamellar vesicle (GUV) and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for RBC dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. To demonstrate that the proposed methods do capture the observed dynamics of vesicles and RBCs, we focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with enclosed volume; 2. RBC shape transitions with different enclosed volume. Finally utilizing the parallel computing capability in LAMMPS, we provide some timing results for parallel coarse-grained simulations to illustrate that it is possible to use LAMMPS to simulate large-scale realistic complex biological membranes for more than 1 ms.

An improved cellular automata model for train operation simulation with dynamic acceleration

NASA Astrophysics Data System (ADS)

Li, Wen-Jun; Nie, Lei

2018-03-01

Urban rail transit plays an important role in the urban public traffic because of its advantages of fast speed, large transport capacity, high safety, reliability and low pollution. This study proposes an improved cellular automaton (CA) model by considering the dynamic characteristic of the train acceleration to analyze the energy consumption and train running time. Constructing an effective model for calculating energy consumption to aid train operation improvement is the basis for studying and analyzing energy-saving measures for urban rail transit system operation.

Potts Model in One-Dimension on Directed Small-World Networks

NASA Astrophysics Data System (ADS)

Aquino, Édio O.; Lima, F. W. S.; Araújo, Ascânio D.; Costa Filho, Raimundo N.

2018-06-01

The critical properties of the Potts model with q=3 and 8 states in one-dimension on directed small-world networks are investigated. This disordered system is simulated by updating it with the Monte Carlo heat bath algorithm. The Potts model on these directed small-world networks presents in fact a second-order phase transition with a new set of critical exponents for q=3 considering a rewiring probability p=0.1. For q=8 the system exhibits only a first-order phase transition independent of p.

A new method for qualitative simulation of water resources systems: 1. Theory

NASA Astrophysics Data System (ADS)

Camara, A. S.; Pinheiro, M.; Antunes, M. P.; Seixas, M. J.

1987-11-01

A new dynamic modeling methodology, SLIN (Simulação Linguistica), allowing for the analysis of systems defined by linguistic variables, is presented. SLIN applies a set of logical rules avoiding fuzzy theoretic concepts. To make the transition from qualitative to quantitative modes, logical rules are used as well. Extensions of the methodology to simulation-optimization applications and multiexpert system modeling are also discussed.

Coexistence of Trees and Grass: Importance of climate and fire within the tropics

NASA Astrophysics Data System (ADS)

Shuman, J. K.; Fisher, R.; Koven, C.; Knox, R. G.; Andre, B.; Kluzek, E. B.

2017-12-01

Tropical forests are characterized by transition zones where dominance shifts between trees and grasses with some areas exhibiting bistability of the two. The cause of this transition and bistability has been linked to the interacting effects of climate, vegetation structure and fire behavior. Utilizing the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a demographic vegetation model, and the CESM ESM, we explore the coexistence of trees and grass across the tropics with an active fire regime. FATES has been updated to use a fire module based on Spitfire. FATES-Spitfire tracks fire ignition, spread and impact based on fuel state and combustion. Fire occurs within the model with variable intensity that kills trees according to the combined effects of cambial damage and crown scorch due to flame height and fire intensity. As a size-structured model, FATES allows for variable mortality based on the size of tree cohorts, where larger trees experience lower morality compared to small trees. Results for simulation scenarios where vegetation is represented by all trees, all grass, or a combination of competing trees and grass are compared to assess changes in biomass, fire regime and tree-grass coexistence. Within the forest-grass transition area there is a critical time during which grass fuels fire spread and prevents the establishment of trees. If trees are able to escape mortality a tree-grass bistable area is successful. The ability to simulate the bistability and transition of trees and grass throughout the tropics is critical to representing vegetation dynamics in response to changing climate and CO2.

Kinetic Monte Carlo Simulations of Rod Eutectics and the Surface Roughening Transition in Binary Alloys

NASA Technical Reports Server (NTRS)

Bentz, Daniel N.; Betush, William; Jackson, Kenneth A.

2003-01-01

In this paper we report on two related topics: Kinetic Monte Carlo simulations of the steady state growth of rod eutectics from the melt, and a study of the surface roughness of binary alloys. We have implemented a three dimensional kinetic Monte Carlo (kMC) simulation with diffusion by pair exchange only in the liquid phase. Entropies of fusion are first chosen to fit the surface roughness of the pure materials, and the bond energies are derived from the equilibrium phase diagram, by treating the solid and liquid as regular and ideal solutions respectively. A simple cubic lattice oriented in the {100} direction is used. Growth of the rods is initiated from columns of pure B material embedded in an A matrix, arranged in a close packed array with semi-periodic boundary conditions. The simulation cells typically have dimensions of 50 by 87 by 200 unit cells. Steady state growth is compliant with the Jackson-Hunt model. In the kMC simulations, using the spin-one Ising model, growth of each phase is faceted or nonfaceted phases depending on the entropy of fusion. There have been many studies of the surface roughening transition in single component systems, but none for binary alloy systems. The location of the surface roughening transition for the phases of a eutectic alloy determines whether the eutectic morphology will be regular or irregular. We have conducted a study of surface roughness on the spin-one Ising Model with diffusion using kMC. The surface roughness was found to scale with the melting temperature of the alloy as given by the liquidus line on the equilibrium phase diagram. The density of missing lateral bonds at the surface was used as a measure of surface roughness.

Applications of neural networks to the studies of phase transitions of two-dimensional Potts models

NASA Astrophysics Data System (ADS)

Li, C.-D.; Tan, D.-R.; Jiang, F.-J.

2018-04-01

We study the phase transitions of two-dimensional (2D) Q-states Potts models on the square lattice, using the first principles Monte Carlo (MC) simulations as well as the techniques of neural networks (NN). We demonstrate that the ideas from NN can be adopted to study these considered phase transitions efficiently. In particular, even with a simple NN constructed in this investigation, we are able to obtain the relevant information of the nature of these phase transitions, namely whether they are first order or second order. Our results strengthen the potential applicability of machine learning in studying various states of matters. Subtlety of applying NN techniques to investigate many-body systems is briefly discussed as well.

International benchmarking of longitudinal train dynamics simulators: results

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin; Chang, Chongyi; Guo, Gang; Sakalo, Alexey; Wei, Wei; Zhao, Xubao; Burgelman, Nico; Wiersma, Pier; Chollet, Hugues; Sebes, Michel; Shamdani, Amir; Melzi, Stefano; Cheli, Federico; di Gialleonardo, Egidio; Bosso, Nicola; Zampieri, Nicolò; Luo, Shihui; Wu, Honghua; Kaza, Guy-Léon

2018-03-01

This paper presents the results of the International Benchmarking of Longitudinal Train Dynamics Simulators which involved participation of nine simulators (TABLDSS, UM, CRE-LTS, TDEAS, PoliTo, TsDyn, CARS, BODYSIM and VOCO) from six countries. Longitudinal train dynamics results and computing time of four simulation cases are presented and compared. The results show that all simulators had basic agreement in simulations of locomotive forces, resistance forces and track gradients. The major differences among different simulators lie in the draft gear models. TABLDSS, UM, CRE-LTS, TDEAS, TsDyn and CARS had general agreement in terms of the in-train forces; minor differences exist as reflections of draft gear model variations. In-train force oscillations were observed in VOCO due to the introduction of wheel-rail contact. In-train force instabilities were sometimes observed in PoliTo and BODYSIM due to the velocity controlled transitional characteristics which could have generated unreasonable transitional stiffness. Regarding computing time per train operational second, the following list is in order of increasing computing speed: VOCO, TsDyn, PoliTO, CARS, BODYSIM, UM, TDEAS, CRE-LTS and TABLDSS (fastest); all simulators except VOCO, TsDyn and PoliTo achieved faster speeds than real-time simulations. Similarly, regarding computing time per integration step, the computing speeds in order are: CRE-LTS, VOCO, CARS, TsDyn, UM, TABLDSS and TDEAS (fastest).

Dynamics of Sheared Granular Materials

NASA Technical Reports Server (NTRS)

Kondic, Lou; Utter, Brian; Behringer, Robert P.

2002-01-01

This work focuses on the properties of sheared granular materials near the jamming transition. The project currently involves two aspects. The first of these is an experiment that is a prototype for a planned ISS (International Space Station) flight. The second is discrete element simulations (DES) that can give insight into the behavior one might expect in a reduced-g environment. The experimental arrangement consists of an annular channel that contains the granular material. One surface, say the upper surface, rotates so as to shear the material contained in the annulus. The lower surface controls the mean density/mean stress on the sample through an actuator or other control system. A novel feature under development is the ability to 'thermalize' the layer, i.e. create a larger amount of random motion in the material, by using the actuating system to provide vibrations as well control the mean volume of the annulus. The stress states of the system are determined by transducers on the non-rotating wall. These measure both shear and normal components of the stress on different size scales. Here, the idea is to characterize the system as the density varies through values spanning dense almost solid to relatively mobile granular states. This transition regime encompasses the regime usually thought of as the glass transition, and/or the jamming transition. Motivation for this experiment springs from ideas of a granular glass transition, a related jamming transition, and from recent experiments. In particular, we note recent experiments carried out by our group to characterize this type of transition and also to demonstrate/ characterize fluctuations in slowly sheared systems. These experiments give key insights into what one might expect in near-zero g. In particular, they show that the compressibility of granular systems diverges at a transition or critical point. It is this divergence, coupled to gravity, that makes it extremely difficult if not impossible to characterize the transition region in an earth-bound experiment. In the DE modeling, we analyze dynamics of a sheared granular system in Couette geometry in two (2D) and three (3D) space dimensions. Here, the idea is to both better understand what we might encounter in a reduced-g environment, and at a deeper level to deduce the physics of sheared systems in a density regime that has not been addressed by past experiments or simulations. One aspect of the simulations addresses sheared 2D system in zero-g environment. For low volume fractions, the expected dynamics of this type of system is relatively well understood. However, as the volume fraction is increased, the system undergoes a phase transition, as explained above. The DES concentrate on the evolution of the system as the solid volume fraction is slowly increased, and in particular on the behavior of very dense systems. For these configurations, the simulations show that polydispersity of the sheared particles is a crucial factor that determines the system response. Figures 1 and 2 below, that present the total force on each grain, show that even relatively small (10 %) nonuniformity of the size of the grains (expected in typical experiments) may lead to significant modifications of the system properties, such as velocity profiles, temperature, force propagation, and formation shear bands. The simulations are extended in a few other directions, in order to provide additional insight to the experimental system analyzed above. In one direction, both gravity, and driving due to vibrations are included. These simulations allow for predictions on the driving regime that is required in the experiments in order to analyze the jamming transition. Furthermore, direct comparison of experiments and DES will allow for verification of the modeling assumptions. We have also extended our modeling efforts to 3D. The (preliminary) results of these simulations of an annular system in zero-g environment will conclude the presentation.

Mathematical model for lift/cruise fan V/STOL aircraft simulator programming data

NASA Technical Reports Server (NTRS)

Bland, M. P.; Fajfar, B.; Konsewicz, R. K.

1976-01-01

Simulation data are reported for the purpose of programming the flight simulator for advanced aircraft for tests of the lift/cruise fan V/STOL Research Technology Aircraft. These simulation tests are to provide insight into problem areas which are encountered in operational use of the aircraft. A mathematical model is defined in sufficient detail to represent all the necessary pertinent aircraft and system characteristics. The model includes the capability to simulate two basic versions of an aircraft propulsion system: (1) the gas coupled configuration which uses insulated air ducts to transmit power between gas generators and fans in the form of high energy engine exhaust and (2) the mechanically coupled power system which uses shafts, clutches, and gearboxes for power transmittal. Both configurations are modeled such that the simulation can include vertical as well as rolling takeoff and landing, hover, powered lift flight, aerodynamic flight, and the transition between powered lift and aerodynamic flight.

Artificial emotion triggered stochastic behavior transitions with motivational gain effects for multi-objective robot tasks

NASA Astrophysics Data System (ADS)

Dağlarli, Evren; Temeltaş, Hakan

2007-04-01

This paper presents artificial emotional system based autonomous robot control architecture. Hidden Markov model developed as mathematical background for stochastic emotional and behavior transitions. Motivation module of architecture considered as behavioral gain effect generator for achieving multi-objective robot tasks. According to emotional and behavioral state transition probabilities, artificial emotions determine sequences of behaviors. Also motivational gain effects of proposed architecture can be observed on the executing behaviors during simulation.

Quantum phases with differing computational power.

PubMed

Cui, Jian; Gu, Mile; Kwek, Leong Chuan; Santos, Marcelo França; Fan, Heng; Vedral, Vlatko

2012-05-01

The observation that concepts from quantum information has generated many alternative indicators of quantum phase transitions hints that quantum phase transitions possess operational significance with respect to the processing of quantum information. Yet, studies on whether such transitions lead to quantum phases that differ in their capacity to process information remain limited. Here we show that there exist quantum phase transitions that cause a distinct qualitative change in our ability to simulate certain quantum systems under perturbation of an external field by local operations and classical communication. In particular, we show that in certain quantum phases of the XY model, adiabatic perturbations of the external magnetic field can be simulated by local spin operations, whereas the resulting effect within other phases results in coherent non-local interactions. We discuss the potential implications to adiabatic quantum computation, where a computational advantage exists only when adiabatic perturbation results in coherent multi-body interactions.

Interface mobility and the liquid-glass transition in a one-component system described by an embedded atom method potential

NASA Astrophysics Data System (ADS)

Mendelev, M. I.; Schmalian, J.; Wang, C. Z.; Morris, J. R.; Ho, K. M.

2006-09-01

We present molecular dynamics (MD) studies of the liquid structure, thermodynamics, and dynamics in a one-component system described by the Ercolessi-Adams embedded atom method potential for Al. We find two distinct noncrystalline phases in this system. One of them is a liquid phase and the second phase has similar structure but different equation of state. Moreover, this phase has qualitatively different dynamics than that in the liquid phase. The transitions between these two noncrystalline phases can be seen during MD simulation. The hysteresis in this transition suggests that this is a first-order transition. This conclusion is strongly supported by simulations of the two phases that demonstrate that these phases may coexist with a well-defined interface. We find the coexistent temperature and the interface mobility. Finally, we discuss how these results can be explained using modern models of vitrification.

Phase transition to turbulence in a pipe

NASA Astrophysics Data System (ADS)

Goldenfeld, Nigel

Leo Kadanoff taught us much about phase transitions, turbulence and collective behavior. Here I explore the transition to turbulence in a pipe, showing how a collective mode determines the universality class. Near the transition, turbulent puffs decay either directly or through splitting, with characteristic time-scales that exhibit a super-exponential dependence on Reynolds number. Direct numerical simulations reveal that a collective mode, a so-called zonal flow emerges at large scales, activated by anisotropic turbulent fluctuations, as represented by Reynolds stress. This zonal flow imposes a shear on the turbulent fluctuations that tends to suppress their anisotropy, leading to a Landau theory of predator-prey type, in the directed percolation universality class. Stochastic simulations of this model reproduce the functional form and phenomenology of pipe flow experiments. Talk based on work performed with Hong-Yan Shih and Tsung-Lin Hsieh. This work was partially supported by the National Science Foundation through Grant NSF-DMR-1044901.

