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

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2010-01-01

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

A Method on Dynamic Path Planning for Robotic Manipulator Autonomous Obstacle Avoidance Based on an Improved RRT Algorithm.

PubMed

Wei, Kun; Ren, Bingyin

2018-02-13

In a future intelligent factory, a robotic manipulator must work efficiently and safely in a Human-Robot collaborative and dynamic unstructured environment. Autonomous path planning is the most important issue which must be resolved first in the process of improving robotic manipulator intelligence. Among the path-planning methods, the Rapidly Exploring Random Tree (RRT) algorithm based on random sampling has been widely applied in dynamic path planning for a high-dimensional robotic manipulator, especially in a complex environment because of its probability completeness, perfect expansion, and fast exploring speed over other planning methods. However, the existing RRT algorithm has a limitation in path planning for a robotic manipulator in a dynamic unstructured environment. Therefore, an autonomous obstacle avoidance dynamic path-planning method for a robotic manipulator based on an improved RRT algorithm, called Smoothly RRT (S-RRT), is proposed. This method that targets a directional node extends and can increase the sampling speed and efficiency of RRT dramatically. A path optimization strategy based on the maximum curvature constraint is presented to generate a smooth and curved continuous executable path for a robotic manipulator. Finally, the correctness, effectiveness, and practicability of the proposed method are demonstrated and validated via a MATLAB static simulation and a Robot Operating System (ROS) dynamic simulation environment as well as a real autonomous obstacle avoidance experiment in a dynamic unstructured environment for a robotic manipulator. The proposed method not only provides great practical engineering significance for a robotic manipulator's obstacle avoidance in an intelligent factory, but also theoretical reference value for other type of robots' path planning.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Propagation Diagnostic Simulations Using High-Resolution Equatorial Plasma Bubble Simulations

NASA Astrophysics Data System (ADS)

Rino, C. L.; Carrano, C. S.; Yokoyama, T.

2017-12-01

In a recent paper, under review, equatorial-plasma-bubble (EPB) simulations were used to conduct a comparative analysis of the EPB spectra characteristics with high-resolution in-situ measurements from the C/NOFS satellite. EPB realizations sampled in planes perpendicular to magnetic field lines provided well-defined EPB structure at altitudes penetrating both high and low-density regions. The average C/NOFS structure in highly disturbed regions showed nearly identical two-component inverse-power-law spectral characteristics as the measured EPB structure. This paper describes the results of PWE simulations using the same two-dimensional cross-field EPB realizations. New Irregularity Parameter Estimation (IPE) diagnostics, which are based on two-dimensional equivalent-phase-screen theory [A theory of scintillation for two-component power law irregularity spectra: Overview and numerical results, by Charles Carrano and Charles Rino, DOI: 10.1002/2015RS005903], have been successfully applied to extract two-component inverse-power-law parameters from measured intensity spectra. The EPB simulations [Low and Midlatitude Ionospheric Plasma DensityIrregularities and Their Effects on Geomagnetic Field, by Tatsuhiro Yokoyama and Claudia Stolle, DOI 10.1007/s11214-016-0295-7] have sufficient resolution to populate the structure scales (tens of km to hundreds of meters) that cause strong scintillation at GPS frequencies. The simulations provide an ideal geometry whereby the ramifications of varying structure along the propagation path can be investigated. It is well known path-integrated one-dimensional spectra increase the one-dimensional index by one. The relation requires decorrelation along the propagation path. Correlated structure would be interpreted as stochastic total-electron-content (TEC). The simulations are performed with unmodified structure. Because the EPB structure is confined to the central region of the sample planes, edge effects are minimized. Consequently, the propagated signal phase can be comparted to path-integrated phase for evaluating TEC extraction. Only the frequency dependence of phase scintillation distinguishes phase scintillation. The simulations allow scale-dependent exploration of remote-sensing diagnostics.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

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

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

Study on the measuring distance for blood glucose infrared spectral measuring by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Li, Xiang

2016-10-01

Blood glucose monitoring is of great importance for controlling diabetes procedure and preventing the complications. At present, the clinical blood glucose concentration measurement is invasive and could be replaced by noninvasive spectroscopy analytical techniques. Among various parameters of optical fiber probe used in spectrum measuring, the measurement distance is the key one. The Monte Carlo technique is a flexible method for simulating light propagation in tissue. The simulation is based on the random walks that photons make as they travel through tissue, which are chosen by statistically sampling the probability distributions for step size and angular deflection per scattering event. The traditional method for determine the optimal distance between transmitting fiber and detector is using Monte Carlo simulation to find out the point where most photons come out. But there is a problem. In the epidermal layer there is no artery, vein or capillary vessel. Thus, when photons propagate and interactive with tissue in epidermal layer, no information is given to the photons. A new criterion is proposed to determine the optimal distance, which is named effective path length in this paper. The path length of each photons travelling in dermis is recorded when running Monte-Carlo simulation, which is the effective path length defined above. The sum of effective path length of every photon at each point is calculated. The detector should be place on the point which has most effective path length. Then the optimal measuring distance between transmitting fiber and detector is determined.

CTViz: A tool for the visualization of transport in nanocomposites.

PubMed

Beach, Benjamin; Brown, Joshua; Tarlton, Taylor; Derosa, Pedro A

2016-05-01

A visualization tool (CTViz) for charge transport processes in 3-D hybrid materials (nanocomposites) was developed, inspired by the need for a graphical application to assist in code debugging and data presentation of an existing in-house code. As the simulation code grew, troubleshooting problems grew increasingly difficult without an effective way to visualize 3-D samples and charge transport in those samples. CTViz is able to produce publication and presentation quality visuals of the simulation box, as well as static and animated visuals of the paths of individual carriers through the sample. CTViz was designed to provide a high degree of flexibility in the visualization of the data. A feature that characterizes this tool is the use of shade and transparency levels to highlight important details in the morphology or in the transport paths by hiding or dimming elements of little relevance to the current view. This is fundamental for the visualization of 3-D systems with complex structures. The code presented here provides these required capabilities, but has gone beyond the original design and could be used as is or easily adapted for the visualization of other particulate transport where transport occurs on discrete paths. Copyright © 2016 Elsevier Inc. All rights reserved.

Development of a new integrated local trajectory planning and tracking control framework for autonomous ground vehicles

NASA Astrophysics Data System (ADS)

Li, Xiaohui; Sun, Zhenping; Cao, Dongpu; Liu, Daxue; He, Hangen

2017-03-01

This study proposes a novel integrated local trajectory planning and tracking control (ILTPTC) framework for autonomous vehicles driving along a reference path with obstacles avoidance. For this ILTPTC framework, an efficient state-space sampling-based trajectory planning scheme is employed to smoothly follow the reference path. A model-based predictive path generation algorithm is applied to produce a set of smooth and kinematically-feasible paths connecting the initial state with the sampling terminal states. A velocity control law is then designed to assign a speed value at each of the points along the generated paths. An objective function considering both safety and comfort performance is carefully formulated for assessing the generated trajectories and selecting the optimal one. For accurately tracking the optimal trajectory while overcoming external disturbances and model uncertainties, a combined feedforward and feedback controller is developed. Both simulation analyses and vehicle testing are performed to verify the effectiveness of the proposed ILTPTC framework, and future research is also briefly discussed.

Girsanov reweighting for path ensembles and Markov state models

NASA Astrophysics Data System (ADS)

Donati, L.; Hartmann, C.; Keller, B. G.

2017-06-01

The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor "on the fly" during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics.

Stochastic Evolutionary Algorithms for Planning Robot Paths

NASA Technical Reports Server (NTRS)

Fink, Wolfgang; Aghazarian, Hrand; Huntsberger, Terrance; Terrile, Richard

2006-01-01

A computer program implements stochastic evolutionary algorithms for planning and optimizing collision-free paths for robots and their jointed limbs. Stochastic evolutionary algorithms can be made to produce acceptably close approximations to exact, optimal solutions for path-planning problems while often demanding much less computation than do exhaustive-search and deterministic inverse-kinematics algorithms that have been used previously for this purpose. Hence, the present software is better suited for application aboard robots having limited computing capabilities (see figure). The stochastic aspect lies in the use of simulated annealing to (1) prevent trapping of an optimization algorithm in local minima of an energy-like error measure by which the fitness of a trial solution is evaluated while (2) ensuring that the entire multidimensional configuration and parameter space of the path-planning problem is sampled efficiently with respect to both robot joint angles and computation time. Simulated annealing is an established technique for avoiding local minima in multidimensional optimization problems, but has not, until now, been applied to planning collision-free robot paths by use of low-power computers.

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

PubMed

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

2017-10-30

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

Diffusing-wave spectroscopy in a standard dynamic light scattering setup

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

From large-eddy simulation to multi-UAVs sampling of shallow cumulus clouds

NASA Astrophysics Data System (ADS)

Lamraoui, Fayçal; Roberts, Greg; Burnet, Frédéric

2016-04-01

In-situ sampling of clouds that can provide simultaneous measurements at satisfying spatio-temporal resolutions to capture 3D small scale physical processes continues to present challenges. This project (SKYSCANNER) aims at bringing together cloud sampling strategies using a swarm of unmanned aerial vehicles (UAVs) based on Large-eddy simulation (LES). The multi-UAV-based field campaigns with a personalized sampling strategy for individual clouds and cloud fields will significantly improve the understanding of the unresolved cloud physical processes. An extensive set of LES experiments for case studies from ARM-SGP site have been performed using MesoNH model at high resolutions down to 10 m. The carried out simulations led to establishing a macroscopic model that quantifies the interrelationship between micro- and macrophysical properties of shallow convective clouds. Both the geometry and evolution of individual clouds are critical to multi-UAV cloud sampling and path planning. The preliminary findings of the current project reveal several linear relationships that associate many cloud geometric parameters to cloud related meteorological variables. In addition, the horizontal wind speed indicates a proportional impact on cloud number concentration as well as triggering and prolonging the occurrence of cumulus clouds. In the framework of the joint collaboration that involves a Multidisciplinary Team (including institutes specializing in aviation, robotics and atmospheric science), this model will be a reference point for multi-UAVs sampling strategies and path planning.