Battery-Charge-State Model

NASA Technical Reports Server (NTRS)

Vivian, H. C.

1985-01-01

Charge-state model for lead/acid batteries proposed as part of effort to make equivalent of fuel gage for battery-powered vehicles. Models based on equations that approximate observable characteristics of battery electrochemistry. Uses linear equations, easier to simulate on computer, and gives smooth transitions between charge, discharge, and recuperation.

Modeling Land Use/Cover Changes in an African Rural Landscape

NASA Astrophysics Data System (ADS)

Kamusoko, C.; Aniya, M.

2006-12-01

Land use/cover changes are analyzed in the Bindura district of Zimbabwe, Africa through the integration of data from a time series of Landsat imagery (1973, 1989 and 2000), a household survey and GIS coverages. We employed a hybrid supervised/unsupervised classification approach to generate land use/cover maps from which landscape metrics were calculated. Population and other household variables were derived from a sample of surveyed villages, while road accessibility and slope were obtained from topographic maps and digital elevation model, respectively. Markov-cellular automata modeling approach that incorporates Markov chain analysis, cellular automata and multi-criteria evaluation (MCE) / multi-objective allocation (MOLA) procedures was used to simulate land use/cover changes. A GIS-based MCE technique computed transition potential maps, whereas transition areas were derived from the 1973-2000 land use/cover maps using the Markov chain analysis. A 5 x 5 cellular automata filter was used to develop a spatially explicit contiguity- weighting factor to change the cells based on its previous state and those of its neighbors, while MOLA resolved land use/cover class allocation conflicts. The kappa index of agreement was used for model validation. Observed trends in land use/cover changes indicate that deforestation and the encroachment of cultivation in woodland areas is a continuous trend in the study area. This suggests that economic activities driven by agricultural expansion were the main causes of landscape fragmentation, leading to landscape degradation. Rigorous calibration of transition potential maps done by a MCE algorithm and Markovian transition probabilities produced accurate inputs for the simulation of land use/cover changes. Overall standard kappa index of agreement ranged from 0.73 to 0.83, which is sufficient for simulating land use/cover changes in the study area. Land use/cover simulations under the 1989 and 2000 scenario indicated further landscape degradation in the rural areas of the Bindura district. Keywords: Zimbabwe, land use/cover changes, landscape fragmentation, GIS, land use/cover change modeling, multi-criteria evaluation/multi-objective allocation procedures, Markov-cellular automata

A Shunt Model of the Inner Medullary Nephron with Pre-Bend Transitions

NASA Astrophysics Data System (ADS)

Gonzalez, M. T.; Hegarty, A. F.; Thomas, S. R.

2009-09-01

Mathematical models of the renal medulla face the problem of representing water and solute transfer among tens of thousands of nephrons and blood vessels of various lengths, arranged in countercurrent fashion. Published models fall into two broad categories with respect to this issue: multi-nephron models, which explicitly represent a large number of individual nephrons, or lumped models with virtual shunts that represent the turning back of nephrons and vessels at varying depths. Shunt models have the advantage of a compact description and relatively rapid execution time but are ill-suited to faithfully represent features such as prebend transitions of epithelial permeabilities in nephrons of different lengths. A new shunt model approach that can accommodate pre-bend transitions of nephrons at all medullary depths is presented in this work together with the results of simulation of predicted flows and concentrations.

One Giant Leap for Categorizers: One Small Step for Categorization Theory

PubMed Central

Smith, J. David; Ell, Shawn W.

2015-01-01

We explore humans’ rule-based category learning using analytic approaches that highlight their psychological transitions during learning. These approaches confirm that humans show qualitatively sudden psychological transitions during rule learning. These transitions contribute to the theoretical literature contrasting single vs. multiple category-learning systems, because they seem to reveal a distinctive learning process of explicit rule discovery. A complete psychology of categorization must describe this learning process, too. Yet extensive formal-modeling analyses confirm that a wide range of current (gradient-descent) models cannot reproduce these transitions, including influential rule-based models (e.g., COVIS) and exemplar models (e.g., ALCOVE). It is an important theoretical conclusion that existing models cannot explain humans’ rule-based category learning. The problem these models have is the incremental algorithm by which learning is simulated. Humans descend no gradient in rule-based tasks. Very different formal-modeling systems will be required to explain humans’ psychology in these tasks. An important next step will be to build a new generation of models that can do so. PMID:26332587

Coevolving complex networks in the model of social interactions

NASA Astrophysics Data System (ADS)

Raducha, Tomasz; Gubiec, Tomasz

2017-04-01

We analyze Axelrod's model of social interactions on coevolving complex networks. We introduce four extensions with different mechanisms of edge rewiring. The models are intended to catch two kinds of interactions-preferential attachment, which can be observed in scientists or actors collaborations, and local rewiring, which can be observed in friendship formation in everyday relations. Numerical simulations show that proposed dynamics can lead to the power-law distribution of nodes' degree and high value of the clustering coefficient, while still retaining the small-world effect in three models. All models are characterized by two phase transitions of a different nature. In case of local rewiring we obtain order-disorder discontinuous phase transition even in the thermodynamic limit, while in case of long-distance switching discontinuity disappears in the thermodynamic limit, leaving one continuous phase transition. In addition, we discover a new and universal characteristic of the second transition point-an abrupt increase of the clustering coefficient, due to formation of many small complete subgraphs inside the network.

Phase transitions of a water overlayer on charged graphene: from electromelting to electrofreezing.

PubMed

Zhu, Xueyan; Yuan, Quanzi; Zhao, Ya-Pu

2014-05-21

We show by using molecular dynamics simulations that a water overlayer on charged graphene experiences first-order ice-to-liquid (electromelting), and then liquid-to-ice (electrofreezing) phase transitions with the increase of the charge value. Corresponding to the ice-liquid-ice transition, the variations of the order parameters indicate an order-disorder-order transition. The key to this novel phenomenon is the surface charge induced change of the orientations of water dipoles, which leads to the change of the water-water interactions from being attractive to repulsive at a critical charge value qc. To further uncover how the orientations of water dipoles influence the interaction strength between water molecules, a theoretical model considering both the Coulomb and van der Waals interactions is established. The results show that with the increase of the charge value, the interaction strength between water molecules decreases below qc, then increases above qc. These two inverse processes lead to electromelting and electrofreezing, respectively. Combining this model with the Eyring equation, the diffusion coefficient is obtained, the variation of which is in qualitative agreement with the simulation results. Our findings not only expand our knowledge of the graphene-water interface, but related analyses could also help recognize the controversial role of the surface charge or electric field in promoting phase transitions of water.

Collective conflict resolution in groups on the move

NASA Astrophysics Data System (ADS)

Pinkoviezky, Itai; Couzin, Iain D.; Gov, Nir S.

2018-03-01

Collective decision-making regarding direction of travel is observed during natural motion of animal and cellular groups. This phenomenon is exemplified, in the simplest case, by a group that contains two informed subgroups that hold conflicting preferred directions of motion. Under such circumstances, simulations, subsequently supported by experimental data with birds and primates, have demonstrated that the resulting motion is either towards a compromise direction or towards one of the preferred targets (even when the two subgroups are equal in size). However, the nature of this transition is not well understood. We present a theoretical study that combines simulations and a spin model for mobile animal groups, the latter providing an equilibrium representation, and exact solution in the thermodynamic limit. This allows us to identify the nature of this transition at a critical angular difference between the two preferred directions: in both flocking and spin models the transition coincides with the change in the group dynamics from Brownian to persistent collective motion. The groups undergo this transition as the number of uninformed individuals (those in the group that do not exhibit a directional preference) increases, which acts as an inverse of the temperature (noise) of the spin model. When the two informed subgroups are not equal in size, there is a tendency for the group to reach the target preferred by the larger subgroup. We find that the spin model captures effectively the essence of the collective decision-making transition and allows us to reveal a noise-dependent trade-off between the decision-making speed and the ability to achieve majority (democratic) consensus.

Collective conflict resolution in groups on the move.

PubMed

Pinkoviezky, Itai; Couzin, Iain D; Gov, Nir S

2018-03-01

Collective decision-making regarding direction of travel is observed during natural motion of animal and cellular groups. This phenomenon is exemplified, in the simplest case, by a group that contains two informed subgroups that hold conflicting preferred directions of motion. Under such circumstances, simulations, subsequently supported by experimental data with birds and primates, have demonstrated that the resulting motion is either towards a compromise direction or towards one of the preferred targets (even when the two subgroups are equal in size). However, the nature of this transition is not well understood. We present a theoretical study that combines simulations and a spin model for mobile animal groups, the latter providing an equilibrium representation, and exact solution in the thermodynamic limit. This allows us to identify the nature of this transition at a critical angular difference between the two preferred directions: in both flocking and spin models the transition coincides with the change in the group dynamics from Brownian to persistent collective motion. The groups undergo this transition as the number of uninformed individuals (those in the group that do not exhibit a directional preference) increases, which acts as an inverse of the temperature (noise) of the spin model. When the two informed subgroups are not equal in size, there is a tendency for the group to reach the target preferred by the larger subgroup. We find that the spin model captures effectively the essence of the collective decision-making transition and allows us to reveal a noise-dependent trade-off between the decision-making speed and the ability to achieve majority (democratic) consensus.

Parser for Sabin-to-Mahoney Transition Model of Quasispecies Replication

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

Ecale Zhou, Carol

2016-01-03

This code is a data parse for preparing output from the Qspp agent-based stochastic simulation model for plotting in Excel. This code is specific to a set of simulations that were run for the purpose of preparing data for a publication. It is necessary to make this code open-source in order to publish the model code (Qspp), which has already been released. There is a necessity of assuring that results from using Qspp for a publication

VizieR Online Data Catalog: Kepler pipeline transit signal recovery. III. (Christiansen+, 2016)

NASA Astrophysics Data System (ADS)

Christiansen, J. L.; Clarke, B. D.; Burke, C. J.; Jenkins, J. M.; Bryson, S. T.; Coughlin, J. L.; Mullally, F.; Thompson, S. E.; Twicken, J. D.; Batalha, N. M.; Haas, M. R.; Catanzarite, J.; Campbell, J. R.; Uddin, A. K.; Zamudio, K.; Smith, J. C.; Henze, C. E.

2018-03-01

Here we describe the third transit injection experiment, which tests the entire Kepler observing baseline (Q1-Q17) for the first time across all 84 CCD channels. It was performed to measure the sensitivity of the Kepler pipeline used to generate the Q1-Q17 Data Release 24 (DR24) catalog of Kepler Objects of Interest (Coughlin et al. 2016, J/ApJS/224/12) available at the NASA Exoplanet Archive (Akeson et al. 2013PASP..125..989A). The average detection efficiency describes the likelihood that the Kepler pipeline would successfully recover a given transit signal. To measure this property we perform a Monte Carlo experiment where we inject the signatures of simulated transiting planets around 198154 target stars, one per star, across the focal plane starting with the Q1-Q17 DR24 calibrated pixels. The simulated transits are generated using the Mandel & Agol (2002ApJ...580L.171M) model. Of the injections, 159013 resulted in three or more injected transits (the minimum required for detection by the pipeline) and were used for the subsequent analysis. (1 data file).

Molecular simulation and mathematical modelling of glass transition temperature depression induced by CO2 plasticization in Polysulfone membranes

NASA Astrophysics Data System (ADS)

Lock, S. S. M.; Lau, K. K.; Lock Sow Mei, Irene; Shariff, A. M.; Yeong, Y. F.; Bustam, A. M.

2017-08-01

A sequence of molecular modelling procedure has been proposed to simulate experimentally validated membrane structure characterizing the effect of CO2 plasticization, whereby it can be subsequently employed to elucidate the depression in glass transition temperature (Tg ). Based on the above motivation, unswollen and swollen Polysulfone membrane structures with different CO2 loadings have been constructed, whereby the accuracy has been validated through good compliance with experimentally measured physical properties. It is found that the presence of CO2 constitutes to enhancement in polymeric chain relaxation, which consequently promotes the enlargement of molecular spacing and causes dilation in the membrane matrix. A series of glass transition temperature treatment has been conducted on the verified molecular structure to elucidate the effect of CO2 loadings to the depression in Tg induced by plasticization. Subsequently, a modified Michealis-Menten (M-M) function has been implemented to quantify the effect of CO2 loading attributed to plasticization towards Tg .

Liquid-Gas-Like Phase Transition in Sand Flow Under Microgravity

NASA Astrophysics Data System (ADS)

Huang, Yu; Zhu, Chongqiang; Xiang, Xiang; Mao, Wuwei

2015-06-01

In previous studies of granular flow, it has been found that gravity plays a compacting role, causing convection and stratification by density. However, there is a lack of research and analysis of the characteristics of different particles' motion under normal gravity contrary to microgravity. In this paper, we conduct model experiments on sand flow using a model test system based on a drop tower under microgravity, within which the characteristics and development processes of granular flow under microgravity are captured by high-speed cameras. The configurations of granular flow are simulated using a modified MPS (moving particle simulation), which is a mesh-free, pure Lagrangian method. Moreover, liquid-gas-like phase transitions in the sand flow under microgravity, including the transitions to "escaped", "jumping", and "scattered" particles are highlighted, and their effects on the weakening of shear resistance, enhancement of fluidization, and changes in particle-wall and particle-particle contact mode are analyzed. This study could help explain the surface geology evolution of small solar bodies and elucidate the nature of granular interaction.

Are rapid transitions between invasive and native species caused by alternative stable states, and does it matter?

PubMed

Hansen, Gretchen J A; Ives, Anthony R; Vander Zanden, M Jake; Carpenter, Stephen R

2013-10-01

Rapid transitions in ecosystem structure, or regime shifts, are a hallmark of alternative stable states (ASS). However, regime shifts can occur even when feedbacks are not strong enough to cause ASS. We investigated the potential for ASS to explain transitions between dominance of an invasive species, rusty crayfish (Orconectes rusticus), and native sunfishes (Lepomis spp.) in northern Wisconsin (USA) lakes. A rapid transition from Lepomis to rusty crayfish dominance occurred as rusty crayfish invaded Trout Lake, and the reverse transition resulted from an eight-year experimental removal of rusty crayfish from Sparkling Lake. We fit a stage-structured population model of species interactions to 31 years of time-series data from each lake. The model identified water level as an important driver, with drought conditions reducing rusty crayfish recruitment and allowing Lepomis dominance. The maximum-likelihood parameter estimates of the negative interaction between rusty crayfish and Lepomis led to ASS in the model, where each species was capable of excluding the other within a narrow range of environmental conditions. However, uncertainty in parameter estimates made it impossible to exclude the potential that rapid transitions were caused by a simpler threshold response lacking alternative equilibria. Simulated forward and backward transitions between species dominance occurred at different environmental conditions (i.e., hysteresis), even when the parameters used for simulation did not predict ASS as a result of slow species responses to environmental drivers. Thus, ASS are possible, but by no means certain, explanations for rapid transitions in this system, and our results highlight the difficulties associated with distinguishing ASS from other types of threshold responses. However, whether regime shifts are caused by ASS may be relatively unimportant in this system, as the range of conditions over which transitions occur is narrow, and under most conditions, the system is predicted to exist in only a single state.