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

NASA Astrophysics Data System (ADS)

Adjanor, G.; Athènes, M.; Calvo, F.

2006-09-01

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

Stochastic and deterministic models for agricultural production networks.

PubMed

Bai, P; Banks, H T; Dediu, S; Govan, A Y; Last, M; Lloyd, A L; Nguyen, H K; Olufsen, M S; Rempala, G; Slenning, B D

2007-07-01

An approach to modeling the impact of disturbances in an agricultural production network is presented. A stochastic model and its approximate deterministic model for averages over sample paths of the stochastic system are developed. Simulations, sensitivity and generalized sensitivity analyses are given. Finally, it is shown how diseases may be introduced into the network and corresponding simulations are discussed.

Scanning electron microscope fine tuning using four-bar piezoelectric actuated mechanism

NASA Astrophysics Data System (ADS)

Hatamleh, Khaled S.; Khasawneh, Qais A.; Al-Ghasem, Adnan; Jaradat, Mohammad A.; Sawaqed, Laith; Al-Shabi, Mohammad

2018-01-01

Scanning Electron Microscopes are extensively used for accurate micro/nano images exploring. Several strategies have been proposed to fine tune those microscopes in the past few years. This work presents a new fine tuning strategy of a scanning electron microscope sample table using four bar piezoelectric actuated mechanisms. The introduced paper presents an algorithm to find all possible inverse kinematics solutions of the proposed mechanism. In addition, another algorithm is presented to search for the optimal inverse kinematic solution. Both algorithms are used simultaneously by means of a simulation study to fine tune a scanning electron microscope sample table through a pre-specified circular or linear path of motion. Results of the study shows that, proposed algorithms were able to minimize the power required to drive the piezoelectric actuated mechanism by a ratio of 97.5% for all simulated paths of motion when compared to general non-optimized solution.

Modeling of Aerosols in Post-Combustor Flow Path and Sampling System

NASA Technical Reports Server (NTRS)

Wey, Thomas; Liu, Nan-Suey

2006-01-01

The development and application of a multi-dimensional capability for modeling and simulation of aviation-sourced particle emissions and their precursors are elucidated. Current focus is on the role of the flow and thermal environments. The cases investigated include a film cooled turbine blade, the first-stage of a high-pressure turbine, the sampling probes, the sampling lines, and a pressure reduction chamber.

Nonequilibrium Phase Transitions in Supercooled Water

NASA Astrophysics Data System (ADS)

Limmer, David; Chandler, David

2012-02-01

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

Heating and thermal control of brazing technique to break contamination path for potential Mars sample return

NASA Astrophysics Data System (ADS)

Bao, Xiaoqi; Badescu, Mircea; Sherrit, Stewart; Bar-Cohen, Yoseph; Campos, Sergio

2017-04-01

The potential return of Mars sample material is of great interest to the planetary science community, as it would enable extensive analysis of samples with highly sensitive laboratory instruments. It is important to make sure such a mission concept would not bring any living microbes, which may possibly exist on Mars, back to Earth's environment. In order to ensure the isolation of Mars microbes from Earth's Atmosphere, a brazing sealing and sterilizing technique was proposed to break the Mars-to-Earth contamination path. Effectively, heating the brazing zone in high vacuum space and controlling the sample temperature for integrity are key challenges to the implementation of this technique. The break-thechain procedures for container configurations, which are being considered, were simulated by multi-physics finite element models. Different heating methods including induction and resistive/radiation were evaluated. The temperature profiles of Martian samples in a proposed container structure were predicted. The results show that the sealing and sterilizing process can be controlled such that the samples temperature is maintained below the level that may cause damage, and that the brazing technique is a feasible approach to breaking the contamination path.

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. PMID:26433027

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. Copyright © 2015 Elsevier Inc. All rights reserved.

Explanation of Two Anomalous Results in Statistical Mediation Analysis.

PubMed

Fritz, Matthew S; Taylor, Aaron B; Mackinnon, David P

2012-01-01

Previous studies of different methods of testing mediation models have consistently found two anomalous results. The first result is elevated Type I error rates for the bias-corrected and accelerated bias-corrected bootstrap tests not found in nonresampling tests or in resampling tests that did not include a bias correction. This is of special concern as the bias-corrected bootstrap is often recommended and used due to its higher statistical power compared with other tests. The second result is statistical power reaching an asymptote far below 1.0 and in some conditions even declining slightly as the size of the relationship between X and M , a , increased. Two computer simulations were conducted to examine these findings in greater detail. Results from the first simulation found that the increased Type I error rates for the bias-corrected and accelerated bias-corrected bootstrap are a function of an interaction between the size of the individual paths making up the mediated effect and the sample size, such that elevated Type I error rates occur when the sample size is small and the effect size of the nonzero path is medium or larger. Results from the second simulation found that stagnation and decreases in statistical power as a function of the effect size of the a path occurred primarily when the path between M and Y , b , was small. Two empirical mediation examples are provided using data from a steroid prevention and health promotion program aimed at high school football players (Athletes Training and Learning to Avoid Steroids; Goldberg et al., 1996), one to illustrate a possible Type I error for the bias-corrected bootstrap test and a second to illustrate a loss in power related to the size of a . Implications of these findings are discussed.

Formation and distribution of fragments in the spontaneous fission of 240 Pu

DOE PAGES

Sadhukhan, Jhilam; Zhang, Chunli; Nazarewicz, Witold; ...

2017-12-18

We use the stochastic Langevin framework to simulate the nuclear evolution after the system tunnels through the multidimensional potential barrier. For a representative sample of different initial configurations along the outer turning-point line, we define effective fission paths by computing a large number of Langevin trajectories. We extract the relative contribution of each such path to the fragment distribution. We then use nucleon localization functions along effective fission pathways to analyze the characteristics of prefragments at prescission configurations.

Path integral Monte Carlo and the electron gas

NASA Astrophysics Data System (ADS)

Brown, Ethan W.

Path integral Monte Carlo is a proven method for accurately simulating quantum mechanical systems at finite-temperature. By stochastically sampling Feynman's path integral representation of the quantum many-body density matrix, path integral Monte Carlo includes non-perturbative effects like thermal fluctuations and particle correlations in a natural way. Over the past 30 years, path integral Monte Carlo has been successfully employed to study the low density electron gas, high-pressure hydrogen, and superfluid helium. For systems where the role of Fermi statistics is important, however, traditional path integral Monte Carlo simulations have an exponentially decreasing efficiency with decreased temperature and increased system size. In this thesis, we work towards improving this efficiency, both through approximate and exact methods, as specifically applied to the homogeneous electron gas. We begin with a brief overview of the current state of atomic simulations at finite-temperature before we delve into a pedagogical review of the path integral Monte Carlo method. We then spend some time discussing the one major issue preventing exact simulation of Fermi systems, the sign problem. Afterwards, we introduce a way to circumvent the sign problem in PIMC simulations through a fixed-node constraint. We then apply this method to the homogeneous electron gas at a large swatch of densities and temperatures in order to map out the warm-dense matter regime. The electron gas can be a representative model for a host of real systems, from simple medals to stellar interiors. However, its most common use is as input into density functional theory. To this end, we aim to build an accurate representation of the electron gas from the ground state to the classical limit and examine its use in finite-temperature density functional formulations. The latter half of this thesis focuses on possible routes beyond the fixed-node approximation. As a first step, we utilize the variational principle inherent in the path integral Monte Carlo method to optimize the nodal surface. By using a ansatz resembling a free particle density matrix, we make a unique connection between a nodal effective mass and the traditional effective mass of many-body quantum theory. We then propose and test several alternate nodal ansatzes and apply them to single atomic systems. Finally, we propose a method to tackle the sign problem head on, by leveraging the relatively simple structure of permutation space. Using this method, we find we can perform exact simulations this of the electron gas and 3He that were previously impossible.

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.

Speech Understanding with a New Implant Technology: A Comparative Study with a New Nonskin Penetrating Baha System

PubMed Central

Caversaccio, Marco

2014-01-01

Objective. To compare hearing and speech understanding between a new, nonskin penetrating Baha system (Baha Attract) to the current Baha system using a skin-penetrating abutment. Methods. Hearing and speech understanding were measured in 16 experienced Baha users. The transmission path via the abutment was compared to a simulated Baha Attract transmission path by attaching the implantable magnet to the abutment and then by adding a sample of artificial skin and the external parts of the Baha Attract system. Four different measurements were performed: bone conduction thresholds directly through the sound processor (BC Direct), aided sound field thresholds, aided speech understanding in quiet, and aided speech understanding in noise. Results. The simulated Baha Attract transmission path introduced an attenuation starting from approximately 5 dB at 1000 Hz, increasing to 20–25 dB above 6000 Hz. However, aided sound field threshold shows smaller differences and aided speech understanding in quiet and in noise does not differ significantly between the two transmission paths. Conclusion. The Baha Attract system transmission path introduces predominately high frequency attenuation. This attenuation can be partially compensated by adequate fitting of the speech processor. No significant decrease in speech understanding in either quiet or in noise was found. PMID:25140314

A computationally efficient Bayesian sequential simulation approach for the assimilation of vast and diverse hydrogeophysical datasets

NASA Astrophysics Data System (ADS)