Topographies and dynamics on multidimensional potential energy surfaces

NASA Astrophysics Data System (ADS)

Ball, Keith Douglas

The stochastic master equation is a valuable tool for elucidating potential energy surface (PES) details that govern structural relaxation in clusters, bulk systems, and protein folding. This work develops a comprehensive framework for studying non-equilibrium relaxation dynamics using the master equation. Since our master equations depend upon accurate partition function models for use in Rice-Ramsperger-Kassel-Marcus (RRK(M) transition state theory, this work introduces several such models employing various harmonic and anharmonic approximations and compares their predicted equilibrium population distributions with those determined from molecular dynamics. This comparison is performed for the fully-delineated surfaces (KCl)5 and Ar9 to evaluate model performance for potential surfaces with long- and short-range interactions, respectively. For each system, several models perform better than a simple harmonic approximation. While no model gives acceptable results for all minima, and optimal modeling strategies differ for (KCl)5 and Ar9, a particular one-parameter model gives the best agreement with simulation for both systems. We then construct master equations from these models and compare their isothermal relaxation predictions for (KCl)5 and Ar9 with molecular dynamics simulations. This is the first comprehensive test of the kinetic performance of partition function models of its kind. Our results show that accurate modeling of transition-state partition functions is more important for (KCl)5 than for Ar9 in reproducing simulation results, due to a marked stiffening anharmonicity in the transition-state normal modes of (KCl)5. For both systems, several models yield qualitative agreement with simulation over a large temperature range. To examine the robustness of the master equation when applied to larger systems, for which full topographical descriptions would be either impossible or infeasible, we compute relaxation predictions for Ar11 using a master equation constructed from data representing the full PES, and compare these predictions to those of reduced master equations based on statistical samples of the full PES. We introduce a sampling method which generates random, Boltzmann-weighted, energetically 'downhill' sequences. The study reveals that, at moderate temperatures, the slowest relaxation timescale converges as the number of sequences in a sample grows to ~1000. Furthermore, the asymptotic timescale is comparable to the full-PES value.

Measurement-noise maximum as a signature of a phase transition.

PubMed

Chen, Zhi; Yu, Clare C

2007-02-02

We propose that a maximum in measurement noise can be used as a signature of a phase transition. As an example, we study the energy and magnetization noise spectra associated with first- and second-order phase transitions by using Monte Carlo simulations of the Ising model and 5-state Potts model in two dimensions. For a finite size system, the total noise power and the low frequency white noise S(f0 and the total noise power vanishes. f(-1)(knee) is approximately the equilibration time.

Linking state-and-transition simulation and timber supply models for forest biomass production scenarios

USGS Publications Warehouse

Costanza, Jennifer; Abt, Robert C.; McKerrow, Alexa; Collazo, Jaime

2015-01-01

We linked state-and-transition simulation models (STSMs) with an economics-based timber supply model to examine landscape dynamics in North Carolina through 2050 for three scenarios of forest biomass production. Forest biomass could be an important source of renewable energy in the future, but there is currently much uncertainty about how biomass production would impact landscapes. In the southeastern US, if forests become important sources of biomass for bioenergy, we expect increased land-use change and forest management. STSMs are ideal for simulating these landscape changes, but the amounts of change will depend on drivers such as timber prices and demand for forest land, which are best captured with forest economic models. We first developed state-and-transition model pathways in the ST-Sim software platform for 49 vegetation and land-use types that incorporated each expected type of landscape change. Next, for the three biomass production scenarios, the SubRegional Timber Supply Model (SRTS) was used to determine the annual areas of thinning and harvest in five broad forest types, as well as annual areas converted among those forest types, agricultural, and urban lands. The SRTS output was used to define area targets for STSMs in ST-Sim under two scenarios of biomass production and one baseline, business-as-usual scenario. We show that ST-Sim output matched SRTS targets in most cases. Landscape dynamics results indicate that, compared with the baseline scenario, forest biomass production leads to more forest and, specifically, more intensively managed forest on the landscape by 2050. Thus, the STSMs, informed by forest economics models, provide important information about potential landscape effects of bioenergy production.

Physically representative atomistic modeling of atomic-scale friction

NASA Astrophysics Data System (ADS)

Dong, Yalin

Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

2D lattice model of a lipid bilayer: Microscopic derivation and thermodynamic exploration

NASA Astrophysics Data System (ADS)

Hakobyan, Davit; Heuer, Andreas

2017-02-01

Based on all-atom Molecular Dynamics (MD) simulations of a lipid bilayer we present a systematic mapping on a 2D lattice model. Keeping the lipid type and the chain order parameter as key variables we derive a free energy functional, containing the enthalpic interaction of adjacent lipids as well as the tail entropy. The functional form of both functions is explicitly determined for saturated and polyunsaturated lipids. By studying the lattice model via Monte Carlo simulations it is possible to reproduce the temperature dependence of the distribution of order parameters of the pure lipids, including the prediction of the gel transition. Furthermore, application to a mixture of saturated and polyunsaturated lipids yields the correct phase separation behavior at lower temperatures with a simulation time reduced by approximately 7 orders of magnitude as compared to the corresponding MD simulations. Even the time-dependence of the de-mixing is reproduced on a semi-quantitative level. Due to the generality of the approach we envisage a large number of further applications, ranging from modeling larger sets of lipids, sterols, and solvent proteins to predicting nucleation barriers for the melting of lipids. Particularly, from the properties of the 2D lattice model one can directly read off the enthalpy and entropy change of the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine gel-to-liquid transition in excellent agreement with experimental and MD results.

A multi-band, multi-level, multi-electron model for efficient FDTD simulations of electromagnetic interactions with semiconductor quantum wells

NASA Astrophysics Data System (ADS)

Ravi, Koustuban; Wang, Qian; Ho, Seng-Tiong

2015-08-01

We report a new computational model for simulations of electromagnetic interactions with semiconductor quantum well(s) (SQW) in complex electromagnetic geometries using the finite-difference time-domain method. The presented model is based on an approach of spanning a large number of electron transverse momentum states in each SQW sub-band (multi-band) with a small number of discrete multi-electron states (multi-level, multi-electron). This enables accurate and efficient two-dimensional (2-D) and three-dimensional (3-D) simulations of nanophotonic devices with SQW active media. The model includes the following features: (1) Optically induced interband transitions between various SQW conduction and heavy-hole or light-hole sub-bands are considered. (2) Novel intra sub-band and inter sub-band transition terms are derived to thermalize the electron and hole occupational distributions to the correct Fermi-Dirac distributions. (3) The terms in (2) result in an explicit update scheme which circumvents numerically cumbersome iterative procedures. This significantly augments computational efficiency. (4) Explicit update terms to account for carrier leakage to unconfined states are derived, which thermalize the bulk and SQW populations to a common quasi-equilibrium Fermi-Dirac distribution. (5) Auger recombination and intervalence band absorption are included. The model is validated by comparisons to analytic band-filling calculations, simulations of SQW optical gain spectra, and photonic crystal lasers.

A 1D thermomechanical network transition constitutive model coupled with multiple structural relaxation for shape memory polymers

NASA Astrophysics Data System (ADS)

Zeng, Hao; Xie, Zhimin; Gu, Jianping; Sun, Huiyu

2018-03-01

A new thermomechanical network transition constitutive model is proposed in the study to describe the viscoelastic behavior of shape memory polymers (SMPs). Based on the microstructure of semi-crystalline SMPs, a new simplified transformation equation is proposed to describe the transform of transient networks. And the generalized fractional Maxwell model is introduced in the paper to estimate the temperature-dependent storage modulus. In addition, a neo-KAHR theory with multiple discrete relaxation processes is put forward to study the structural relaxation of the nonlinear thermal strain in cooling/heating processes. The evolution equations of the time- and temperature-dependent stress and strain response are developed. In the model, the thermodynamical and mechanical characteristics of SMPs in the typical thermomechanical cycle are described clearly and the irreversible deformation is studied in detail. Finally, the typical thermomechanical cycles are simulated using the present constitutive model, and the simulation results agree well with the experimental results.

The "Grey Zone" cold air outbreak global model intercomparison: A cross evaluation using large-eddy simulations

NASA Astrophysics Data System (ADS)

Tomassini, Lorenzo; Field, Paul R.; Honnert, Rachel; Malardel, Sylvie; McTaggart-Cowan, Ron; Saitou, Kei; Noda, Akira T.; Seifert, Axel

2017-03-01

A stratocumulus-to-cumulus transition as observed in a cold air outbreak over the North Atlantic Ocean is compared in global climate and numerical weather prediction models and a large-eddy simulation model as part of the Working Group on Numerical Experimentation "Grey Zone" project. The focus of the project is to investigate to what degree current convection and boundary layer parameterizations behave in a scale-adaptive manner in situations where the model resolution approaches the scale of convection. Global model simulations were performed at a wide range of resolutions, with convective parameterizations turned on and off. The models successfully simulate the transition between the observed boundary layer structures, from a well-mixed stratocumulus to a deeper, partly decoupled cumulus boundary layer. There are indications that surface fluxes are generally underestimated. The amount of both cloud liquid water and cloud ice, and likely precipitation, are under-predicted, suggesting deficiencies in the strength of vertical mixing in shear-dominated boundary layers. But also regulation by precipitation and mixed-phase cloud microphysical processes play an important role in the case. With convection parameterizations switched on, the profiles of atmospheric liquid water and cloud ice are essentially resolution-insensitive. This, however, does not imply that convection parameterizations are scale-aware. Even at the highest resolutions considered here, simulations with convective parameterizations do not converge toward the results of convection-off experiments. Convection and boundary layer parameterizations strongly interact, suggesting the need for a unified treatment of convective and turbulent mixing when addressing scale-adaptivity.

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

PubMed

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

2015-03-04

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

Ages and transit times as important diagnostics of model performance for predicting carbon dynamics in terrestrial vegetation models

NASA Astrophysics Data System (ADS)

Ceballos-Núñez, Verónika; Richardson, Andrew D.; Sierra, Carlos A.

2018-03-01

The global carbon cycle is strongly controlled by the source/sink strength of vegetation as well as the capacity of terrestrial ecosystems to retain this carbon. These dynamics, as well as processes such as the mixing of old and newly fixed carbon, have been studied using ecosystem models, but different assumptions regarding the carbon allocation strategies and other model structures may result in highly divergent model predictions. We assessed the influence of three different carbon allocation schemes on the C cycling in vegetation. First, we described each model with a set of ordinary differential equations. Second, we used published measurements of ecosystem C compartments from the Harvard Forest Environmental Measurement Site to find suitable parameters for the different model structures. And third, we calculated C stocks, release fluxes, radiocarbon values (based on the bomb spike), ages, and transit times. We obtained model simulations in accordance with the available data, but the time series of C in foliage and wood need to be complemented with other ecosystem compartments in order to reduce the high parameter collinearity that we observed, and reduce model equifinality. Although the simulated C stocks in ecosystem compartments were similar, the different model structures resulted in very different predictions of age and transit time distributions. In particular, the inclusion of two storage compartments resulted in the prediction of a system mean age that was 12-20 years older than in the models with one or no storage compartments. The age of carbon in the wood compartment of this model was also distributed towards older ages, whereas fast cycling compartments had an age distribution that did not exceed 5 years. As expected, models with C distributed towards older ages also had longer transit times. These results suggest that ages and transit times, which can be indirectly measured using isotope tracers, serve as important diagnostics of model structure and could largely help to reduce uncertainties in model predictions. Furthermore, by considering age and transit times of C in vegetation compartments as distributions, not only their mean values, we obtain additional insights into the temporal dynamics of carbon use, storage, and allocation to plant parts, which not only depends on the rate at which this C is transferred in and out of the compartments but also on the stochastic nature of the process itself.

Nonequilibrium transition induced by mass media in a model for social influence

NASA Astrophysics Data System (ADS)

González-Avella, J. C.; Cosenza, M. G.; Tucci, K.

2005-12-01

We study the effect of mass media, modeled as an applied external field, on a social system based on Axelrod’s model for the dissemination of culture. The numerical simulations show that the system undergoes a nonequilibrium phase transition between an ordered phase (homogeneous culture) specified by the mass media and a disordered (culturally fragmented) one. The critical boundary separating these phases is calculated on the parameter space of the system, given by the intensity of the mass media influence and the number of options per cultural attribute. Counterintuitively, mass media can induce cultural diversity when its intensity is above some threshold value. The nature of the phase transition changes from continuous to discontinuous at some critical value of the number of options.

Assessment of the Ability of Contemporary Climate Models to Assess Adequately the Risk of Possible Regional Anomalies and Trends

NASA Astrophysics Data System (ADS)

Mokhov, I. I.

2018-04-01

The results describing the ability of contemporary global and regional climate models not only to assess the risk of general trends of changes but also to predict qualitatively new regional effects are presented. In particular, model simulations predicted spatially inhomogeneous changes in the wind and wave conditions in the Arctic basins, which have been confirmed in recent years. According to satellite and reanalysis data, a qualitative transition to the regime predicted by model simulations occurred about a decade ago.

Quantitative modeling of soil genesis processes

NASA Technical Reports Server (NTRS)

Levine, E. R.; Knox, R. G.; Kerber, A. G.

1992-01-01

For fine spatial scale simulation, a model is being developed to predict changes in properties over short-, meso-, and long-term time scales within horizons of a given soil profile. Processes that control these changes can be grouped into five major process clusters: (1) abiotic chemical reactions; (2) activities of organisms; (3) energy balance and water phase transitions; (4) hydrologic flows; and (5) particle redistribution. Landscape modeling of soil development is possible using digitized soil maps associated with quantitative soil attribute data in a geographic information system (GIS) framework to which simulation models are applied.

Numerical Model of Transitory Flood Flow in 2005 on River Timis

NASA Astrophysics Data System (ADS)

Ghitescu, Marie-Alice; Lazar, Gheorghe; Titus Constantin, Albert; Nicoara, Serban-Vlad

2017-10-01

The paper presents numerical modelling of fluid flow transiting on the Timis River, downstream Lugoj section - N.H. COSTEIU, the occurrence of accidental flood waves from 4 April to 11 April 2005. Numerical simulation aims to estimate water levels on the route pattern on some areas and areas associated respectively floodplain adjacent construction site on the right bank of Timis river, on existing conditions in 2005. The model simulation from 2005 flood event shows that the model can be used for future inundation studies in this locality.

L-H transitions driven by ion heating in scrape-off layer turbulence (SOLT) model simulations

NASA Astrophysics Data System (ADS)

Russell, D. A.; D'Ippolito, D. A.; Myra, J. R.

2015-11-01

The original SOLT model now includes the evolution of ion pressure consistent with drift-ordering. It is a two-dimensional, electrostatic reduced model wherein closure relations, obtained by integrating the equations along the B-field, model parallel physics that includes sheath-mediated current and heat flux in the scrape-off-layer and electron drift waves inside the separatrix. Low (L) and high (H) confinement regimes are observed in SOLT simulations, depending on the strength of an ion pressure (i.e., ion heating) source localized inside the separatrix: With increasing heating, particle and energy confinement times at first decrease in the L-mode then rise in the H-mode. The L-H transition is marked by distinct changes in sheared-flow profiles. The addition of ion pressure dynamics enables modeling the self-consistent interaction between the ion diamagnetic drift and the radial electric field (mean and zonal flows). The roles of these sheared flows in mediating the L-H transition are explored. A new diagnostic, based on the density correlation function, is applied to study blob velocities in different regimes. Work supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Sciences, under Award Number DE-FG02-97ER54392.

Computer-Assisted Simulation Methods of Learning Process

ERIC Educational Resources Information Center

Mayer, Robert V.

2015-01-01

In this article we analyse: 1) one-component models of training; 2) the multi-component models considering transition of weak knowledge in strong and vice versa; and 3) the models considering change of working efficiency of the pupil during the day. The results of imitating modeling are presented, graphs of dependences of the pupil's knowledge on…

The ground state of the Frenkel-Kontorova model

NASA Astrophysics Data System (ADS)

Babushkin, A. Yu.; Abkaryan, A. K.; Dobronets, B. S.; Krasikov, V. S.; Filonov, A. N.

2016-09-01

The continual approximation of the ground state of the discrete Frenkel-Kontorova model is tested using a symmetric algorithm of numerical simulation. A "kaleidoscope effect" is found, which means that the curves representing the dependences of the relative extension of an N-atom chain vary periodically with increasing N. Stairs of structural transitions for N ≫ 1 are analyzed by the channel selection method with the approximation N = ∞. Images of commensurable and incommensurable structures are constructed. The commensurable-incommensurable phase transitions are stepwise.

Unconstrained Structure Formation in Coarse-Grained Protein Simulations

NASA Astrophysics Data System (ADS)

Bereau, Tristan

The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid model. The lipid force field was systematically tuned to reproduce the structural and mechanical properties of phosphatidylcholine bilayers. The two models were cross-parametrized against atomistic potential of mean force curves for the insertion of single amino acid side chains into a bilayer. Coarse-grained transmembrane protein simulations were then compared with experiments and atomistic simulations to validate the force field. The transferability of the two models across amino acid sequences and lipid species permits the investigation of a wide variety of scenarios, while the absence of explicit solvent allows for studies of large-scale phenomena.

On the existence of vapor-liquid phase transition in dusty plasmas

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

Kundu, M.; Sen, A.; Ganesh, R.

2014-10-15

The phenomenon of phase transition in a dusty-plasma system (DPS) has attracted some attention in the past. Earlier Farouki and Hamaguchi [J. Chem. Phys. 101, 9876 (1994)] have demonstrated the existence of a liquid to solid transition in DPS where the dust particles interact through a Yukawa potential. However, the question of the existence of a vapor-liquid (VL) transition in such a system remains unanswered and relatively unexplored so far. We have investigated this problem by performing extensive molecular dynamics simulations which show that the VL transition does not have a critical curve in the pressure versus volume diagram formore » a large range of the Yukawa screening parameter κ and the Coulomb coupling parameter Γ. Thus, the VL phase transition is found to be super-critical, meaning that this transition is continuous in the dusty plasma model given by Farouki and Hamaguchi. We provide an approximate analytic explanation of this finding by means of a simple model calculation.« less

Early Warning Signals for Regime Transition in the Stable Boundary Layer: A Model Study

NASA Astrophysics Data System (ADS)

van Hooijdonk, I. G. S.; Moene, A. F.; Scheffer, M.; Clercx, H. J. H.; van de Wiel, B. J. H.

2017-02-01

The evening transition is investigated in an idealized model for the nocturnal boundary layer. From earlier studies it is known that the nocturnal boundary layer may manifest itself in two distinct regimes, depending on the ambient synoptic conditions: strong-wind or overcast conditions typically lead to weakly stable, turbulent nights; clear-sky and weak-wind conditions, on the other hand, lead to very stable, weakly turbulent conditions. Previously, the dynamical behaviour near the transition between these regimes was investigated in an idealized setting, relying on Monin-Obukhov (MO) similarity to describe turbulent transport. Here, we investigate a similar set-up, using direct numerical simulation; in contrast to MO-based models, this type of simulation does not need to rely on turbulence closure assumptions. We show that previous predictions are verified, but now independent of turbulence parametrizations. Also, it appears that a regime shift to the very stable state is signaled in advance by specific changes in the dynamics of the turbulent boundary layer. Here, we show how these changes may be used to infer a quantitative estimate of the transition point from the weakly stable boundary layer to the very stable boundary layer. In addition, it is shown that the idealized, nocturnal boundary-layer system shares important similarities with generic non-linear dynamical systems that exhibit critical transitions. Therefore, the presence of other, generic early warning signals is tested as well. Indeed, indications are found that such signals are present in stably stratified turbulent flows.

Numerical Simulation of Complex Turbomachinery Flows

NASA Technical Reports Server (NTRS)

Chernobrovkin, A. A.; Lakshiminarayana, B.

1999-01-01

An unsteady, multiblock, Reynolds Averaged Navier Stokes solver based on Runge-Kutta scheme and Pseudo-time step for turbo-machinery applications was developed. The code was validated and assessed against analytical and experimental data. It was used to study a variety of physical mechanisms of unsteady, three-dimensional, turbulent, transitional, and cooling flows in compressors and turbines. Flow over a cylinder has been used to study effects of numerical aspects on accuracy of prediction of wake decay and transition, and to modify K-epsilon models. The following simulations have been performed: (a) Unsteady flow in a compressor cascade: Three low Reynolds number turbulence models have been assessed and data compared with Euler/boundary layer predictions. Major flow features associated with wake induced transition were predicted and studied; (b) Nozzle wake-rotor interaction in a turbine: Results compared to LDV data in design and off-design conditions, and cause and effect of unsteady flow in turbine rotors were analyzed; (c) Flow in the low-pressure turbine: Assessed capability of the code to predict transitional, attached and separated flows at a wide range of low Reynolds numbers and inlet freestream turbulence intensity. Several turbulence and transition models have been employed and comparisons made to experiments; (d) leading edge film cooling at compound angle: Comparisons were made with experiments, and the flow physics of the associated vortical structures were studied; and (e) Tip leakage flow in a turbine. The physics of the secondary flow in a rotor was studied and sources of loss identified.

Modeling, Simulation, and Control of a Solar Electric Propulsion Vehicle in Near-Earth Vicinity Including Solar Array Degradation

NASA Technical Reports Server (NTRS)

Witzberger, Kevin (Inventor); Hojnicki, Jeffery (Inventor); Manzella, David (Inventor)

2016-01-01

Modeling and control software that integrates the complexities of solar array models, a space environment, and an electric propulsion system into a rigid body vehicle simulation and control model is provided. A rigid body vehicle simulation of a solar electric propulsion (SEP) vehicle may be created using at least one solar array model, at least one model of a space environment, and at least one model of a SEP propulsion system. Power availability and thrust profiles may be determined based on the rigid body vehicle simulation as the SEP vehicle transitions from a low Earth orbit (LEO) to a higher orbit or trajectory. The power availability and thrust profiles may be displayed such that a user can use the displayed power availability and thrust profiles to determine design parameters for an SEP vehicle mission.

Computation and modeling of aero-thermal fields in turbine cascades and strongly curved ducts

NASA Technical Reports Server (NTRS)

Luo, J.; Lakshminarayana, B.

1994-01-01

Advanced turbulence models are crucial for accurate prediction of rocket engine flows, due to existence of very large extra strain rates, such as strong streamline curvature. Numerical simulation of the turbulent flow in a strongly curved turn-around duct (TAD) has been carried out with a Reynolds stress model (RSM), an algebraic Reynolds stress model (ARSM) and a kappa-epsilon model. the RSM model and the ARSM model are found to capture the turbulence damping due to the convex curvature, but underpredict the turbulence enhancement caused by the concave curvature. To capture the concave curvature effects, it is necessary to modify the epsilon-equation. The modification of episilon-equation suggested by Launder, et.al, provides the correct trend, but over-corrects the curvature effects. A comparative study of two modes of transition in gas turbine, the by-pass transition and the separation-induced transition, has been carried out with several low-Reynolds-number (LRN) kappa-epsilon models. Effects of blade surface pressure gradient, freestream turbulence and Reynolds number on the blade boundary layer development, and particularly the inception of transition are examined in detail. The present study indicates that the turbine blade transition, in the presence of high freestream turbulence, is predicted well with LRN kappa-epsilon models employed.

Comprehensive Validation of an Intermittency Transport Model for Transitional Low-Pressure Turbine Flows

NASA Technical Reports Server (NTRS)

Suzen, Y. B.; Huang, P. G.

2005-01-01

A transport equation for the intermittency factor is employed to predict transitional flows under the effects of pressure gradients, freestream turbulence intensities, Reynolds number variations, flow separation and reattachment. and unsteady wake-blade interactions representing diverse operating conditions encountered in low-pressure turbines. The intermittent behaviour of the transitional flows is taken into account and incorporated into computations by modifying the eddy viscosity, Mu(sub t), with the intermittency factor, gamma. Turbulent quantities are predicted by using Menter's two-equation turbulence model (SST). The onset location of transition is obtained from correlations based on boundary-layer momentum thickness, acceleration parameter, and turbulence intensity. The intermittency factor is obtained from a transport model which can produce both the experimentally observed streamwise variation of intermittency and a realistic profile in the cross stream direction. The intermittency transport model is tested and validated against several well documented low pressure turbine experiments ranging from flat plate cases to unsteady wake-blade interaction experiments. Overall, good agreement between the experimental data and computational results is obtained illustrating the predicting capabilities of the model and the current intermittency transport modelling approach for transitional flow simulations.

Recharge heterogeneity and high intensity rainfall events increase contamination risk for Mediterranean groundwater resources

NASA Astrophysics Data System (ADS)

Hartmann, Andreas; Jasechko, Scott; Gleeson, Tom; Wada, Yoshihide; Andreo, Bartolomé; Barberá, Juan Antonio; Brielmann, Heike; Charlier, Jean-Baptiste; Darling, George; Filippini, Maria; Garvelmann, Jakob; Goldscheider, Nico; Kralik, Martin; Kunstmann, Harald; Ladouche, Bernard; Lange, Jens; Mudarra, Matías; Francisco Martín, José; Rimmer, Alon; Sanchez, Damián; Stumpp, Christine; Wagener, Thorsten

2017-04-01

Karst develops through the dissolution of carbonate rock and results in pronounced spatiotemporal heterogeneity of hydrological processes. Karst groundwater in Europe is a major source of fresh water contributing up to half of the total drinking water supply in some countries like Austria or Slovenia. Previous work showed that karstic recharge processes enhance and alter the sensitivity of recharge to climate variability. The enhanced preferential flow from the surface to the aquifer may be followed by enhanced risk of groundwater contamination. In this study we assess the contamination risk of karst aquifers over Europe and the Mediterranean using simulated transit time distributions. Using a new type of semi-distributed model that considers the spatial heterogeneity of karst hydraulic properties, we were able to simulate karstic groundwater recharge including its heterogeneous spatiotemporal dynamics. The model is driven by gridded daily climate data from the Global Land Data Assimilation System (GLDAS). Transit time distributions are calculated using virtual tracer experiments. We evaluated our simulations by independent information on transit times derived from observed time series of water isotopes of >70 karst springs over Europe. The simulations indicate that, compared to humid, mountain and desert regions, the Mediterranean region shows a stronger risk of contamination in Europe because preferential flow processes are most pronounced given thin soil layers and the seasonal abundance of high intensity rainfall events in autumn and winter. Our modelling approach includes strong simplifications and its results cannot easily be generalized but it still highlights that the combined effects of variable climate and heterogeneous catchment properties constitute a strong risk on water quality.

Effect of the Bering Strait on the AMOC hysteresis and glacial climate stability (Invited)

NASA Astrophysics Data System (ADS)

Hu, A.; Meehl, G. A.; Han, W.; Timmermann, A.; Otto-Bliesner, B. L.; Liu, Z.; Abe-Ouchi, A.

2013-12-01

Abrupt climate transitions, such as Dansgaard-Oeschger and Heinrich events, occurred frequently during the last glacial period, especially from 80 - 11 thousand years before present, but were nearly absent during Holocene and the early stages of last glacial period. Here we show, with a fully coupled climate model, that closing the Bering Strait and preventing its throughflow between the Pacific and Arctic Oceans during the glacial period can lead to the emergence of stronger hysteresis behavior of the Atlantic meridional overturning circulation (AMOC) to create conditions that are conducive to triggering abrupt climate transitions. Hence, it is argued that even for greenhouse warming, abrupt climate transitions similar to those in the last glacial time are unlikely to occur as the Bering Strait remains open. Qualitatively the same result is arrived in new simulations by employing the glacial background conditions using the same climate model. Theoretical and simulated AMOC hysteresis curves (a, b) and the associated changes of Greenland surface temperature and meridional heat transport at 65°N in the Atlantic (c, d). In panel a), 'S' is the bifurcation point beyond which AMOC collapses and the '+/-F' values indicate the freshwater forcing strength. In panels b), c), and d), the black/red (blue/green) lines are for the closed (open) BS simulation. The black/blue (red/green) lines represent the phase of freshwater forcing increase (decrease) in these simulations. Note that a change of the freshwater forcing by 0.1 Sv (Sv≡106m3s-1) in this figure takes place over 500 model years.

Growing a market economy

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

Basu, N.; Pryor, R.J.

1997-09-01

This report presents a microsimulation model of a transition economy. Transition is defined as the process of moving from a state-enterprise economy to a market economy. The emphasis is on growing a market economy starting from basic microprinciples. The model described in this report extends and modifies the capabilities of Aspen, a new agent-based model that is being developed at Sandia National Laboratories on a massively parallel Paragon computer. Aspen is significantly different from traditional models of the economy. Aspen`s emphasis on disequilibrium growth paths, its analysis based on evolution and emergent behavior rather than on a mechanistic view ofmore » society, and its use of learning algorithms to simulate the behavior of some agents rather than an assumption of perfect rationality make this model well-suited for analyzing economic variables of interest from transition economies. Preliminary results from several runs of the model are included.« less

Two-Dimensional Wetting Transition Modeling with the Potts Model

NASA Astrophysics Data System (ADS)

Lopes, Daisiane M.; Mombach, José C. M.

2017-12-01

A droplet of a liquid deposited on a surface structured in pillars may have two states of wetting: (1) Cassie-Baxter (CB), the liquid remains on top of the pillars, also known as heterogeneous wetting, or (2) Wenzel, the liquid fills completely the cavities of the surface, also known as homogeneous wetting. Studies show that between these two states, there is an energy barrier that, when overcome, results in the transition of states. The transition can be achieved by changes in geometry parameters of the surface, by vibrations of the surface or by evaporation of the liquid. In this paper, we present a comparison of two-dimensional simulations of the Cassie-Wenzel transition on pillar-structured surfaces using the cellular Potts model (CPM) with studies performed by Shahraz et al. In our work, we determine a transition diagram by varying the surface parameters such as the interpillar distance ( G) and the pillar height ( H). Our results were compared to those obtained by Shahraz et al. obtaining good agreement.

Observation and modeling of deflagration-to-detonation transition (DDT) in low-density HMX

NASA Astrophysics Data System (ADS)

Tringe, Joseph W.; Vandersall, Kevin S.; Reaugh, John E.; Levie, Harold W.; Henson, Bryan F.; Smilowitz, Laura B.; Parker, Gary R.