Nussbaumer, Raphaël; Gloaguen, Erwan; Mariéthoz, Grégoire; Holliger, Klaus

2016-04-01

Bayesian sequential simulation (BSS) is a powerful geostatistical technique, which notably has shown significant potential for the assimilation of datasets that are diverse with regard to the spatial resolution and their relationship. However, these types of applications of BSS require a large number of realizations to adequately explore the solution space and to assess the corresponding uncertainties. Moreover, such simulations generally need to be performed on very fine grids in order to adequately exploit the technique's potential for characterizing heterogeneous environments. Correspondingly, the computational cost of BSS algorithms in their classical form is very high, which so far has limited an effective application of this method to large models and/or vast datasets. In this context, it is also important to note that the inherent assumption regarding the independence of the considered datasets is generally regarded as being too strong in the context of sequential simulation. To alleviate these problems, we have revisited the classical implementation of BSS and incorporated two key features to increase the computational efficiency. The first feature is a combined quadrant spiral - superblock search, which targets run-time savings on large grids and adds flexibility with regard to the selection of neighboring points using equal directional sampling and treating hard data and previously simulated points separately. The second feature is a constant path of simulation, which enhances the efficiency for multiple realizations. We have also modified the aggregation operator to be more flexible with regard to the assumption of independence of the considered datasets. This is achieved through log-linear pooling, which essentially allows for attributing weights to the various data components. Finally, a multi-grid simulating path was created to enforce large-scale variance and to allow for adapting parameters, such as, for example, the log-linear weights or the type of simulation path at various scales. The newly implemented search method for kriging reduces the computational cost from an exponential dependence with regard to the grid size in the original algorithm to a linear relationship, as each neighboring search becomes independent from the grid size. For the considered examples, our results show a sevenfold reduction in run time for each additional realization when a constant simulation path is used. The traditional criticism that constant path techniques introduce a bias to the simulations was explored and our findings do indeed reveal a minor reduction in the diversity of the simulations. This bias can, however, be largely eliminated by changing the path type at different scales through the use of the multi-grid approach. Finally, we show that adapting the aggregation weight at each scale considered in our multi-grid approach allows for reproducing both the variogram and histogram, and the spatial trend of the underlying data.

Comparison of Monte Carlo simulation of gamma ray attenuation coefficients of amino acids with XCOM program and experimental data

NASA Astrophysics Data System (ADS)

Elbashir, B. O.; Dong, M. G.; Sayyed, M. I.; Issa, Shams A. M.; Matori, K. A.; Zaid, M. H. M.

2018-06-01

The mass attenuation coefficients (μ/ρ), effective atomic numbers (Zeff) and electron densities (Ne) of some amino acids obtained experimentally by the other researchers have been calculated using MCNP5 simulations in the energy range 0.122-1.330 MeV. The simulated values of μ/ρ, Zeff, and Ne were compared with the previous experimental work for the amino acids samples and a good agreement was noticed. Moreover, the values of mean free path (MFP) for the samples were calculated using MCNP5 program and compared with the theoretical results obtained by XCOM. The investigation of μ/ρ, Zeff, Ne and MFP values of amino acids using MCNP5 simulations at various photon energies when compared with the XCOM values and previous experimental data for the amino acids samples revealed that MCNP5 code provides accurate photon interaction parameters for amino acids.

Simulating Mission Command for Planning and Analysis

DTIC Science & Technology

2015-06-01

mission plan. 14. SUBJECT TERMS Mission Planning, CPM , PERT, Simulation, DES, Simkit, Triangle Distribution, Critical Path 15. NUMBER OF...Battalion Task Force CO Company CPM Critical Path Method DES Discrete Event Simulation FA BAT Field Artillery Battalion FEL Future Event List FIST...management tools that can be utilized to find the critical path in military projects. These are the Critical Path Method ( CPM ) and the Program Evaluation and

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

PubMed

Hobolth, Asger; Stone, Eric A

2009-09-01

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

Path selection system simulation and evaluation for a Martian roving vehicle

NASA Technical Reports Server (NTRS)

Boheim, S. L.; Prudon, W. C.

1972-01-01

The simulation and evaluation of proposed path selection systems for an autonomous Martian roving vehicle was developed. The package incorporates a number of realistic features, such as the simulation of random effects due to vehicle bounce and sensor-reading uncertainty, to increase the reliability of the results. Qualitative and quantitative evaluation criteria were established. The performance of three different path selection systems was evaluated to determine the effectiveness of the simulation package, and to form some preliminary conclusions regarding the tradeoffs involved in a path selection system design.

Design and simulation of a descent controller for strategic four-dimensional aircraft navigation. M.S. Thesis

NASA Technical Reports Server (NTRS)

Lax, F. M.

1975-01-01

A time-controlled navigation system applicable to the descent phase of flight for airline transport aircraft was developed and simulated. The design incorporates the linear discrete-time sampled-data version of the linearized continuous-time system describing the aircraft's aerodynamics. Using optimal linear quadratic control techniques, an optimal deterministic control regulator which is implementable on an airborne computer is designed. The navigation controller assists the pilot in complying with assigned times of arrival along a four-dimensional flight path in the presence of wind disturbances. The strategic air traffic control concept is also described, followed by the design of a strategic control descent path. A strategy for determining possible times of arrival at specified waypoints along the descent path and for generating the corresponding route-time profiles that are within the performance capabilities of the aircraft is presented. Using a mathematical model of the Boeing 707-320B aircraft along with a Boeing 707 cockpit simulator interfaced with an Adage AGT-30 digital computer, a real-time simulation of the complete aircraft aerodynamics was achieved. The strategic four-dimensional navigation controller for longitudinal dynamics was tested on the nonlinear aircraft model in the presence of 15, 30, and 45 knot head-winds. The results indicate that the controller preserved the desired accuracy and precision of a time-controlled aircraft navigation system.

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

PubMed

Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca

2015-01-01

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.

Influence of the Strain History on TWIP Steel Deformation Mechanisms in the Deep-Drawing Process

NASA Astrophysics Data System (ADS)

Lapovok, R.; Timokhina, I.; Mester, A.-K.; Weiss, M.; Shekhter, A.

2018-03-01

A study of preferable deformation modes on strain path and strain level in a TWIP steel sheet was performed. Different strain paths were obtained by stretch forming of specimens with various shapes and tensile tests. TEM analysis was performed on samples cut from various locations in the deformed specimens, which had different strain paths and strain levels and the preferable deformation modes were identified. Stresses caused by various strain paths were considered and an analytical analysis performed to identify the preferable deformation modes for the case of single crystal. For a single crystal, in assumption of the absence of lattice rotation, the strain path and the level of accumulated equivalent strain define the preferable deformation mode. For a polycrystalline material, such analytical analysis is not possible due to the large number of grains and, therefore, numerical simulation was employed. For the polycrystalline material, the role of strain path diminishes due to the presence of a large number of grains with random orientations and the effect of accumulated strain becomes dominant. However, at small strains the strain path still defines the level of twinning activity. TEM analysis experimentally confirmed that various deformation modes lead to different deformation strengthening mechanisms.

Influence of the Strain History on TWIP Steel Deformation Mechanisms in the Deep-Drawing Process

NASA Astrophysics Data System (ADS)

Lapovok, R.; Timokhina, I.; Mester, A.-K.; Weiss, M.; Shekhter, A.

2018-06-01

A study of preferable deformation modes on strain path and strain level in a TWIP steel sheet was performed. Different strain paths were obtained by stretch forming of specimens with various shapes and tensile tests. TEM analysis was performed on samples cut from various locations in the deformed specimens, which had different strain paths and strain levels and the preferable deformation modes were identified. Stresses caused by various strain paths were considered and an analytical analysis performed to identify the preferable deformation modes for the case of single crystal. For a single crystal, in assumption of the absence of lattice rotation, the strain path and the level of accumulated equivalent strain define the preferable deformation mode. For a polycrystalline material, such analytical analysis is not possible due to the large number of grains and, therefore, numerical simulation was employed. For the polycrystalline material, the role of strain path diminishes due to the presence of a large number of grains with random orientations and the effect of accumulated strain becomes dominant. However, at small strains the strain path still defines the level of twinning activity. TEM analysis experimentally confirmed that various deformation modes lead to different deformation strengthening mechanisms.

Numerical and experimental study on the wave attenuation in bone--FDTD simulation of ultrasound propagation in cancellous bone.

PubMed

Nagatani, Yoshiki; Mizuno, Katsunori; Saeki, Takashi; Matsukawa, Mami; Sakaguchi, Takefumi; Hosoi, Hiroshi

2008-11-01

In cancellous bone, longitudinal waves often separate into fast and slow waves depending on the alignment of bone trabeculae in the propagation path. This interesting phenomenon becomes an effective tool for the diagnosis of osteoporosis because wave propagation behavior depends on the bone structure. Since the fast wave mainly propagates in trabeculae, this wave is considered to reflect the structure of trabeculae. For a new diagnosis method using the information of this fast wave, therefore, it is necessary to understand the generation mechanism and propagation behavior precisely. In this study, the generation process of fast wave was examined by numerical simulations using elastic finite-difference time-domain (FDTD) method and experimental measurements. As simulation models, three-dimensional X-ray computer tomography (CT) data of actual bone samples were used. Simulation and experimental results showed that the attenuation of fast wave was always higher in the early state of propagation, and they gradually decreased as the wave propagated in bone. This phenomenon is supposed to come from the complicated propagating paths of fast waves in cancellous bone.