2017-01-01

We employ simultaneous flash x-ray radiography and streak imaging, together with a multi-phase finite element model, to understand deflagration-to-detonation transition (DDT) phenomena in low-density (˜1.2 gm/cm3) powder of the explosive cyclotetramethylene-tetranitramine (HMX). HMX powder was lightly hand-tamped in a 12.7 mm diameter column, relatively lightly-confined in an optically-transparent polycarbonate cylinder with wall thickness 25.4 mm. We observe apparent compaction of the powder in advance of the detonation transition by the motion of small steel spheres pre-emplaced throughout the length of explosive. High-speed imaging along the explosive cylinder length provides a more temporally continuous record of the transition that is correlated with the high-resolution x-ray image record. Preliminary simulation of these experiments with the HERMES model implemented in the ALE3D code enables improved understanding of the explosive particle burning, compaction and detonation phenomena which are implied by the observed reaction rate and transition location within the cylinder.

Computer simulation of liquid metals

NASA Astrophysics Data System (ADS)

Belashchenko, D. K.

2013-12-01

Methods for and the results of the computer simulation of liquid metals are reviewed. Two basic methods, classical molecular dynamics with known interparticle potentials and the ab initio method, are considered. Most attention is given to the simulated results obtained using the embedded atom model (EAM). The thermodynamic, structural, and diffusion properties of liquid metal models under normal and extreme (shock) pressure conditions are considered. Liquid-metal simulated results for the Groups I - IV elements, a number of transition metals, and some binary systems (Fe - C, Fe - S) are examined. Possibilities for the simulation to account for the thermal contribution of delocalized electrons to energy and pressure are considered. Solidification features of supercooled metals are also discussed.

Phase-field simulations of velocity selection in rapidly solidified binary alloys

NASA Astrophysics Data System (ADS)

Fan, Jun; Greenwood, Michael; Haataja, Mikko; Provatas, Nikolas

2006-09-01

Time-dependent simulations of two-dimensional isothermal Ni-Cu dendrites are simulated using a phase-field model solved with a finite-difference adaptive mesh refinement technique. Dendrite tip velocity selection is examined and found to exhibit a transition between two markedly different regimes as undercooling is increased. At low undercooling, the dendrite tip growth rate is consistent with the kinetics of the classical Stefan problem, where the interface is assume to be in local equilibrium. At high undercooling, the growth velocity selected approaches a linear dependence on melt undercooling, consistent with the continuous growth kinetics of Aziz and with a one-dimensional steady-state phase-field asymptotic analysis of Ahmad [Phys. Rev. E 58, 3436 (1998)]. Our simulations are also consistent with other previously observed behaviors of dendritic growth as undercooling is increased. These include the transition of dendritic morphology to absolute stability and nonequilibrium solute partitioning. Our results show that phase-field models of solidification, which inherently contain a nonzero interface width, can be used to study the dynamics of complex solidification phenomena involving both equilibrium and nonequilibrium interface growth kinetics.

Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations

PubMed Central

Baumketner, Andrij; Nesmelov, Yuri

2011-01-01

The recovery stroke is a key step in the functional cycle of muscle motor protein myosin, during which pre-recovery conformation of the protein is changed into the active post-recovery conformation, ready to exersice force. We study the microscopic details of this transition using molecular dynamics simulations of atomistic models in implicit and explicit solvent. In more than 2 μs of aggregate simulation time, we uncover evidence that the recovery stroke is a two-step process consisting of two stages separated by a time delay. In our simulations, we directly observe the first stage at which switch II loop closes in the presence of adenosine triphosphate at the nucleotide binding site. The resulting configuration of the nucleotide binding site is identical to that detected experimentally. Distribution of inter-residue distances measured in the force generating region of myosin is in good agreement with the experimental data. The second stage of the recovery stroke structural transition, rotation of the converter domain, was not observed in our simulations. Apparently it occurs on a longer time scale. We suggest that the two parts of the recovery stroke need to be studied using separate computational models. PMID:21922589

Computer simulation studies of the growth of strained layers by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Faux, D. A.; Gaynor, G.; Carson, C. L.; Hall, C. K.; Bernholc, J.

1990-08-01

Two new types of discrete-space Monte Carlo computer simulation are presented for the modeling of the early stages of strained-layer growth by molecular-beam epitaxy. The simulations are more economical on computer resources than continuous-space Monte Carlo or molecular dynamics. Each model is applied to the study of growth onto a substrate in two dimensions with use of Lennard-Jones interatomic potentials. Up to seven layers are deposited for a variety of lattice mismatches, temperatures, and growth rates. Both simulations give similar results. At small lattice mismatches (<~4%) the growth is in registry with the substrate, while at high mismatches (>~6%) the growth is incommensurate with the substrate. At intermediate mismatches, a transition from registered to incommensurate growth is observed which commences at the top of the crystal and propagates down to the first layer. Faster growth rates are seen to inhibit this transition. The growth mode is van der Merwe (layer-by-layer) at 2% lattice mismatch, but at larger mismatches Volmer-Weber (island) growth is preferred. The Monte Carlo simulations are assessed in the light of these results and the ease at which they can be extended to three dimensions and to more sophisticated potentials is discussed.

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

PubMed Central

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-01-01

We studied the microsecond folding dynamics of three β hairpins (Trp zippers 1–3, TZ1–TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1–TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations. PMID:15020773

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-03-01

We studied the microsecond folding dynamics of three hairpins (Trp zippers 1-3, TZ1-TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1-TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.

Life's attractors : understanding developmental systems through reverse engineering and in silico evolution.

PubMed

Jaeger, Johannes; Crombach, Anton

2012-01-01

We propose an approach to evolutionary systems biology which is based on reverse engineering of gene regulatory networks and in silico evolutionary simulations. We infer regulatory parameters for gene networks by fitting computational models to quantitative expression data. This allows us to characterize the regulatory structure and dynamical repertoire of evolving gene regulatory networks with a reasonable amount of experimental and computational effort. We use the resulting network models to identify those regulatory interactions that are conserved, and those that have diverged between different species. Moreover, we use the models obtained by data fitting as starting points for simulations of evolutionary transitions between species. These simulations enable us to investigate whether such transitions are random, or whether they show stereotypical series of regulatory changes which depend on the structure and dynamical repertoire of an evolving network. Finally, we present a case study-the gap gene network in dipterans (flies, midges, and mosquitoes)-to illustrate the practical application of the proposed methodology, and to highlight the kind of biological insights that can be gained by this approach.

Transit losses and traveltimes for water-supply releases Marion Lake during drought conditions, Cottonwood River, east-central Kansas

USGS Publications Warehouse

Jordan, P.R.; Hart, R.J.

1985-01-01

A streamflow routing model was used to calculate the transit losses and traveltimes. Channel and aquifer characteristics, and the model control parameters, were estimated from available data and then verified to the extent possible by comparing model simulated streamflow to observed streamflow at streamflow gaging stations. Transit losses and traveltimes for varying reservoir release rates and durations then were simulated for two different antecedent streamflow (drought) conditions. For the severe-drought antecedent-streamflow condition, it was assumed that only the downstream water use requirement would be released from the reservoir. For a less severe drought (LSD) antecedent streamflow condition, it was assumed than any releases from Marion Lake for water supply use downstream, would be in addition to a nominal dry weather release of 5 cu ft/sec. Water supply release rates of 10 and 25 cu ft/sec for the severe drought condition and 5, 10, and 25 cu ft/sec for the less severe drought condition were simulated for periods of 28 and 183 days commencing on July 1. Transit losses for the severe drought condition for all reservoir release rates and durations ranged from 12% to 78% of the maximum downstream flow rate and from 27% to 91% of the total volume of reservoir storage released. For the LSD condition, transit losses ranged from 7% to 29% of the maximum downstream flow rate and from 10% to 48% of the total volume of release. The 183-day releases had larger total transit losses, but losses on a percentage basis were less than the losses for the 28-day release period for both antecedent streamflow conditions. Traveltimes to full response (80% of the maximum downstream flow rate), however, showed considerable variation. For the release of 5 cu ft/sec during LSD conditions, base flow exceeded 80% of the maximum flow rate near the confluence; the traveltime to full response was undefined for those simulations. For the releases of 10 and 25 cu ft/sec during the same drought condition, traveltimes to full response ranged from 4.4 to 6.5 days. For releases of 10 and 25 cu ft/sec during severe drought conditions, traveltimes to full response near the confluence with the Neosho River ranged from 8.3 to 93 days. (Lantz-PTT)

Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation: Report of an FDA Public Workshop.

PubMed

Zhang, X; Duan, J; Kesisoglou, F; Novakovic, J; Amidon, G L; Jamei, M; Lukacova, V; Eissing, T; Tsakalozou, E; Zhao, L; Lionberger, R

2017-08-01

On May 19, 2016, the US Food and Drug Administration (FDA) hosted a public workshop, entitled "Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation." The topic of mechanistic oral absorption modeling, which is one of the major applications of physiologically based pharmacokinetic (PBPK) modeling and simulation, focuses on predicting oral absorption by mechanistically integrating gastrointestinal transit, dissolution, and permeation processes, incorporating systems, active pharmaceutical ingredient (API), and the drug product information, into a systemic mathematical whole-body framework. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

Simulating the Seismic Signal of Phase Transitions in the Deepest Mantle (Invited)

NASA Astrophysics Data System (ADS)

Walker, A.; Dobson, D. P.; Nowacki, A.; Wookey, J. M.; Forte, A. M.; Kendall, J. M.

2013-12-01

The discovery of the perovskite to post-perovskite phase transition in (Mg,Fe)SiO3 explains many of the seismic observations of the lowermost mantle including the presence of multiple seismic discontinuities and significant seismic anisotropy. However, the explanations of many detailed features remain elusive. The recent discovery of a topotactic relationship between the orientation of perovskite and post-perovskite crystals in a partially transformed analogue opens the possibility of texture inheritance through the phase transition [1]. This must be captured in simulations designed to explain the anisotropy of the lowermost mantle, especially those which link mantle dynamics with seismic observations. We have extended our previous work linking models of flow in the lowermost mantle with simulations of texture development and predictions of seismic anisotropy [2] to account for the topotaxy between perovskite and post-perovskite. In particular, we compare four cases: (1) As in [2], anisotropy is only generated in post-perovskite by dislocation mediated deformation dominated by one of a number of slip systems, phase transitions destroy texture and ferropericlase and perovskite dominated rocks are isotropic. (2) Although phase transitions destroy texture, ferropericlase and/or perovskite deform by dislocation motion permitting the generation of seismic anisotropy in warmer regions of the mantle where post-perovskite is unstable. We account for the possibility of the inversion of slip-system activities in ferropericlase at high pressure as suggested by models of dislocation motion based on atomic scale simulations [3]. (3) Allow texture development by dislocation motion in perovskite and post-perovskite and texture inheritance through phase transitions by the mechanism described in [1]. However, we assume that the bulk of the lower mantle deforms by a mechanism that does not lead to the development of texture and so begin the simulation from a random distribution of crystal orientations the first time the post-perovskite stability field is encountered for downward migrating packages of mantle. (4) Allow the bulk of the lower mantle to deform by dislocation creep such that material entering the lowermost mantle for the first time is already textured, allow this texture to be inherited and further modified by strain and phase transitions. These calculations show clear differences in global and local scale elastic anisotropy in the lowermost mantle between cases where texture is allowed to persist through the phase transitions and those where it is not. On a global scale and when radial anisotropy is imposed the inclusion of topotaxy results in a dramatic decrease in the strength of the degree two signal and better agreement between observations and the model for post-perovskite deformation where dislocations moving on (001) dominate. On a smaller scale we see potential signs of reflectors generated by a change in anisotropy between perovskite that has inherited a strong starting texture from post-perovskite and overlaying perovskite that has never undergone the phase transition. These observations suggest that the incorporation of texture inheritance will be an important feature of future models of anisotropy in the lowermost mantle. [1] Dobson et al. 2013 Nature Geosci. 6:575-578 [2] Walker et al. 2011 Gcubed. 12:Q10006 [3] Cordier et al. 2012 Nature 481:177-180

Chiral spin liquids at finite temperature in a three-dimensional Kitaev model

NASA Astrophysics Data System (ADS)

Kato, Yasuyuki; Kamiya, Yoshitomo; Nasu, Joji; Motome, Yukitoshi

2017-11-01

Chiral spin liquids (CSLs) in three dimensions and thermal phase transitions to paramagnet are studied by unbiased Monte Carlo simulations. For an extension of the Kitaev model to a three-dimensional tricoordinate network dubbed the hypernonagon lattice, we derive low-energy effective models in two different anisotropic limits. We show that the effective interactions between the emergent Z2 degrees of freedom called fluxes are unfrustrated in one limit, while highly frustrated in the other. In both cases, we find a first-order phase transition to the CSL, where both time-reversal and parity symmetries are spontaneously broken. In the frustrated case, however, the CSL state is highly exotic—the flux configuration is subextensively degenerate while showing a directional order with broken C3 rotational symmetry. Our results provide two contrasting archetypes of CSLs in three dimensions, both of which allow approximation-free simulation for investigating the thermodynamics.

Complex Langevin simulation of a random matrix model at nonzero chemical potential

NASA Astrophysics Data System (ADS)

Bloch, J.; Glesaaen, J.; Verbaarschot, J. J. M.; Zafeiropoulos, S.

2018-03-01

In this paper we test the complex Langevin algorithm for numerical simulations of a random matrix model of QCD with a first order phase transition to a phase of finite baryon density. We observe that a naive implementation of the algorithm leads to phase quenched results, which were also derived analytically in this article. We test several fixes for the convergence issues of the algorithm, in particular the method of gauge cooling, the shifted representation, the deformation technique and reweighted complex Langevin, but only the latter method reproduces the correct analytical results in the region where the quark mass is inside the domain of the eigenvalues. In order to shed more light on the issues of the methods we also apply them to a similar random matrix model with a milder sign problem and no phase transition, and in that case gauge cooling solves the convergence problems as was shown before in the literature.

Optimal community structure for social contagions

NASA Astrophysics Data System (ADS)

Su, Zhen; Wang, Wei; Li, Lixiang; Stanley, H. Eugene; Braunstein, Lidia A.

2018-05-01

Community structure is an important factor in the behavior of real-world networks because it strongly affects the stability and thus the phase transition order of the spreading dynamics. We here propose a reversible social contagion model of community networks that includes the factor of social reinforcement. In our model an individual adopts a social contagion when the number of received units of information exceeds its adoption threshold. We use mean-field approximation to describe our proposed model, and the results agree with numerical simulations. The numerical simulations and theoretical analyses both indicate that there is a first-order phase transition in the spreading dynamics, and that a hysteresis loop emerges in the system when there is a variety of initially adopted seeds. We find an optimal community structure that maximizes spreading dynamics. We also find a rich phase diagram with a triple point that separates the no-diffusion phase from the two diffusion phases.