Analysis of explicit model predictive control for path-following control

PubMed Central

2018-01-01

In this paper, explicit Model Predictive Control(MPC) is employed for automated lane-keeping systems. MPC has been regarded as the key to handle such constrained systems. However, the massive computational complexity of MPC, which employs online optimization, has been a major drawback that limits the range of its target application to relatively small and/or slow problems. Explicit MPC can reduce this computational burden using a multi-parametric quadratic programming technique(mp-QP). The control objective is to derive an optimal front steering wheel angle at each sampling time so that autonomous vehicles travel along desired paths, including straight, circular, and clothoid parts, at high entry speeds. In terms of the design of the proposed controller, a method of choosing weighting matrices in an optimization problem and the range of horizons for path-following control are described through simulations. For the verification of the proposed controller, simulation results obtained using other control methods such as MPC, Linear-Quadratic Regulator(LQR), and driver model are employed, and CarSim, which reflects the features of a vehicle more realistically than MATLAB/Simulink, is used for reliable demonstration. PMID:29534080

Analysis of explicit model predictive control for path-following control.

PubMed

Lee, Junho; Chang, Hyuk-Jun

2018-01-01

In this paper, explicit Model Predictive Control(MPC) is employed for automated lane-keeping systems. MPC has been regarded as the key to handle such constrained systems. However, the massive computational complexity of MPC, which employs online optimization, has been a major drawback that limits the range of its target application to relatively small and/or slow problems. Explicit MPC can reduce this computational burden using a multi-parametric quadratic programming technique(mp-QP). The control objective is to derive an optimal front steering wheel angle at each sampling time so that autonomous vehicles travel along desired paths, including straight, circular, and clothoid parts, at high entry speeds. In terms of the design of the proposed controller, a method of choosing weighting matrices in an optimization problem and the range of horizons for path-following control are described through simulations. For the verification of the proposed controller, simulation results obtained using other control methods such as MPC, Linear-Quadratic Regulator(LQR), and driver model are employed, and CarSim, which reflects the features of a vehicle more realistically than MATLAB/Simulink, is used for reliable demonstration.

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

PubMed Central

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

2011-01-01

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

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

PubMed

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

2011-02-17

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

Comparison study of photon attenuation characteristics of Lead-Boron Polyethylene by MCNP code, XCOM and experimental data

NASA Astrophysics Data System (ADS)

Zhang, Lei; Jia, Mingchun; Gong, Junjun; Xia, Wenming

2017-08-01

The linear attenuation coefficient, mass attenuation coefficient and mean free path of various Lead-Boron Polyethylene (PbBPE) samples which can be used as the photon shielding materials in marine reactor have been simulated using the Monte Carlo N-Particle (MCNP)-5 code. The MCNP simulation results are in good agreement with the XCOM values and the reported experimental data for source Cesium-137 and Cobalt-60. Thus, this method based on MCNP can be used to simulate the photon attenuation characteristics of various types of PbBPE materials.

A Framework for Simulation of Aircraft Flyover Noise Through a Non-Standard Atmosphere

NASA Technical Reports Server (NTRS)

Arntzen, Michael; Rizzi, Stephen A.; Visser, Hendrikus G.; Simons, Dick G.

2012-01-01

This paper describes a new framework for the simulation of aircraft flyover noise through a non-standard atmosphere. Central to the framework is a ray-tracing algorithm which defines multiple curved propagation paths, if the atmosphere allows, between the moving source and listener. Because each path has a different emission angle, synthesis of the sound at the source must be performed independently for each path. The time delay, spreading loss and absorption (ground and atmosphere) are integrated along each path, and applied to each synthesized aircraft noise source to simulate a flyover. A final step assigns each resulting signal to its corresponding receiver angle for the simulation of a flyover in a virtual reality environment. Spectrograms of the results from a straight path and a curved path modeling assumption are shown. When the aircraft is at close range, the straight path results are valid. Differences appear especially when the source is relatively far away at shallow elevation angles. These differences, however, are not significant in common sound metrics. While the framework used in this work performs off-line processing, it is conducive to real-time implementation.

Annealed importance sampling with constant cooling rate

NASA Astrophysics Data System (ADS)

Giovannelli, Edoardo; Cardini, Gianni; Gellini, Cristina; Pietraperzia, Giangaetano; Chelli, Riccardo

2015-02-01

Annealed importance sampling is a simulation method devised by Neal [Stat. Comput. 11, 125 (2001)] to assign weights to configurations generated by simulated annealing trajectories. In particular, the equilibrium average of a generic physical quantity can be computed by a weighted average exploiting weights and estimates of this quantity associated to the final configurations of the annealed trajectories. Here, we review annealed importance sampling from the perspective of nonequilibrium path-ensemble averages [G. E. Crooks, Phys. Rev. E 61, 2361 (2000)]. The equivalence of Neal's and Crooks' treatments highlights the generality of the method, which goes beyond the mere thermal-based protocols. Furthermore, we show that a temperature schedule based on a constant cooling rate outperforms stepwise cooling schedules and that, for a given elapsed computer time, performances of annealed importance sampling are, in general, improved by increasing the number of intermediate temperatures.

Nonequilibrium umbrella sampling in spaces of many order parameters

NASA Astrophysics Data System (ADS)

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

2009-02-01

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

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

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2008-01-01

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

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

PubMed

Kamberaj, Hiqmet

2018-05-01

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

Development of an Implantable WBAN Path-Loss Model for Capsule Endoscopy

NASA Astrophysics Data System (ADS)

Aoyagi, Takahiro; Takizawa, Kenichi; Kobayashi, Takehiko; Takada, Jun-Ichi; Hamaguchi, Kiyoshi; Kohno, Ryuji

An implantable WBAN path-loss model for a capsule endoscopy which is used for examining digestive organs, is developed by conducting simulations and experiments. First, we performed FDTD simulations on implant WBAN propagation by using a numerical human model. Second, we performed FDTD simulations on a vessel that represents the human body. Third, we performed experiments using a vessel of the same dimensions as that used in the simulations. On the basis of the results of these simulations and experiments, we proposed the gradient and intercept parameters of the simple path-loss in-body propagation model.

Developing effective sampling designs for monitoring natural resources in Alaskan national parks: an example using simulations and vegetation data

USGS Publications Warehouse

Thompson, William L.; Miller, Amy E.; Mortenson, Dorothy C.; Woodward, Andrea

2011-01-01

Monitoring natural resources in Alaskan national parks is challenging because of their remoteness, limited accessibility, and high sampling costs. We describe an iterative, three-phased process for developing sampling designs based on our efforts to establish a vegetation monitoring program in southwest Alaska. In the first phase, we defined a sampling frame based on land ownership and specific vegetated habitats within the park boundaries and used Path Distance analysis tools to create a GIS layer that delineated portions of each park that could be feasibly accessed for ground sampling. In the second phase, we used simulations based on landcover maps to identify size and configuration of the ground sampling units (single plots or grids of plots) and to refine areas to be potentially sampled. In the third phase, we used a second set of simulations to estimate sample size and sampling frequency required to have a reasonable chance of detecting a minimum trend in vegetation cover for a specified time period and level of statistical confidence. Results of the first set of simulations indicated that a spatially balanced random sample of single plots from the most common landcover types yielded the most efficient sampling scheme. Results of the second set of simulations were compared with field data and indicated that we should be able to detect at least a 25% change in vegetation attributes over 31. years by sampling 8 or more plots per year every five years in focal landcover types. This approach would be especially useful in situations where ground sampling is restricted by access.

Sensor-Oriented Path Planning for Multiregion Surveillance with a Single Lightweight UAV SAR

PubMed Central

Li, Jincheng; Chen, Jie; Wang, Pengbo; Li, Chunsheng

2018-01-01

In the surveillance of interested regions by unmanned aerial vehicle (UAV), system performance relies greatly on the motion control strategy of the UAV and the operation characteristics of the onboard sensors. This paper investigates the 2D path planning problem for the lightweight UAV synthetic aperture radar (SAR) system in an environment of multiple regions of interest (ROIs), the sizes of which are comparable to the radar swath width. Taking into account the special requirements of the SAR system on the motion of the platform, we model path planning for UAV SAR as a constrained multiobjective optimization problem (MOP). Based on the fact that the UAV route can be designed in the map image, an image-based path planner is proposed in this paper. First, the neighboring ROIs are merged by the morphological operation. Then, the parts of routes for data collection of the ROIs can be located according to the geometric features of the ROIs and the observation geometry of UAV SAR. Lastly, the route segments for ROIs surveillance are connected by a path planning algorithm named the sampling-based sparse A* search (SSAS) algorithm. Simulation experiments in real scenarios demonstrate that the proposed sensor-oriented path planner can improve the reconnaissance performance of lightweight UAV SAR greatly compared with the conventional zigzag path planner. PMID:29439447

Sensor-Oriented Path Planning for Multiregion Surveillance with a Single Lightweight UAV SAR.

PubMed

Li, Jincheng; Chen, Jie; Wang, Pengbo; Li, Chunsheng

2018-02-11

In the surveillance of interested regions by unmanned aerial vehicle (UAV), system performance relies greatly on the motion control strategy of the UAV and the operation characteristics of the onboard sensors. This paper investigates the 2D path planning problem for the lightweight UAV synthetic aperture radar (SAR) system in an environment of multiple regions of interest (ROIs), the sizes of which are comparable to the radar swath width. Taking into account the special requirements of the SAR system on the motion of the platform, we model path planning for UAV SAR as a constrained multiobjective optimization problem (MOP). Based on the fact that the UAV route can be designed in the map image, an image-based path planner is proposed in this paper. First, the neighboring ROIs are merged by the morphological operation. Then, the parts of routes for data collection of the ROIs can be located according to the geometric features of the ROIs and the observation geometry of UAV SAR. Lastly, the route segments for ROIs surveillance are connected by a path planning algorithm named the sampling-based sparse A* search (SSAS) algorithm. Simulation experiments in real scenarios demonstrate that the proposed sensor-oriented path planner can improve the reconnaissance performance of lightweight UAV SAR greatly compared with the conventional zigzag path planner.

SSAGES: Software Suite for Advanced General Ensemble Simulations.

PubMed

Sidky, Hythem; Colón, Yamil J; Helfferich, Julian; Sikora, Benjamin J; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S; Reid, Daniel R; Sevgen, Emre; Thapar, Vikram; Webb, Michael A; Whitmer, Jonathan K; de Pablo, Juan J

2018-01-28

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

Laboratory simulation of irradiation-induced dielectric breakdown in spacecraft charging

NASA Technical Reports Server (NTRS)

Yadlowsky, E. J.; Churchill, R. J.; Hazelton, R. C.

1980-01-01

The discharging of dielectric samples irradiated by a beam of monoenergetic electrons is investigated. The development of a model, or models, which describe the discharge phenomena occuring on the irradiated dielectric targets is discussed. The electrical discharge characteristics of irradiated dielectric samples are discussed and the electrical discharge paths along dielectric surfaces and within the dielectric material are determined. The origin and destination of the surface emitted particles is examined and the charge and energy balance in the system is evaluated.

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

PubMed Central

Ovchinnikov, Victor; Karplus, Martin

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

Ovchinnikov, Victor; Karplus, Martin

2014-05-01

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

Methodology for Augmenting Existing Paths with Additional Parallel Transects

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

Wilson, John E.

2013-09-30

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

Pitch attitude, flight path, and airspeed control during approach and landing of a powered lift STOL aircraft

NASA Technical Reports Server (NTRS)

Franklin, J. A.; Innis, R. C.

1972-01-01

Analytical investigations and piloted moving base simulator evaluations were conducted for manual control of pitch attitude, flight path, and airspeed for the approach and landing of a powered lift jet STOL aircraft. Flight path and speed response characteristics were described analytically and were evaluated for the simulation experiments which were carried out on a large motion simulator. The response characteristics were selected and evaluated for a specified path and speed control technique. These charcteristics were: (1) the initial pitch response and steady pitch rate sensitivity for control of attitude with a pitch rate command/ attitude hold system, (2) the initial flight path response, flight path overshoot, and flight path-airspeed coupling in response to a change in thrust, and (3) the sensitivity of airspeed to pitch attitude changes. Results are presented in the form of pilot opinion ratings and commentary, substantiated where appropriate by response time histories and aircraft states at the point of touchdown.

Spectroscopic fingerprints of toroidal nuclear quantum delocalization via ab initio path integral simulations.

PubMed

Schütt, Ole; Sebastiani, Daniel

2013-04-05

We investigate the quantum-mechanical delocalization of hydrogen in rotational symmetric molecular systems. To this purpose, we perform ab initio path integral molecular dynamics simulations of a methanol molecule to characterize the quantum properties of hydrogen atoms in a representative system by means of their real-space and momentum-space densities. In particular, we compute the spherically averaged momentum distribution n(k) and the pseudoangular momentum distribution n(kθ). We interpret our results by comparing them to path integral samplings of a bare proton in an ideal torus potential. We find that the hydroxyl hydrogen exhibits a toroidal delocalization, which leads to characteristic fingerprints in the line shapes of the momentum distributions. We can describe these specific spectroscopic patterns quantitatively and compute their onset as a function of temperature and potential energy landscape. The delocalization patterns in the projected momentum distribution provide a promising computational tool to address the intriguing phenomenon of quantum delocalization in condensed matter and its spectroscopic characterization. As the momentum distribution n(k) is also accessible through Nuclear Compton Scattering experiments, our results will help to interpret and understand future measurements more thoroughly. Copyright © 2012 Wiley Periodicals, Inc.

Reconfigurable radio receiver with fractional sample rate converter and multi-rate ADC based on LO-derived sampling clock

NASA Astrophysics Data System (ADS)

Park, Sungkyung; Park, Chester Sungchung

2018-03-01

A composite radio receiver back-end and digital front-end, made up of a delta-sigma analogue-to-digital converter (ADC) with a high-speed low-noise sampling clock generator, and a fractional sample rate converter (FSRC), is proposed and designed for a multi-mode reconfigurable radio. The proposed radio receiver architecture contributes to saving the chip area and thus lowering the design cost. To enable inter-radio access technology handover and ultimately software-defined radio reception, a reconfigurable radio receiver consisting of a multi-rate ADC with its sampling clock derived from a local oscillator, followed by a rate-adjustable FSRC for decimation, is designed. Clock phase noise and timing jitter are examined to support the effectiveness of the proposed radio receiver. A FSRC is modelled and simulated with a cubic polynomial interpolator based on Lagrange method, and its spectral-domain view is examined in order to verify its effect on aliasing, nonlinearity and signal-to-noise ratio, giving insight into the design of the decimation chain. The sampling clock path and the radio receiver back-end data path are designed in a 90-nm CMOS process technology with 1.2V supply.

The tropical forest and fire emissions experiment: Laboratory fire measurement and synthesis of campaign data

Treesearch

R. J. Yokelson; T. J. Christian; T. G. Karl; A. Guenther

2008-01-01

As part of the Tropical Forest and Fire Emissions Experiment (TROFFEE), tropical forest fuels were burned in a large, biomass-fire simulation facility and the smoke was characterized with open-path Fourier transform infrared spectroscopy (FTIR), proton-transfer reaction mass spectrometry (PTR-MS), gas chromatography (GC), GC/PTRMS, and filter sampling of the particles...

Planning Under Uncertainty: Methods and Applications

DTIC Science & Technology

2010-06-09

begun research into fundamental algorithms for optimization and re?optimization of continuous optimization problems (such as linear and quadratic... algorithm yields a 14.3% improvement over the original design while saving 68.2 % of the simulation evaluations compared to standard sample-path...They provide tools for building and justifying computational algorithms for such problems. Year. 2010 Month: 03 Final Research under this grant

Influence of particle shape on the microstructure evolution and the mechanical properties of granular materials

NASA Astrophysics Data System (ADS)

Tian, Jianqiu; Liu, Enlong; Jiang, Lian; Jiang, Xiaoqiong; Sun, Yi; Xu, Ran

2018-06-01

In order to study the influence of particle shape on the microstructure evolution and the mechanical properties of granular materials, a two-dimensional DEM analysis of samples with three particle shapes, including circular particles, triangular particles, and elongated particles, is proposed here to simulate the direct shear tests of coarse-grained soils. For the numerical test results, analyses are conducted in terms of particle rotations, fabric evolution, and average path length evolution. A modified Rowe's stress-dilatancy equation is also proposed and successfully fitted onto simulation data.

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Kremer, Kurt; Potestio, Raffaello; Tuckerman, Mark E.

2017-12-01

Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

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

Akagi, Sheryl; Burling, Ian R.; Mendoza, Albert

We report trace-gas emission factors from three pine-understory prescribed fires in South Carolina, U.S. measured during the fall of 2011. The fires were an attempt to simulate high-intensity burns and the fuels included mature pine stands not frequently subjected to prescribed fire that were lit following a sustained period of drought. In this work we focus on the emission factor measurements made using a fixed open-path gas analyzer Fourier transform infrared (FTIR) system. We compare these emission factors with those measured using a roving, point sampling, land-based FTIR and an airborne FTIR that were deployed on the same fires. Wemore » also compare to emission factors measured by a similar open-path FTIR system deployed on savanna fires in Africa. The data suggest that the method in which the smoke is sampled can strongly influence the relative abundance of the emissions that are observed. The airborne FTIR probed the bulk of the emissions, which were lofted in the convection column and the downwind chemistry while the roving ground-based point sampling FTIR measured the contribution of individual residual smoldering combustion fuel elements scattered throughout the burn site. The open-path FTIR provided a fixed path-integrated sample of emissions produced directly upwind mixed with emissions that were redirected by wind gusts, or right after ignition and before the adjacent plume achieved significant vertical development. It typically probed two distinct combustion regimes, “flaming-like” (immediately after adjacent ignition) and “smoldering-like”, denoted “early” and “late”, respectively. The calculated emission factors from open-path measurements were closer to the airborne than to the point measurements, but this could vary depending on the calculation method or from fire to fire given the changing MCE and dynamics over the duration of a typical burn. The emission factors for species whose emissions are not highly fuel dependent (e.g. CH4 and CH3OH) from all three systems can be plotted versus modified combustion efficiency and fit to a single consistent trend suggesting that differences between the systems for these species may be mainly due to the unique mix of flaming and smoldering that each system sampled. For other more fuel dependent species, the different fuels sampled also likely contributed to platform differences in emission factors. The path-integrated sample of the ground-level smoke layer adjacent to the fire provided by the open-path measurements is important for estimating fire-line exposure to smoke for wildland fire personnel. We provide a table of estimated fire-line exposures for numerous known air toxics based on synthesizing results from several studies. Our data suggest that peak exposures are more likely to challenge permissible exposure limits for wildland fire personnel than shift-average exposures.« less

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

DOE PAGES

McGibbon, J.; Bretherton, C. S.

2017-03-17

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

Manual flying of curved precision approaches to landing with electromechanical instrumentation. A piloted simulation study

NASA Technical Reports Server (NTRS)

Knox, Charles E.

1993-01-01

A piloted simulation study was conducted to examine the requirements for using electromechanical flight instrumentation to provide situation information and flight guidance for manually controlled flight along curved precision approach paths to a landing. Six pilots were used as test subjects. The data from these tests indicated that flight director guidance is required for the manually controlled flight of a jet transport airplane on curved approach paths. Acceptable path tracking performance was attained with each of the three situation information algorithms tested. Approach paths with both multiple sequential turns and short final path segments were evaluated. Pilot comments indicated that all the approach paths tested could be used in normal airline operations.