Trap-assisted transition between Schottky emission and Fowler-Nordheim tunneling in the interfacial-memristor based on Bi2S3 nano-networks

NASA Astrophysics Data System (ADS)

Tian, Ye; Jiang, Lianjun; Zhang, Xuejun; Zhang, Guangfu; Zhu, Qiuxiang

2018-03-01

For the usage of the memristors in functional circuits, a predictive physical model is of great importance. However, other than the developments of the memristive models accounting bulky effects, the achievements on simulating the interfacial memristance are still insufficient. Here we provide a physical model to describe the electrical switching of the memristive interface. It considers the trap-assisted transition between Schottky emission and Fowler-Nordheim tunneling, and successfully reproduces the memristive behaviors occurring on the interface between Bi2S3 nano-networks and F-doped SnO2. Such success not only allows us uncover several features of the memristive interface including the distribution nature of the traps, barrier height/thickness and so on, but also provides a foundation from which we can quantitatively simulate the real interfacial memristor.

Multi-agent electricity market modeling with EMCAS.

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

North, M.; Macal, C.; Conzelmann, G.

2002-09-05

Electricity systems are a central component of modern economies. Many electricity markets are transitioning from centrally regulated systems to decentralized markets. Furthermore, several electricity markets that have recently undergone this transition have exhibited extremely unsatisfactory results, most notably in California. These high stakes transformations require the introduction of largely untested regulatory structures. Suitable tools that can be used to test these regulatory structures before they are applied to real systems are required. Multi-agent models can provide such tools. To better understand the requirements such as tool, a live electricity market simulation was created. This experience helped to shape the developmentmore » of the multi-agent Electricity Market Complex Adaptive Systems (EMCAS) model. To explore EMCAS' potential, several variations of the live simulation were created. These variations probed the possible effects of changing power plant outages and price setting rules on electricity market prices.« less

Performance Impact of Deflagration to Detonation Transition Enhancing Obstacles

NASA Technical Reports Server (NTRS)

Paxson, Daniel E.; Schauer, Frederick; Hopper, David

2012-01-01

A sub-model is developed to account for the drag and heat transfer enhancement resulting from deflagration-to-detonation (DDT) inducing obstacles commonly used in pulse detonation engines (PDE). The sub-model is incorporated as a source term in a time-accurate, quasi-onedimensional, CFD-based PDE simulation. The simulation and sub-model are then validated through comparison with a particular experiment in which limited DDT obstacle parameters were varied. The simulation is then used to examine the relative contributions from drag and heat transfer to the reduced thrust which is observed. It is found that heat transfer is far more significant than aerodynamic drag in this particular experiment.

UTM, a universal simulator for lightcurves of transiting systems

NASA Astrophysics Data System (ADS)

Deeg, Hans

2009-02-01

The Universal Transit Modeller (UTM) is a light-curve simulator for all kinds of transiting or eclipsing configurations between arbitrary numbers of several types of objects, which may be stars, planets, planetary moons, and planetary rings. Applications of UTM to date have been mainly in the generation of light-curves for the testing of detection algorithms. For the preparation of such test for the Corot Mission, a special version has been used to generate multicolour light-curves in Corot's passbands. A separate fitting program, UFIT (Universal Fitter) is part of the UTM distribution and may be used to derive best fits to light-curves for any set of continuously variable parameters. UTM/UFIT is written in IDL code and its source is released in the public domain under the GNU General Public License.

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2011-10-01

We use numerical simulation to examine the possibility of a reversible liquid-liquid transition in supercooled water and related systems. In particular, for two atomistic models of water, we have computed free energies as functions of multiple order parameters, where one is density and another distinguishes crystal from liquid. For a range of temperatures and pressures, separate free energy basins for liquid and crystal are found, conditions of phase coexistence between these phases are demonstrated, and time scales for equilibration are determined. We find that at no range of temperatures and pressures is there more than a single liquid basin, even at conditions where amorphous behavior is unstable with respect to the crystal. We find a similar result for a related model of silicon. This result excludes the possibility of the proposed liquid-liquid critical point for the models we have studied. Further, we argue that behaviors others have attributed to a liquid-liquid transition in water and related systems are in fact reflections of transitions between liquid and crystal.

Universality of the Berezinskii-Kosterlitz-Thouless type of phase transition in the dipolar XY-model

NASA Astrophysics Data System (ADS)

Vasiliev, A. Yu; Tarkhov, A. E.; Menshikov, L. I.; Fedichev, P. O.; Fischer, Uwe R.

2014-05-01

We investigate the nature of the phase transition occurring in a planar XY-model spin system with dipole-dipole interactions. It is demonstrated that a Berezinskii-Kosterlitz-Thouless (BKT) type of phase transition always takes place at a finite temperature separating the ordered (ferro) and the disordered (para) phases. The low-temperature phase corresponds to an ordered state with thermal fluctuations, composed of a ‘gas’ of bound vortex-antivortex pairs, which would, when considered isolated, be characterized by a constant vortex-antivortex attraction force which is due to the dipolar interaction term in the Hamiltonian. Using a topological charge model, we show that small bound pairs are easily polarized, and screen the vortex-antivortex interaction in sufficiently large pairs. Screening changes the linear attraction potential of vortices to a logarithmic one, and leads to the familiar pair dissociation mechanism of the BKT type phase transition. The topological charge model is confirmed by numerical simulations, in which we demonstrate that the transition temperature slightly increases when compared with the BKT result for short-range interactions.

Liquid-liquid phase transition in an ionic model of silica

NASA Astrophysics Data System (ADS)

Chen, Renjie; Lascaris, Erik; Palmer, Jeremy C.

2017-06-01

Recent equation of state calculations [E. Lascaris, Phys. Rev. Lett. 116, 125701 (2016)] for an ionic model of silica suggest that it undergoes a density-driven, liquid-liquid phase transition (LLPT) similar to the controversial transition hypothesized to exist in deeply supercooled water. Here, we perform extensive free energy calculations to scrutinize the model's low-temperature phase behavior and confirm the existence of a first-order phase transition between two liquids with identical compositions but different densities. The low-density liquid (LDL) exhibits tetrahedral order, which is partially disrupted in the high-density liquid (HDL) by the intrusion of additional particles into the primary neighbor shell. Histogram reweighting methods are applied to locate conditions of HDL-LDL coexistence and the liquid spinodals that bound the two-phase region. Spontaneous liquid-liquid phase separation is also observed directly in large-scale molecular dynamics simulations performed inside the predicted two-phase region. Given its clear LLPT, we anticipate that this model may serve as a paradigm for understanding whether similar transitions occur in water and other tetrahedral liquids.

Bond and flux-disorder effects on the superconductor-insulator transition of a honeycomb array of Josephson junctions

NASA Astrophysics Data System (ADS)

Granato, Enzo

2018-05-01

We study the effects of disorder on the zero-temperature quantum phase transition of a honeycomb array of Josephson junctions in a magnetic field with an average of fo flux quantum per plaquette. Bond disorder due to spatial variations in the Josephson couplings and magnetic flux disorder due to variations in the plaquette areas are considered. The model can describe the superconductor-insulator transition in ultra-thin films with a triangular pattern of nanoholes. Path integral Monte Carlo simulations of the equivalent (2 + 1)-dimensional classical model are used to study the critical behavior and estimate the universal resistivity at the transition. The results show that bond disorder leads to a rounding of the first-order phase transition for fo = 1 / 3 to a continuous transition. For integer fo, the decrease of the critical coupling parameter with flux disorder is significantly different from that of the same model defined on a square lattice. The results are compared with recent experimental observations on nanohole thin films with geometrical disorder and external magnetic field.

Transition to synchrony in degree-frequency correlated Sakaguchi-Kuramoto model

NASA Astrophysics Data System (ADS)

Kundu, Prosenjit; Khanra, Pitambar; Hens, Chittaranjan; Pal, Pinaki

2017-11-01

We investigate transition to synchrony in degree-frequency correlated Sakaguchi-Kuramoto (SK) model on complex networks both analytically and numerically. We analytically derive self-consistent equations for group angular velocity and order parameter for the model in the thermodynamic limit. Using the self-consistent equations we investigate transition to synchronization in SK model on uncorrelated scale-free (SF) and Erdős-Rényi (ER) networks in detail. Depending on the degree distribution exponent (γ ) of SF networks and phase-frustration parameter, the population undergoes from first-order transition [explosive synchronization (ES)] to second-order transition and vice versa. In ER networks transition is always second order irrespective of the values of the phase-lag parameter. We observe that the critical coupling strength for the onset of synchronization is decreased by phase-frustration parameter in case of SF network where as in ER network, the phase-frustration delays the onset of synchronization. Extensive numerical simulations using SF and ER networks are performed to validate the analytical results. An analytical expression of critical coupling strength for the onset of synchronization is also derived from the self-consistent equations considering the vanishing order parameter limit.

Evaluation of aquifer heterogeneity effects on river flow loss using a transition probability framework

USGS Publications Warehouse

Engdahl, N.B.; Vogler, E.T.; Weissmann, G.S.

2010-01-01

River-aquifer exchange is considered within a transition probability framework along the Rio Grande in Albuquerque, New Mexico, to provide a stochastic estimate of aquifer heterogeneity and river loss. Six plausible hydrofacies configurations were determined using categorized drill core and wetland survey data processed through the TPROGS geostatistical package. A base case homogeneous model was also constructed for comparison. River loss was simulated for low, moderate, and high Rio Grande stages and several different riverside drain stage configurations. Heterogeneity effects were quantified by determining the mean and variance of the K field for each realization compared to the root-mean-square (RMS) error of the observed groundwater head data. Simulation results showed that the heterogeneous models produced smaller estimates of loss than the homogeneous approximation. Differences between heterogeneous and homogeneous model results indicate that the use of a homogeneous K in a regional-scale model may result in an overestimation of loss but comparable RMS error. We find that the simulated river loss is dependent on the aquifer structure and is most sensitive to the volumetric proportion of fines within the river channel. Copyright 2010 by the American Geophysical Union.

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

DOE PAGES

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; ...

2016-02-16

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

Electric train energy consumption modeling

DOE PAGES

Wang, Jinghui; Rakha, Hesham A.

2017-05-01

For this paper we develop an electric train energy consumption modeling framework considering instantaneous regenerative braking efficiency in support of a rail simulation system. The model is calibrated with data from Portland, Oregon using an unconstrained non-linear optimization procedure, and validated using data from Chicago, Illinois by comparing model predictions against the National Transit Database (NTD) estimates. The results demonstrate that regenerative braking efficiency varies as an exponential function of the deceleration level, rather than an average constant as assumed in previous studies. The model predictions are demonstrated to be consistent with the NTD estimates, producing a predicted error ofmore » 1.87% and -2.31%. The paper demonstrates that energy recovery reduces the overall power consumption by 20% for the tested Chicago route. Furthermore, the paper demonstrates that the proposed modeling approach is able to capture energy consumption differences associated with train, route and operational parameters, and thus is applicable for project-level analysis. The model can be easily implemented in traffic simulation software, used in smartphone applications and eco-transit programs given its fast execution time and easy integration in complex frameworks.« less

Electric train energy consumption modeling

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

Wang, Jinghui; Rakha, Hesham A.

For this paper we develop an electric train energy consumption modeling framework considering instantaneous regenerative braking efficiency in support of a rail simulation system. The model is calibrated with data from Portland, Oregon using an unconstrained non-linear optimization procedure, and validated using data from Chicago, Illinois by comparing model predictions against the National Transit Database (NTD) estimates. The results demonstrate that regenerative braking efficiency varies as an exponential function of the deceleration level, rather than an average constant as assumed in previous studies. The model predictions are demonstrated to be consistent with the NTD estimates, producing a predicted error ofmore » 1.87% and -2.31%. The paper demonstrates that energy recovery reduces the overall power consumption by 20% for the tested Chicago route. Furthermore, the paper demonstrates that the proposed modeling approach is able to capture energy consumption differences associated with train, route and operational parameters, and thus is applicable for project-level analysis. The model can be easily implemented in traffic simulation software, used in smartphone applications and eco-transit programs given its fast execution time and easy integration in complex frameworks.« less

Dealing with Time in Health Economic Evaluation: Methodological Issues and Recommendations for Practice.

PubMed

O'Mahony, James F; Newall, Anthony T; van Rosmalen, Joost

2015-12-01

Time is an important aspect of health economic evaluation, as the timing and duration of clinical events, healthcare interventions and their consequences all affect estimated costs and effects. These issues should be reflected in the design of health economic models. This article considers three important aspects of time in modelling: (1) which cohorts to simulate and how far into the future to extend the analysis; (2) the simulation of time, including the difference between discrete-time and continuous-time models, cycle lengths, and converting rates and probabilities; and (3) discounting future costs and effects to their present values. We provide a methodological overview of these issues and make recommendations to help inform both the conduct of cost-effectiveness analyses and the interpretation of their results. For choosing which cohorts to simulate and how many, we suggest analysts carefully assess potential reasons for variation in cost effectiveness between cohorts and the feasibility of subgroup-specific recommendations. For the simulation of time, we recommend using short cycles or continuous-time models to avoid biases and the need for half-cycle corrections, and provide advice on the correct conversion of transition probabilities in state transition models. Finally, for discounting, analysts should not only follow current guidance and report how discounting was conducted, especially in the case of differential discounting, but also seek to develop an understanding of its rationale. Our overall recommendations are that analysts explicitly state and justify their modelling choices regarding time and consider how alternative choices may impact on results.

Simulation of Tip-Sample Interaction in the Atomic Force Microscope

NASA Technical Reports Server (NTRS)

Good, Brian S.; Banerjea, Amitava

1994-01-01

Recent simulations of the interaction between planar surfaces and model Atomic Force Microscope (AFM) tips have suggested that there are conditions under which the tip may become unstable and 'avalanche' toward the sample surface. Here we investigate via computer simulation the stability of a variety of model AFM tip configurations with respect to the avalanche transition for a number of fcc metals. We perform Monte-Carlo simulations at room temperature using the Equivalent Crystal Theory (ECT) of Smith and Banerjea. Results are compared with recent experimental results as well as with our earlier work on the avalanche of parallel planar surfaces. Our results on a model single-atom tip are in excellent agreement with recent experiments on tunneling through mechanically-controlled break junctions.

Toward XML Representation of NSS Simulation Scenario for Mission Scenario Exchange Capability

DTIC Science & Technology

2003-09-01

app.html Deitel , H. M., Deitel , P. J., Nieto, T. R., Lin, T. M., Sadhu, P. (2001). XML How to Program . Upper Saddle River: Prentice Hall...Combat XXI Program ...........................13 2. Transition NSS to a Java Environment ...........................................13 3. Shift to an...STATEMENT The Naval Simulation System (NSS) is a powerful computer program developed by the Navy to provide a force-on-force modeling and simulation

Performance of Renormalization Group Algebraic Turbulence Model on Boundary Layer Transition Simulation

NASA Technical Reports Server (NTRS)

Ahn, Kyung H.

1994-01-01

The RNG-based algebraic turbulence model, with a new method of solving the cubic equation and applying new length scales, is introduced. An analysis is made of the RNG length scale which was previously reported and the resulting eddy viscosity is compared with those from other algebraic turbulence models. Subsequently, a new length scale is introduced which actually uses the two previous RNG length scales in a systematic way to improve the model performance. The performance of the present RNG model is demonstrated by simulating the boundary layer flow over a flat plate and the flow over an airfoil.