SSAGES: Software Suite for Advanced General Ensemble Simulations

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

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniquesmore » as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.« less

SSAGES: Software Suite for Advanced General Ensemble Simulations

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.

2018-01-01

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

A hydrogeologic approach to identify land uses that overlie ground-water flow paths, Broward County, Florida

USGS Publications Warehouse

Sonenshein, R.S.

1995-01-01

A hydrogeologic approach that integrates the use of hydrogeologic and spatial tools aids in the identification of land uses that overlie ground- water flow paths and permits a better understanding of ground-water flow systems. A mathematical model was used to simulate the ground-water flow system in Broward County, particle-tracking software was used to determine flow paths leading to the monitor wells in Broward County, and a Geographic Information System was used to identify which land uses overlie the flow paths. A procedure using a geographic information system to evaluate the output from a ground-water flow model has been documented. The ground-water flow model was used to represent steady-state conditions during selected wet- and dry-season months, and an advective flow particle- tracking program was used to simulate the direction of ground-water flow in the aquifer system. Digital spatial data layers were created from the particle pathlines that lead to the vicinity of the open interval of selected wells in the Broward County ground-water quality monitoring network. Buffer zone data layers were created, surrounding the particle pathlines to represent the area of contribution to the water sampled from the monitor wells. Spatial data layers, combined with a land-use data layer, were used to identify the land uses that overlie the ground-water flow paths leading to the monitor wells. The simulation analysis was performed on five Broward County wells with different hydraulic parameters to determine the source of ground-water stress, determine selected particle pathlines, and identify land use in buffer zones in the vicinity of the wells. The flow paths that lead to the grid cells containing wells G-2355, G-2373, and G-2373A did not vary between the wet- and dry-season conditions. Changes in the area of contribution for wells G-2345X and G-2369 were attributed to variations in rainfall patterns, well-field pumpage, and surface-water management practices. Additionally, using a different open interval at a site, such as for wells G-2373 and G-2373A, can result in a very different area that overlies the flow path leading to the monitor well.

Generation of RGB-D data for SLAM using robotic framework V-REP

NASA Astrophysics Data System (ADS)

Gritsenko, Pavel S.; Gritsenko, Igor S.; Seidakhmet, Askar Zh.; Abduraimov, Azizbek E.

2017-09-01

In this article, we will present a methodology to debug RGB-D SLAM systems as well as to generate testing data. We have created a model of a laboratory with an area of 250 m2 (25 × 10) with set of objects of different type. V-REP Microsoft Kinect sensor simulation model was used as a basis for robot vision system. Motion path of the sensor model has multiple loops. We have written a program in V-Rep native language Lua to record data array from the Microsoft Kinect sensor model. The array includes both RGB and Depth streams with full resolution (640 × 480) for every 10 cm of the path. The simulated path has absolute accuracy, since it is a simulation, and is represented by an array of transformation matrices (4 × 4). The length of the data array is 1000 steps or 100 m. The path simulates frequently occurring cases in SLAM, including loops. It is worth noting that the path was modeled for a mobile robot and it is represented by a 2D path parallel to the floor at a height of 40 cm.

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

PubMed Central

Cao, Youfang; Liang, Jie

2013-01-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape. PMID:23862966

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

NASA Astrophysics Data System (ADS)

Cao, Youfang; Liang, Jie

2013-07-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method.

PubMed

Cao, Youfang; Liang, Jie

2013-07-14

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

Combined Monte Carlo and path-integral method for simulated library of time-resolved reflectance curves from layered tissue models

NASA Astrophysics Data System (ADS)

Wilson, Robert H.; Vishwanath, Karthik; Mycek, Mary-Ann

2009-02-01

Monte Carlo (MC) simulations are considered the "gold standard" for mathematical description of photon transport in tissue, but they can require large computation times. Therefore, it is important to develop simple and efficient methods for accelerating MC simulations, especially when a large "library" of related simulations is needed. A semi-analytical method involving MC simulations and a path-integral (PI) based scaling technique generated time-resolved reflectance curves from layered tissue models. First, a zero-absorption MC simulation was run for a tissue model with fixed scattering properties in each layer. Then, a closed-form expression for the average classical path of a photon in tissue was used to determine the percentage of time that the photon spent in each layer, to create a weighted Beer-Lambert factor to scale the time-resolved reflectance of the simulated zero-absorption tissue model. This method is a unique alternative to other scaling techniques in that it does not require the path length or number of collisions of each photon to be stored during the initial simulation. Effects of various layer thicknesses and absorption and scattering coefficients on the accuracy of the method will be discussed.

Channel Modeling of Miniaturized Battery-Powered Capacitive Human Body Communication Systems.

PubMed

Park, Jiwoong; Garudadri, Harinath; Mercier, Patrick P

2017-02-01

The purpose of this contribution is to estimate the path loss of capacitive human body communication (HBC) systems under practical conditions. Most prior work utilizes large grounded instruments to perform path loss measurements, resulting in overly optimistic path loss estimates for wearable HBC devices. In this paper, small battery-powered transmitter and receiver devices are implemented to measure path loss under realistic assumptions. A hybrid electrostatic finite element method simulation model is presented that validates measurements and enables rapid and accurate characterization of future capacitive HBC systems. Measurements from form-factor-accurate prototypes reveal path loss results between 31.7 and 42.2 dB from 20 to 150 MHz. Simulation results matched measurements within 2.5 dB. Comeasurements using large grounded benchtop vector network analyzer (VNA) and large battery-powered spectrum analyzer (SA) underestimate path loss by up to 33.6 and 8.2 dB, respectively. Measurements utilizing a VNA with baluns, or large battery-powered SAs with baluns still underestimate path loss by up to 24.3 and 6.7 dB, respectively. Measurements of path loss in capacitive HBC systems strongly depend on instrumentation configurations. It is thus imperative to simulate or measure path loss in capacitive HBC systems utilizing realistic geometries and grounding configurations. HBC has a great potential for many emerging wearable devices and applications; accurate path loss estimation will improve system-level design leading to viable products.

Multivariate statistical analysis and hydrogeochemical modelling of seawater-freshwater mixing along selected flow paths: Case of Korba coastal aquifer Tunisia

NASA Astrophysics Data System (ADS)

Slama, Fairouz; Bouhlila, Rachida

2017-11-01

Groundwater sampling and piezometric measurements were carried out along two flow paths (corresponding to two transects) in Korba coastal plain (Northeast of Tunisia). The study aims to identify hydrochemical processes occurring when seawater and freshwater mix. Those processes can be used as indicators of seawater intrusion progression and freshwater flushing into seawater accompanying Submarine Groundwater Discharge (SGD). Seawater fractions in the groundwater were calculated using the chloride concentration. Hierarchical cluster analysis (HCA) was applied to isolate wells potentially affected by seawater. In addition, PHREEQC was used to simulate the theoretical mixing between two end members: seawater and a fresh-brackish groundwater sample. Geochemical conventional diagrams showed that the groundwater chemistry is explained by a mixing process between two end members. Results also revealed the presence of other geochemical processes, correlated to the hydrodynamic flow paths. Direct cation exchange was linked to seawater intrusion, and reverse cation exchange was associated to the freshwater flushing into seawater. The presence of these processes indicated that seawater intrusion was in progress. An excess of Ca, that could not be explained by only cation exchange processes, was observed in both transects. Dedolomitization combined to gypsum leaching is the possible explanation of the groundwater Ca enrichment. Finally, redox processes were also found to contribute to the groundwater composition along flow paths.

Effects of forming history on crash simulation of a vehicle

NASA Astrophysics Data System (ADS)

Gökler, M. İ.; Doğan, U. Ç.; Darendeliler, H.

2016-08-01

The effects of forming on the crash simulation of a vehicle have been investigated by considering the load paths produced by sheet metal forming process. The frontal crash analysis has been performed by the finite element method, firstly without considering the forming history, to find out the load paths that absorb the highest energy. The sheet metal forming simulations have been realized for each structural component of the load paths and the frontal crash analysis has been repeated by including forming history. The results of the simulations with and without forming effects have been compared with the physical crash test results available in literature.

Stability of simulated flight path control at +3 Gz in a human centrifuge.

PubMed

Guardiera, Simon; Dalecki, Marc; Bock, Otmar

2010-04-01

Earlier studies have shown that naïve subjects and experienced jet pilots produce exaggerated manual forces when exposed to increased acceleration (+Gz). This study was designed to evaluate whether this exaggeration affects the stability of simulated flight path control. We evaluated naïve subjects' performance in a flight simulator which either remained stationary (+1 Gz), or rotated to induce an acceleration in accordance to the simulated flight path with a mean acceleration of about +3 Gz. In either case, subjects were requested to produce a series of altitude changes in pursuit of a visual target airplane. Resulting flight paths were analyzed to determine the largest oscillation after an altitude change (Oscillation) and the mean deviation between subject and target flight path (Tracking Error). Flight stability after an altitude change was degraded in +3 Gz compared to +1 Gz, as evidenced by larger Oscillations (+11%) and increased Tracking Errors (+80%). These deficits correlated significantly with subjects' +3 Gz deficits in a manual-force production task. We conclude that force exaggeration in +3 Gz may impair flight stability during simulated jet maneuvers in naïve subjects, most likely as a consequence of vestibular stimulation.

Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin.

PubMed

Orlowski, Slawomir; Nowak, Wieslaw

2007-07-01

Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.

A path-level exact parallelization strategy for sequential simulation

NASA Astrophysics Data System (ADS)

Peredo, Oscar F.; Baeza, Daniel; Ortiz, Julián M.; Herrero, José R.

2018-01-01

Sequential Simulation is a well known method in geostatistical modelling. Following the Bayesian approach for simulation of conditionally dependent random events, Sequential Indicator Simulation (SIS) method draws simulated values for K categories (categorical case) or classes defined by K different thresholds (continuous case). Similarly, Sequential Gaussian Simulation (SGS) method draws simulated values from a multivariate Gaussian field. In this work, a path-level approach to parallelize SIS and SGS methods is presented. A first stage of re-arrangement of the simulation path is performed, followed by a second stage of parallel simulation for non-conflicting nodes. A key advantage of the proposed parallelization method is to generate identical realizations as with the original non-parallelized methods. Case studies are presented using two sequential simulation codes from GSLIB: SISIM and SGSIM. Execution time and speedup results are shown for large-scale domains, with many categories and maximum kriging neighbours in each case, achieving high speedup results in the best scenarios using 16 threads of execution in a single machine.

A hip joint simulator study using simplified loading and motion cycles generating physiological wear paths and rates.

PubMed

Barbour, P S; Stone, M H; Fisher, J

1999-01-01

In some designs of hip joint simulator the cost of building a highly complex machine has been offset with the requirement for a large number of test stations. The application of the wear results generated by these machines depends on their ability to reproduce physiological wear rates and processes. In this study a hip joint simulator has been shown to reproduce physiological wear using only one load vector and two degrees of motion with simplified input cycles. The actual path of points on the femoral head relative to the acetabular cup were calculated and compared for physiological and simplified input cycles. The in vitro wear rates were found to be highly dependent on the shape of these paths and similarities could be drawn between the shape of the physiological paths and the simplified elliptical paths.

Path-integral method for the source apportionment of photochemical pollutants

NASA Astrophysics Data System (ADS)

Dunker, A. M.

2015-06-01

A new, path-integral method is presented for apportioning the concentrations of pollutants predicted by a photochemical model to emissions from different sources. A novel feature of the method is that it can apportion the difference in a species concentration between two simulations. For example, the anthropogenic ozone increment, which is the difference between a simulation with all emissions present and another simulation with only the background (e.g., biogenic) emissions included, can be allocated to the anthropogenic emission sources. The method is based on an existing, exact mathematical equation. This equation is applied to relate the concentration difference between simulations to line or path integrals of first-order sensitivity coefficients. The sensitivities describe the effects of changing the emissions and are accurately calculated by the decoupled direct method. The path represents a continuous variation of emissions between the two simulations, and each path can be viewed as a separate emission-control strategy. The method does not require auxiliary assumptions, e.g., whether ozone formation is limited by the availability of volatile organic compounds (VOCs) or nitrogen oxides (NOx), and can be used for all the species predicted by the model. A simplified configuration of the Comprehensive Air Quality Model with Extensions (CAMx) is used to evaluate the accuracy of different numerical integration procedures and the dependence of the source contributions on the path. A Gauss-Legendre formula using three or four points along the path gives good accuracy for apportioning the anthropogenic increments of ozone, nitrogen dioxide, formaldehyde, and nitric acid. Source contributions to these increments were obtained for paths representing proportional control of all anthropogenic emissions together, control of NOx emissions before VOC emissions, and control of VOC emissions before NOx emissions. There are similarities in the source contributions from the three paths but also differences due to the different chemical regimes resulting from the emission-control strategies.

Path-integral method for the source apportionment of photochemical pollutants

NASA Astrophysics Data System (ADS)

Dunker, A. M.

2014-12-01

A new, path-integral method is presented for apportioning the concentrations of pollutants predicted by a photochemical model to emissions from different sources. A novel feature of the method is that it can apportion the difference in a species concentration between two simulations. For example, the anthropogenic ozone increment, which is the difference between a simulation with all emissions present and another simulation with only the background (e.g., biogenic) emissions included, can be allocated to the anthropogenic emission sources. The method is based on an existing, exact mathematical equation. This equation is applied to relate the concentration difference between simulations to line or path integrals of first-order sensitivity coefficients. The sensitivities describe the effects of changing the emissions and are accurately calculated by the decoupled direct method. The path represents a continuous variation of emissions between the two simulations, and each path can be viewed as a separate emission-control strategy. The method does not require auxiliary assumptions, e.g., whether ozone formation is limited by the availability of volatile organic compounds (VOC's) or nitrogen oxides (NOx), and can be used for all the species predicted by the model. A simplified configuration of the Comprehensive Air Quality Model with Extensions is used to evaluate the accuracy of different numerical integration procedures and the dependence of the source contributions on the path. A Gauss-Legendre formula using 3 or 4 points along the path gives good accuracy for apportioning the anthropogenic increments of ozone, nitrogen dioxide, formaldehyde, and nitric acid. Source contributions to these increments were obtained for paths representing proportional control of all anthropogenic emissions together, control of NOx emissions before VOC emissions, and control of VOC emissions before NOx emissions. There are similarities in the source contributions from the three paths but also differences due to the different chemical regimes resulting from the emission-control strategies.

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics

NASA Astrophysics Data System (ADS)

Tao, Xuecheng; Shushkov, Philip; Miller, Thomas F.

2018-03-01

We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation. An advantage of the isomorphic Hamiltonian is that it can easily be combined with existing mixed quantum-classical dynamics methods, such as surface hopping or Ehrenfest dynamics, to enable the simulation of electronically non-adiabatic processes with nuclear quantum effects. We present numerical applications of the isomorphic Hamiltonian to model two- and three-level systems, with encouraging results that include improvement upon a previously reported combination of RPMD with surface hopping in the deep-tunneling regime.

Multiple point statistical simulation using uncertain (soft) conditional data

NASA Astrophysics Data System (ADS)

Hansen, Thomas Mejer; Vu, Le Thanh; Mosegaard, Klaus; Cordua, Knud Skou

2018-05-01

Geostatistical simulation methods have been used to quantify spatial variability of reservoir models since the 80s. In the last two decades, state of the art simulation methods have changed from being based on covariance-based 2-point statistics to multiple-point statistics (MPS), that allow simulation of more realistic Earth-structures. In addition, increasing amounts of geo-information (geophysical, geological, etc.) from multiple sources are being collected. This pose the problem of integration of these different sources of information, such that decisions related to reservoir models can be taken on an as informed base as possible. In principle, though difficult in practice, this can be achieved using computationally expensive Monte Carlo methods. Here we investigate the use of sequential simulation based MPS simulation methods conditional to uncertain (soft) data, as a computational efficient alternative. First, it is demonstrated that current implementations of sequential simulation based on MPS (e.g. SNESIM, ENESIM and Direct Sampling) do not account properly for uncertain conditional information, due to a combination of using only co-located information, and a random simulation path. Then, we suggest two approaches that better account for the available uncertain information. The first make use of a preferential simulation path, where more informed model parameters are visited preferentially to less informed ones. The second approach involves using non co-located uncertain information. For different types of available data, these approaches are demonstrated to produce simulation results similar to those obtained by the general Monte Carlo based approach. These methods allow MPS simulation to condition properly to uncertain (soft) data, and hence provides a computationally attractive approach for integration of information about a reservoir model.

Environmental factors and flow paths related to Escherichia coli concentrations at two beaches on Lake St. Clair, Michigan, 2002–2005

USGS Publications Warehouse

Holtschlag, David J.; Shively, Dawn; Whitman, Richard L.; Haack, Sheridan K.; Fogarty, Lisa R.

2008-01-01

Regression analyses and hydrodynamic modeling were used to identify environmental factors and flow paths associated with Escherichia coli (E. coli) concentrations at Memorial and Metropolitan Beaches on Lake St. Clair in Macomb County, Mich. Lake St. Clair is part of the binational waterway between the United States and Canada that connects Lake Huron with Lake Erie in the Great Lakes Basin. Linear regression, regression-tree, and logistic regression models were developed from E. coli concentration and ancillary environmental data. Linear regression models on log10 E. coli concentrations indicated that rainfall prior to sampling, water temperature, and turbidity were positively associated with bacteria concentrations at both beaches. Flow from Clinton River, changes in water levels, wind conditions, and log10 E. coli concentrations 2 days before or after the target bacteria concentrations were statistically significant at one or both beaches. In addition, various interaction terms were significant at Memorial Beach. Linear regression models for both beaches explained only about 30 percent of the variability in log10 E. coli concentrations. Regression-tree models were developed from data from both Memorial and Metropolitan Beaches but were found to have limited predictive capability in this study. The results indicate that too few observations were available to develop reliable regression-tree models. Linear logistic models were developed to estimate the probability of E. coli concentrations exceeding 300 most probable number (MPN) per 100 milliliters (mL). Rainfall amounts before bacteria sampling were positively associated with exceedance probabilities at both beaches. Flow of Clinton River, turbidity, and log10 E. coli concentrations measured before or after the target E. coli measurements were related to exceedances at one or both beaches. The linear logistic models were effective in estimating bacteria exceedances at both beaches. A receiver operating characteristic (ROC) analysis was used to determine cut points for maximizing the true positive rate prediction while minimizing the false positive rate. A two-dimensional hydrodynamic model was developed to simulate horizontal current patterns on Lake St. Clair in response to wind, flow, and water-level conditions at model boundaries. Simulated velocity fields were used to track hypothetical massless particles backward in time from the beaches along flow paths toward source areas. Reverse particle tracking for idealized steady-state conditions shows changes in expected flow paths and traveltimes with wind speeds and directions from 24 sectors. The results indicate that three to four sets of contiguous wind sectors have similar effects on flow paths in the vicinity of the beaches. In addition, reverse particle tracking was used for transient conditions to identify expected flow paths for 10 E. coli sampling events in 2004. These results demonstrate the ability to track hypothetical particles from the beaches, backward in time, to likely source areas. This ability, coupled with a greater frequency of bacteria sampling, may provide insight into changes in bacteria concentrations between source and sink areas.