Simulation evaluation of two VTOL control/display systems in IMC approach and shipboard landing

NASA Technical Reports Server (NTRS)

Merrick, V. K.

1984-01-01

Two control/display systems, which differed in overall complexity but were both designed for VTOL flight operations to and from small ships in instrument meteorological conditions (IMC), were tested using the Ames Flight Simulator for Advanced Aircraft (FSAA). Both systems have attitude command in transition and horizontal-velocity command in hover; the more complex system also has longitudinal-acceleration and flightpath-angle command in transition, and vertical-velocity command in hover. The most important overall distinction between the two systems for the viewpoint of implementation is that in one - the more complex - engine power and nozzle position are operated indirectly through flight controllers, whereas in the other they are operated directly by the pilot. Simulated landings were made on a moving model of a DD 963 Spruance-class destroyer. Acceptable transitions can be performed in turbulence of 3 m/sec rms using either system. Acceptable landings up to sea state 6 can be performed using the more complex system, and up to sea state 5 using the other system.

Model-Based Economic Evaluation of Treatments for Depression: A Systematic Literature Review.

PubMed

Kolovos, Spyros; Bosmans, Judith E; Riper, Heleen; Chevreul, Karine; Coupé, Veerle M H; van Tulder, Maurits W

2017-09-01

An increasing number of model-based studies that evaluate the cost effectiveness of treatments for depression are being published. These studies have different characteristics and use different simulation methods. We aimed to systematically review model-based studies evaluating the cost effectiveness of treatments for depression and examine which modelling technique is most appropriate for simulating the natural course of depression. The literature search was conducted in the databases PubMed, EMBASE and PsycInfo between 1 January 2002 and 1 October 2016. Studies were eligible if they used a health economic model with quality-adjusted life-years or disability-adjusted life-years as an outcome measure. Data related to various methodological characteristics were extracted from the included studies. The available modelling techniques were evaluated based on 11 predefined criteria. This methodological review included 41 model-based studies, of which 21 used decision trees (DTs), 15 used cohort-based state-transition Markov models (CMMs), two used individual-based state-transition models (ISMs), and three used discrete-event simulation (DES) models. Just over half of the studies (54%) evaluated antidepressants compared with a control condition. The data sources, time horizons, cycle lengths, perspectives adopted and number of health states/events all varied widely between the included studies. DTs scored positively in four of the 11 criteria, CMMs in five, ISMs in six, and DES models in seven. There were substantial methodological differences between the studies. Since the individual history of each patient is important for the prognosis of depression, DES and ISM simulation methods may be more appropriate than the others for a pragmatic representation of the course of depression. However, direct comparisons between the available modelling techniques are necessary to yield firm conclusions.

Hybrid Defect Phase Transition: Renormalization Group and Monte Carlo Analysis

NASA Astrophysics Data System (ADS)

Kaufman, Miron; Diep, H. T.

2010-03-01

For the q-state Potts model with 2 < q <= 4 on the square lattice with a defect line, the order parameter on the defect line jumps discontinuously from zero to a nonzero value while the defect energy varies continuously with the temperature at the critical temperature. Monte-Carlo simulations (H. T. Diep, M. Kaufman, Phys Rev E 2009) of the q-state Potts model on a square lattice with a line of defects verify the renormalization group prediction (M. Kaufman, R. B. Griffiths, Phys Rev B 1982) on the occurrence of the hybrid transition on the defect line. This is interesting since for those q values the bulk transition is continuous. This hybrid (continuous - discontinuous) defect transition is induced by the infinite range correlations at the bulk critical point.

Quantum phase transitions in a two-dimensional quantum XYX model: ground-state fidelity and entanglement.

PubMed

Li, Bo; Li, Sheng-Hao; Zhou, Huan-Qiang

2009-06-01

A systematic analysis is performed for quantum phase transitions in a two-dimensional anisotropic spin-1/2 antiferromagnetic XYX model in an external magnetic field. With the help of an innovative tensor network algorithm, we compute the fidelity per lattice site to demonstrate that the field-induced quantum phase transition is unambiguously characterized by a pinch point on the fidelity surface, marking a continuous phase transition. We also compute an entanglement estimator, defined as a ratio between the one-tangle and the sum of squared concurrences, to identify both the factorizing field and the critical point, resulting in a quantitative agreement with quantum Monte Carlo simulation. In addition, the local order parameter is "derived" from the tensor network representation of the system's ground-state wave functions.

Bypass transition and spot nucleation in boundary layers

NASA Astrophysics Data System (ADS)

Kreilos, Tobias; Khapko, Taras; Schlatter, Philipp; Duguet, Yohann; Henningson, Dan S.; Eckhardt, Bruno

2016-08-01

The spatiotemporal aspects of the transition to turbulence are considered in the case of a boundary-layer flow developing above a flat plate exposed to free-stream turbulence. Combining results on the receptivity to free-stream turbulence with the nonlinear concept of a transition threshold, a physically motivated model suggests a spatial distribution of spot nucleation events. To describe the evolution of turbulent spots a probabilistic cellular automaton is introduced, with all parameters directly obtained from numerical simulations of the boundary layer. The nucleation rates are then combined with the cellular automaton model, yielding excellent quantitative agreement with the statistical characteristics for different free-stream turbulence levels. We thus show how the recent theoretical progress on transitional wall-bounded flows can be extended to the much wider class of spatially developing boundary-layer flows.

Effects of Drake Passage on a strongly eddying global ocean

NASA Astrophysics Data System (ADS)

Viebahn, Jan; von der Heydt, Anna S.; Dijkstra, Henk A.

2015-04-01

During the past 65 Million (Ma) years, Earth's climate has undergone a major change from warm 'greenhouse' to colder 'icehouse' conditions with extensive ice sheets in the polar regions of both hemispheres. The Eocene-Oligocene (~34 Ma) and Oligocene-Miocene (~23 Ma) boundaries reflect major transitions in Cenozoic global climate change. Proposed mechanisms of these transitions include reorganization of ocean circulation due to critical gateway opening/deepening, changes in atmospheric CO2-concentration, and feedback mechanisms related to land-ice formation. Drake Passage (DP) is an intensively studied gateway because it plays a central role in closing the transport pathways of heat and chemicals in the ocean. The climate response to a closed DP has been explored with a variety of general circulation models, however, all of these models employ low model-grid resolutions such that the effects of subgrid-scale fluctuations ('eddies') are parameterized. We present results of the first high-resolution (0.1° horizontally) realistic global ocean model simulation with a closed DP in which the eddy field is largely resolved. The simulation extends over more than 200 years such that the strong transient adjustment process is passed and a near-equilibrium ocean state is reached. The effects of DP are diagnosed by comparing with both an open DP high-resolution control simulation (of same length) and corresponding low-resolution simulations. By focussing on the heat/tracer transports we demonstrate that the results are twofold: Considering spatially integrated transports the overall response to a closed DP is well captured by low-resolution simulations. However, looking at the actual spatial distributions drastic differences appear between far-scattered high-resolution and laminar-uniform low-resolution fields. We conclude that sparse and highly localized tracer proxy observations have to be interpreted carefully with the help of high-resolution model simulations.

Simulating and validating coastal gradients in wind energy resources

NASA Astrophysics Data System (ADS)

Hahmann, Andrea; Floors, Rogier; Karagali, Ioanna; Vasiljevic, Nikola; Lea, Guillaume; Simon, Elliot; Courtney, Michael; Badger, Merete; Peña, Alfredo; Hasager, Charlotte

2016-04-01

The experimental campaign of the RUNE (Reducing Uncertainty of Near-shore wind resource Estimates) project took place on the western coast of Denmark during the winter 2015-2016. The campaign used onshore scanning lidar technology combined with ocean and satellite information and produced a unique dataset to study the transition in boundary layer dynamics across the coastal zone. The RUNE project aims at reducing the uncertainty of near-shore wind resource estimates produced by mesoscale modeling. With this in mind, simulations using the Weather Research and Forecasting (WRF) model were performed to identify the sensitivity in the coastal gradients of wind energy resources to various model parameters and model inputs. Among these: model horizontal grid spacing and the planetary boundary layer and surface-layer scheme. We report on the differences amongst these simulations and preliminary results on the comparison of the model simulations with the RUNE observations of lidar and satellite measurements and near coastal tall mast.

Numerical investigation of hydrodynamic flow over an AUV moving in the water-surface vicinity considering the laminar-turbulent transition

NASA Astrophysics Data System (ADS)

Salari, Mahmoud; Rava, Amin

2017-09-01

Nowadays, Autonomous Underwater Vehicles (AUVs) are frequently used for exploring the oceans. The hydrodynamics of AUVs moving in the vicinity of the water surface are significantly different at higher depths. In this paper, the hydrodynamic coefficients of an AUV in non-dimensional depths of 0.75, 1, 1.5, 2, and 4D are obtained for movement close to the free-surface. Reynolds Averaged Navier Stokes Equations (RANS) are discretized using the finite volume approach and the water-surface effects modeled using the Volume of Fraction (VOF) method. As the operating speeds of AUVs are usually low, the boundary layer over them is not fully laminar or fully turbulent, so the effect of boundary layer transition from laminar to turbulent flow was considered in the simulations. Two different turbulence/transition models were used: 1) a full-turbulence model, the k-ɛ model, and 2) a turbulence/transition model, Menter's Transition-SST model. The results show that the Menter's Transition-SST model has a better consistency with experimental results. In addition, the wave-making effects of these bodies are studied at different immersion depths in the sea-surface vicinity or at finite depths. It is observed that the relevant pitch moments and lift coefficients are non-zero for these axi-symmetric bodies when they move close to the sea-surface. This is not expected for greater depths.

General trends of dihedral conformational transitions in a globular protein.

PubMed

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C; McCammon, J Andrew

2016-04-01

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. © 2016 Wiley Periodicals, Inc.

General trends of dihedral conformational transitions in a globular protein

DOE PAGES

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; ...

2016-02-15

In this paper, dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed bymore » the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. In conclusion, these general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.« less

Model averaging in the presence of structural uncertainty about treatment effects: influence on treatment decision and expected value of information.

PubMed

Price, Malcolm J; Welton, Nicky J; Briggs, Andrew H; Ades, A E

2011-01-01

Standard approaches to estimation of Markov models with data from randomized controlled trials tend either to make a judgment about which transition(s) treatments act on, or they assume that treatment has a separate effect on every transition. An alternative is to fit a series of models that assume that treatment acts on specific transitions. Investigators can then choose among alternative models using goodness-of-fit statistics. However, structural uncertainty about any chosen parameterization will remain and this may have implications for the resulting decision and the need for further research. We describe a Bayesian approach to model estimation, and model selection. Structural uncertainty about which parameterization to use is accounted for using model averaging and we developed a formula for calculating the expected value of perfect information (EVPI) in averaged models. Marginal posterior distributions are generated for each of the cost-effectiveness parameters using Markov Chain Monte Carlo simulation in WinBUGS, or Monte-Carlo simulation in Excel (Microsoft Corp., Redmond, WA). We illustrate the approach with an example of treatments for asthma using aggregate-level data from a connected network of four treatments compared in three pair-wise randomized controlled trials. The standard errors of incremental net benefit using structured models is reduced by up to eight- or ninefold compared to the unstructured models, and the expected loss attaching to decision uncertainty by factors of several hundreds. Model averaging had considerable influence on the EVPI. Alternative structural assumptions can alter the treatment decision and have an overwhelming effect on model uncertainty and expected value of information. Structural uncertainty can be accounted for by model averaging, and the EVPI can be calculated for averaged models. Copyright © 2011 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Study on the effect of transition curve to the dynamic characteristics of high-temperature superconducting maglev

NASA Astrophysics Data System (ADS)

Qian, Nan; Zheng, Botian; Gou, Yanfeng; Chen, Ping; Zheng, Jun; Deng, Zigang

2015-12-01

High temperature superconducting (HTS) maglev technology is becoming more and more mature, and many key technologies have been deeply studied. However, the transition curve plays a key role in HTS maglev system, and related studies have not been carried out. In this paper series of simulations were conducted to test the lateral and vertical vibration of HTS maglev when passing through curves. Two magnetic guideways, of which one has transition curves but the other does not, are designed to test the vibration characteristics of a mini HTS maglev model running though curves. Results show that after adding transition curves between straight line and circular curve the vibration of HTS maglev model in lateral and vertical directions are all weakened in different degrees. It proves that adding transition curve into HTS maglev system is favorable and necessary.

Resolution requirements for numerical simulations of transition

NASA Technical Reports Server (NTRS)

Zang, Thomas A.; Krist, Steven E.; Hussaini, M. Yousuff

1989-01-01

The resolution requirements for direct numerical simulations of transition to turbulence are investigated. A reliable resolution criterion is determined from the results of several detailed simulations of channel and boundary-layer transition.

Using multi-disciplinary optimization and numerical simulation on the transiting exoplanet survey satellite

NASA Astrophysics Data System (ADS)

Stoeckel, Gerhard P.; Doyle, Keith B.

2017-08-01

The Transiting Exoplanet Survey Satellite (TESS) is an instrument consisting of four, wide fieldof- view CCD cameras dedicated to the discovery of exoplanets around the brightest stars, and understanding the diversity of planets and planetary systems in our galaxy. Each camera utilizes a seven-element lens assembly with low-power and low-noise CCD electronics. Advanced multivariable optimization and numerical simulation capabilities accommodating arbitrarily complex objective functions have been added to the internally developed Lincoln Laboratory Integrated Modeling and Analysis Software (LLIMAS) and used to assess system performance. Various optical phenomena are accounted for in these analyses including full dn/dT spatial distributions in lenses and charge diffusion in the CCD electronics. These capabilities are utilized to design CCD shims for thermal vacuum chamber testing and flight, and verify comparable performance in both environments across a range of wavelengths, field points and temperature distributions. Additionally, optimizations and simulations are used for model correlation and robustness optimizations.

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.

Universal phase transition in community detectability under a stochastic block model.

PubMed

Chen, Pin-Yu; Hero, Alfred O

2015-03-01

We prove the existence of an asymptotic phase-transition threshold on community detectability for the spectral modularity method [M. E. J. Newman, Phys. Rev. E 74, 036104 (2006) and Proc. Natl. Acad. Sci. (USA) 103, 8577 (2006)] under a stochastic block model. The phase transition on community detectability occurs as the intercommunity edge connection probability p grows. This phase transition separates a subcritical regime of small p, where modularity-based community detection successfully identifies the communities, from a supercritical regime of large p where successful community detection is impossible. We show that, as the community sizes become large, the asymptotic phase-transition threshold p* is equal to √[p1p2], where pi(i=1,2) is the within-community edge connection probability. Thus the phase-transition threshold is universal in the sense that it does not depend on the ratio of community sizes. The universal phase-transition phenomenon is validated by simulations for moderately sized communities. Using the derived expression for the phase-transition threshold, we propose an empirical method for estimating this threshold from real-world data.

Non-Fickian dispersion of groundwater age

PubMed Central

Engdahl, Nicholas B.; Ginn, Timothy R.; Fogg, Graham E.