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

PubMed

Rydzewski, J; Nowak, W

2016-04-12

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

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

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

Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate ismore » about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.« less

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

PubMed

Gao, Yi Qin

2008-04-07

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

Cooperative path planning for multi-USV based on improved artificial bee colony algorithm

NASA Astrophysics Data System (ADS)

Cao, Lu; Chen, Qiwei

2018-03-01

Due to the complex constraints, more uncertain factors and critical real-time demand of path planning for multiple unmanned surface vehicle (multi-USV), an improved artificial bee colony (I-ABC) algorithm were proposed to solve the model of cooperative path planning for multi-USV. First the Voronoi diagram of battle field space is conceived to generate the optimal area of USVs paths. Then the chaotic searching algorithm is used to initialize the collection of paths, which is regard as foods of the ABC algorithm. With the limited data, the initial collection can search the optimal area of paths perfectly. Finally simulations of the multi-USV path planning under various threats have been carried out. Simulation results verify that the I-ABC algorithm can improve the diversity of nectar source and the convergence rate of algorithm. It can increase the adaptability of dynamic battlefield and unexpected threats for USV.

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

NASA Astrophysics Data System (ADS)

Wang, Ting; Plecháč, Petr

2017-12-01

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

Model-Averaged ℓ1 Regularization using Markov Chain Monte Carlo Model Composition

PubMed Central

Fraley, Chris; Percival, Daniel

2014-01-01

Bayesian Model Averaging (BMA) is an effective technique for addressing model uncertainty in variable selection problems. However, current BMA approaches have computational difficulty dealing with data in which there are many more measurements (variables) than samples. This paper presents a method for combining ℓ1 regularization and Markov chain Monte Carlo model composition techniques for BMA. By treating the ℓ1 regularization path as a model space, we propose a method to resolve the model uncertainty issues arising in model averaging from solution path point selection. We show that this method is computationally and empirically effective for regression and classification in high-dimensional datasets. We apply our technique in simulations, as well as to some applications that arise in genomics. PMID:25642001

Aircraft path planning for optimal imaging using dynamic cost functions

NASA Astrophysics Data System (ADS)

Christie, Gordon; Chaudhry, Haseeb; Kochersberger, Kevin

2015-05-01

Unmanned aircraft development has accelerated with recent technological improvements in sensing and communications, which has resulted in an "applications lag" for how these aircraft can best be utilized. The aircraft are becoming smaller, more maneuverable and have longer endurance to perform sensing and sampling missions, but operating them aggressively to exploit these capabilities has not been a primary focus in unmanned systems development. This paper addresses a means of aerial vehicle path planning to provide a realistic optimal path in acquiring imagery for structure from motion (SfM) reconstructions and performing radiation surveys. This method will allow SfM reconstructions to occur accurately and with minimal flight time so that the reconstructions can be executed efficiently. An assumption is made that we have 3D point cloud data available prior to the flight. A discrete set of scan lines are proposed for the given area that are scored based on visibility of the scene. Our approach finds a time-efficient path and calculates trajectories between scan lines and over obstacles encountered along those scan lines. Aircraft dynamics are incorporated into the path planning algorithm as dynamic cost functions to create optimal imaging paths in minimum time. Simulations of the path planning algorithm are shown for an urban environment. We also present our approach for image-based terrain mapping, which is able to efficiently perform a 3D reconstruction of a large area without the use of GPS data.

Aviation Safety Simulation Model

NASA Technical Reports Server (NTRS)

Houser, Scott; Yackovetsky, Robert (Technical Monitor)

2001-01-01

The Aviation Safety Simulation Model is a software tool that enables users to configure a terrain, a flight path, and an aircraft and simulate the aircraft's flight along the path. The simulation monitors the aircraft's proximity to terrain obstructions, and reports when the aircraft violates accepted minimum distances from an obstruction. This model design facilitates future enhancements to address other flight safety issues, particularly air and runway traffic scenarios. This report shows the user how to build a simulation scenario and run it. It also explains the model's output.

Effect of hurricane paths on storm surge response at Tianjin, China

NASA Astrophysics Data System (ADS)

Feng, Xingru; Yin, Baoshu; Yang, Dezhou

2012-06-01

A hurricane induced storm surge simulation system was developed for Tianjin coast, which consists of a hurricane model and a storm surge model. The peak storm surge result of the simulation agreed well with that of the observation. Three observed paths (Rita, Mimie and WINNIE) and a hypothetical path (Rita2) were chosen as the selective hurricane paths according to their positions relative to Tianjin. The sensitivity of Tianjin storm surge to the four paths was investigated using the validated storm surge simulation system. Three groups of experiments were done. In group one, the models were forced by the wind field and air pressure; in group two and three the models were forced by the wind only and the air pressure only respectively. In the experiments, the hurricane moved with a fixed speed and an intensity of 50 year return period. The simulation results show that path of the type Rita2 is the easiest to cause storm surge disaster in Tianjin, and the effect of air pressure forcing is most evident for path of the type Rita in Tianjin storm surge process. The above conclusions were analyzed through the evolution of the wind fields and the air pressure distributions. Comparing the experiment results of Group one, two and three, it can be seen that the storm surge is mainly induced by the wind forcing and the nonlinear interaction between the effect of wind forcing and air pressure forcing on the storm surge tends to weaken the storm surge.

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions.

PubMed

Jiang, Hao; Haji-Akbari, Amir; Debenedetti, Pablo G; Panagiotopoulos, Athanassios Z

2018-01-28

We used molecular dynamics simulations and the path sampling technique known as forward flux sampling to study homogeneous nucleation of NaCl crystals from supersaturated aqueous solutions at 298 K and 1 bar. Nucleation rates were obtained for a range of salt concentrations for the Joung-Cheatham NaCl force field combined with the Extended Simple Point Charge (SPC/E) water model. The calculated nucleation rates are significantly lower than the available experimental measurements. The estimates for the nucleation rates in this work do not rely on classical nucleation theory, but the pathways observed in the simulations suggest that the nucleation process is better described by classical nucleation theory than an alternative interpretation based on Ostwald's step rule, in contrast to some prior simulations of related models. In addition to the size of NaCl nucleus, we find that the crystallinity of a nascent cluster plays an important role in the nucleation process. Nuclei with high crystallinity were found to have higher growth probability and longer lifetimes, possibly because they are less exposed to hydration water.

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions

NASA Astrophysics Data System (ADS)

Jiang, Hao; Haji-Akbari, Amir; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2018-01-01

We used molecular dynamics simulations and the path sampling technique known as forward flux sampling to study homogeneous nucleation of NaCl crystals from supersaturated aqueous solutions at 298 K and 1 bar. Nucleation rates were obtained for a range of salt concentrations for the Joung-Cheatham NaCl force field combined with the Extended Simple Point Charge (SPC/E) water model. The calculated nucleation rates are significantly lower than the available experimental measurements. The estimates for the nucleation rates in this work do not rely on classical nucleation theory, but the pathways observed in the simulations suggest that the nucleation process is better described by classical nucleation theory than an alternative interpretation based on Ostwald's step rule, in contrast to some prior simulations of related models. In addition to the size of NaCl nucleus, we find that the crystallinity of a nascent cluster plays an important role in the nucleation process. Nuclei with high crystallinity were found to have higher growth probability and longer lifetimes, possibly because they are less exposed to hydration water.

The Microstructural Evolution of Quartzite During Gradually Increasing Stress.

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Geometrical Effect on Thermal Conductivity of Unidirectional Fiber-Reinforced Polymer Composite along Different In-plane Orientations

NASA Astrophysics Data System (ADS)

Fang, Zenong; Li, Min; Wang, Shaokai; Li, Yanxia; Wang, Xiaolei; Gu, Yizhuo; Liu, Qianli; Tian, Jie; Zhang, Zuoguang

2017-11-01

This paper focuses on the anisotropic characteristics of the in-plane thermal conductivity of fiber-reinforced polymer composite based on experiment and simulation. Thermal conductivity along different in-plane orientations was measured by laser flash analysis (LFA) and steady-state heat flow method. Their heat transfer processes were simulated to reveal the geometrical effect on thermal conduction. The results show that the in-plane thermal conduction of unidirectional carbon-fiber-reinforced polymer composite is greatly influenced by the sample geometry at an in-plane orientation angle between 0° to 90°. By defining radius-to-thickness as a dimensionless shape factor for the LFA sample, the apparent thermal conductivity shows a dramatic change when the shape factor is close to the tangent of the orientation angle (tanθ). Based on finite element analysis, this phenomenon was revealed to correlate with the change of the heat transfer process. When the shape factor is larger than tanθ, the apparent thermal conductivity is consistent with the estimated value according to the theoretical model. For a sample with a shape factor smaller than tanθ, the apparent thermal conductivity shows a slow growth around a low value, which seriously deviates from the theory estimation. This phenomenon was revealed to correlate with the change of the heat transfer process from a continuous path to a zigzag path. These results will be helpful in optimizing the ply scheme of composite laminates for thermal management applications.

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

NASA Technical Reports Server (NTRS)

Mccreight, L. R. (Inventor)

1974-01-01

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

Effects of changes in pumping on regional groundwater-flow paths, 2005 and 2010, and areas contributing recharge to discharging wells, 1990–2010, in the vicinity of North Penn Area 7 Superfund site, Montgomery County, Pennsylvania

USGS Publications Warehouse

Senior, Lisa A.; Goode, Daniel J.

2017-06-06

A previously developed regional groundwater flow model was used to simulate the effects of changes in pumping rates on groundwater-flow paths and extent of recharge discharging to wells for a contaminated fractured bedrock aquifer in southeastern Pennsylvania. Groundwater in the vicinity of the North