2014-01-01

We expand the governing equation of groundwater age to account for non-Fickian dispersive fluxes using continuous random walks. Groundwater age is included as an additional (fifth) dimension on which the volumetric mass density of water is distributed and we follow the classical random walk derivation now in five dimensions. The general solution of the random walk recovers the previous conventional model of age when the low order moments of the transition density functions remain finite at their limits and describes non-Fickian age distributions when the transition densities diverge. Previously published transition densities are then used to show how the added dimension in age affects the governing differential equations. Depending on which transition densities diverge, the resulting models may be nonlocal in time, space, or age and can describe asymptotic or pre-asymptotic dispersion. A joint distribution function of time and age transitions is developed as a conditional probability and a natural result of this is that time and age must always have identical transition rate functions. This implies that a transition density defined for age can substitute for a density in time and this has implications for transport model parameter estimation. We present examples of simulated age distributions from a geologically based, heterogeneous domain that exhibit non-Fickian behavior and show that the non-Fickian model provides better descriptions of the distributions than the Fickian model. PMID:24976651

Lattice Boltzmann study on Kelvin-Helmholtz instability: roles of velocity and density gradients.

PubMed

Gan, Yanbiao; Xu, Aiguo; Zhang, Guangcai; Li, Yingjun

2011-05-01

A two-dimensional lattice Boltzmann model with 19 discrete velocities for compressible fluids is proposed. The fifth-order weighted essentially nonoscillatory (5th-WENO) finite difference scheme is employed to calculate the convection term of the lattice Boltzmann equation. The validity of the model is verified by comparing simulation results of the Sod shock tube with its corresponding analytical solutions [G. A. Sod, J. Comput. Phys. 27, 1 (1978).]. The velocity and density gradient effects on the Kelvin-Helmholtz instability (KHI) are investigated using the proposed model. Sharp density contours are obtained in our simulations. It is found that the linear growth rate γ for the KHI decreases by increasing the width of velocity transition layer D(v) but increases by increasing the width of density transition layer D(ρ). After the initial transient period and before the vortex has been well formed, the linear growth rates γ(v) and γ(ρ), vary with D(v) and D(ρ) approximately in the following way, lnγ(v)=a-bD(v) and γ(ρ)=c+elnD(ρ)(D(ρ)D(ρ)(E) the linear growth rate γ(ρ) does not vary significantly any more. One can use the hybrid effects of velocity and density transition layers to stabilize the KHI. Our numerical simulation results are in general agreement with the analytical results [L. F. Wang et al., Phys. Plasma 17, 042103 (2010)]. © 2011 American Physical Society

Dynamical critical exponent of the Jaynes-Cummings-Hubbard model

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

Hohenadler, M.; Aichhorn, M.; Schmidt, S.

2011-10-15

An array of high-Q electromagnetic resonators coupled to qubits gives rise to the Jaynes-Cummings-Hubbard model describing a superfluid to Mott-insulator transition of lattice polaritons. From mean-field and strong-coupling expansions, the critical properties of the model are expected to be identical to the scalar Bose-Hubbard model. A recent Monte Carlo study of the superfluid density on the square lattice suggested that this does not hold for the fixed-density transition through the Mott lobe tip. Instead, mean-field behavior with a dynamical critical exponent z=2 was found. We perform large-scale quantum Monte Carlo simulations to investigate the critical behavior of the superfluid densitymore » and the compressibility. We find z=1 at the tip of the insulating lobe. Hence the transition falls in the three-dimensional XY universality class, analogous to the Bose-Hubbard model.« less

Three-state Potts model on non-local directed small-world lattices

NASA Astrophysics Data System (ADS)

Ferraz, Carlos Handrey Araujo; Lima, José Luiz Sousa

2017-10-01

In this paper, we study the non-local directed Small-World (NLDSW) disorder effects in the three-state Potts model as a form to capture the essential features shared by real complex systems where non-locality effects play a important role in the behavior of these systems. Using Monte Carlo techniques and finite-size scaling analysis, we estimate the infinite lattice critical temperatures and the leading critical exponents in this model. In particular, we investigate the first- to second-order phase transition crossover when NLDSW links are inserted. A cluster-flip algorithm was used to reduce the critical slowing down effect in our simulations. We find that for a NLDSW disorder densities p

The nature of the continuous non-equilibrium phase transition of Axelrod's model

NASA Astrophysics Data System (ADS)

Peres, Lucas R.; Fontanari, José F.

2015-09-01

Axelrod's model in the square lattice with nearest-neighbors interactions exhibits culturally homogeneous as well as culturally fragmented absorbing configurations. In the case in which the agents are characterized by F = 2 cultural features and each feature assumes k states drawn from a Poisson distribution of parameter q, these regimes are separated by a continuous transition at qc = 3.10 +/- 0.02 . Using Monte Carlo simulations and finite-size scaling we show that the mean density of cultural domains μ is an order parameter of the model that vanishes as μ ∼ (q - q_c)^β with β = 0.67 +/- 0.01 at the critical point. In addition, for the correlation length critical exponent we find ν = 1.63 +/- 0.04 and for Fisher's exponent, τ = 1.76 +/- 0.01 . This set of critical exponents places the continuous phase transition of Axelrod's model apart from the known universality classes of non-equilibrium lattice models.

Moving base simulation of an ASTOVL lift-fan aircraft

NASA Technical Reports Server (NTRS)

Chung, William W. Y.; Borchers, Paul F.; Franklin, James A.

1995-01-01

Using a generalized simulation model, a moving-base simulation of a lift-fan short takeoff/vertical landing fighter aircraft was conducted on the Vertical Motion Simulator at Ames Research Center. Objectives of the experiment were to (1) assess the effects of lift-fan propulsion system design features on aircraft control during transition and vertical flight including integration of lift fan/lift/cruise engine/aerodynamic controls and lift fan/lift/cruise engine dynamic response, (2) evaluate pilot-vehicle interface with the control system and head-up display including control modes for low-speed operational tasks and control mode/display integration, and (3) conduct operational evaluations of this configuration during takeoff, transition, and landing similar to those carried out previously by the Ames team for the mixed-flow, vectored thrust, and augmentor-ejector concepts. Based on results of the simulation, preliminary assessments of acceptable and borderline lift-fan and lift/cruise engine thrust response characteristics were obtained. Maximum pitch, roll, and yaw control power used during transition, hover, and vertical landing were documented. Control and display mode options were assessed for their compatibility with a range of land-based and shipboard operations from takeoff to cruise through transition back to hover and vertical landing. Flying qualities were established for candidate control modes and displays for instrument approaches and vertical landings aboard an LPH assault ship and DD-963 destroyer. Test pilot and engineer teams from the Naval Air Warfare Center, Boeing, Lockheed, McDonnell Douglas, and the British Defence Research Agency participated in the program.

When teams shift among processes: insights from simulation and optimization.

PubMed

Kennedy, Deanna M; McComb, Sara A

2014-09-01

This article introduces process shifts to study the temporal interplay among transition and action processes espoused in the recurring phase model proposed by Marks, Mathieu, and Zacarro (2001). Process shifts are those points in time when teams complete a focal process and change to another process. By using team communication patterns to measure process shifts, this research explores (a) when teams shift among different transition processes and initiate action processes and (b) the potential of different interventions, such as communication directives, to manipulate process shift timing and order and, ultimately, team performance. Virtual experiments are employed to compare data from observed laboratory teams not receiving interventions, simulated teams receiving interventions, and optimal simulated teams generated using genetic algorithm procedures. Our results offer insights about the potential for different interventions to affect team performance. Moreover, certain interventions may promote discussions about key issues (e.g., tactical strategies) and facilitate shifting among transition processes in a manner that emulates optimal simulated teams' communication patterns. Thus, we contribute to theory regarding team processes in 2 important ways. First, we present process shifts as a way to explore the timing of when teams shift from transition to action processes. Second, we use virtual experimentation to identify those interventions with the greatest potential to affect performance by changing when teams shift among processes. Additionally, we employ computational methods including neural networks, simulation, and optimization, thereby demonstrating their applicability in conducting team research. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Implementation of real-time energy management strategy based on reinforcement learning for hybrid electric vehicles and simulation validation

PubMed Central

Kong, Zehui; Liu, Teng

2017-01-01

To further improve the fuel economy of series hybrid electric tracked vehicles, a reinforcement learning (RL)-based real-time energy management strategy is developed in this paper. In order to utilize the statistical characteristics of online driving schedule effectively, a recursive algorithm for the transition probability matrix (TPM) of power-request is derived. The reinforcement learning (RL) is applied to calculate and update the control policy at regular time, adapting to the varying driving conditions. A facing-forward powertrain model is built in detail, including the engine-generator model, battery model and vehicle dynamical model. The robustness and adaptability of real-time energy management strategy are validated through the comparison with the stationary control strategy based on initial transition probability matrix (TPM) generated from a long naturalistic driving cycle in the simulation. Results indicate that proposed method has better fuel economy than stationary one and is more effective in real-time control. PMID:28671967

Implementation of real-time energy management strategy based on reinforcement learning for hybrid electric vehicles and simulation validation.

PubMed

Kong, Zehui; Zou, Yuan; Liu, Teng

2017-01-01

To further improve the fuel economy of series hybrid electric tracked vehicles, a reinforcement learning (RL)-based real-time energy management strategy is developed in this paper. In order to utilize the statistical characteristics of online driving schedule effectively, a recursive algorithm for the transition probability matrix (TPM) of power-request is derived. The reinforcement learning (RL) is applied to calculate and update the control policy at regular time, adapting to the varying driving conditions. A facing-forward powertrain model is built in detail, including the engine-generator model, battery model and vehicle dynamical model. The robustness and adaptability of real-time energy management strategy are validated through the comparison with the stationary control strategy based on initial transition probability matrix (TPM) generated from a long naturalistic driving cycle in the simulation. Results indicate that proposed method has better fuel economy than stationary one and is more effective in real-time control.

Explicit filtering in large eddy simulation using a discontinuous Galerkin method

NASA Astrophysics Data System (ADS)

Brazell, Matthew J.

The discontinuous Galerkin (DG) method is a formulation of the finite element method (FEM). DG provides the ability for a high order of accuracy in complex geometries, and allows for highly efficient parallelization algorithms. These attributes make the DG method attractive for solving the Navier-Stokes equations for large eddy simulation (LES). The main goal of this work is to investigate the feasibility of adopting an explicit filter in the numerical solution of the Navier-Stokes equations with DG. Explicit filtering has been shown to increase the numerical stability of under-resolved simulations and is needed for LES with dynamic sub-grid scale (SGS) models. The explicit filter takes advantage of DG's framework where the solution is approximated using a polyno- mial basis where the higher modes of the solution correspond to a higher order polynomial basis. By removing high order modes, the filtered solution contains low order frequency content much like an explicit low pass filter. The explicit filter implementation is tested on a simple 1-D solver with an initial condi- tion that has some similarity to turbulent flows. The explicit filter does restrict the resolution as well as remove accumulated energy in the higher modes from aliasing. However, the ex- plicit filter is unable to remove numerical errors causing numerical dissipation. A second test case solves the 3-D Navier-Stokes equations of the Taylor-Green vortex flow (TGV). The TGV is useful for SGS model testing because it is initially laminar and transitions into a fully turbulent flow. The SGS models investigated include the constant coefficient Smagorinsky model, dynamic Smagorinsky model, and dynamic Heinz model. The constant coefficient Smagorinsky model is over dissipative, this is generally not desirable however it does add stability. The dynamic Smagorinsky model generally performs better, especially during the laminar-turbulent transition region as expected. The dynamic Heinz model which is based on an improved model, handles the laminar-turbulent transition region well while also showing additional robustness.

Modeling Conformational Transitions and Energetics of Ligand Binding with the Glutamate Receptor Ligand Binding Domain

NASA Astrophysics Data System (ADS)

Kurnikova, Maria

2009-03-01

Understanding of protein motion and energetics of conformational transitions is crucial to understanding protein function. The glutamate receptor ligand binding domain (GluR2 S1S2) is a two lobe protein, which binds ligand at the interface of two lobes and undergoes conformational transition. The cleft closure conformational transition of S1S2 has been implicated in gating of the ion channel formed by the transmembrane domain of the receptor. In this study we present a composite multi-faceted theoretical analysis of the detailed mechanism of this conformational transition based on rigid cluster decomposition of the protein structure [1] and identifying hydrogen bonds that are responsible for stabilizing the closed conformation [2]. Free energy of the protein reorganization upon ligand binding was calculated using combined Thermodynamic Integration (TI) and Umbrella Sampling (US) simulations [3]. Ligand -- protein interactions in the binding cleft were analyzed using Molecular Dynamics, continuum electrostatics and QM/MM models [4]. All model calculations compare well with corresponding experimental measurements. [4pt] [1] Protein Flexibility using Constraints from Molecular Dynamics Simulations T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. G. Kurnikova , Phys. Biol., 2, S137 (2005)[0pt] [2] Theoretical Study of the Glutamate Receptor Ligand Binding Domain Flexibility and Conformational Reorganization T. Mamonova, K. Speranskiy, and M. Kurnikova , Prot.: Struct., Func., Bioinf., 73,656 (2008)[0pt] [3] Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain T. Mamonova, M. Yonkunas, and M. Kurnikova Biochemistry 47, 11077 (2008)[0pt] [4] On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain K. Speranskiy and M. Kurnikova Biochemistry 44, 11208 (2005)

Paramagnetic and glass transitions in sudoku

NASA Astrophysics Data System (ADS)

Williams, A.; Ackland, G. J.

2012-09-01

We study the statistical mechanics of a model glassy system based on sudoku, a familiar and popular mathematical puzzle. Sudoku puzzles provide a very rare example of a class of frustrated systems with a unique ground state without symmetry. Here, the puzzle is recast as a thermodynamic system where the number of violated rules defines the energy. We use Monte Carlo simulation to show that the “sudoku Hamiltonian” exhibits two transitions as a function of temperature, a paramagnetic, and a glass transition. Of these, the intermediate condensed phase is the only one that visits the ground state (i.e., it solves the puzzle, though this is not the purpose of the study). Both transitions are associated with an entropy change, paramagnetism measured from the dynamics of the Monte Carlo run, showing a peak in specific heat, while the residual glass entropy is determined by finding multiple instances of the glass by repeated annealing. There are relatively few such simple models for frustrated or glassy systems that exhibit both ordering and glass transitions; sudoku puzzles are unique for the ease with which they can be obtained, with the proof of the existence of a unique ground state via the satisfiability of all constraints. Simulations suggest that in the glass phase there is an increase in information entropy with lowering temperature. In fact, we have shown that sudoku puzzles have the type of rugged energy landscape with multiple minima that typifies glasses in many physical systems. This puzzling result is a manifestation of the paradox of the residual glass entropy. These readily available puzzles can now be used as solvable model Hamiltonian systems for studying the glass transition.

Empirical methods for modeling landscape change, ecosystem services, and biodiversity

Treesearch

David Lewis; Ralph Alig

2009-01-01

The purpose of this paper is to synthesize recent economics research aimed at integrating discrete-choice econometric models of land-use change with spatially-explicit landscape simulations and quantitative ecology. This research explicitly models changes in the spatial pattern of landscapes in two steps: 1) econometric estimation of parcel-scale transition...

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter.

PubMed

Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D

2015-01-01

Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis.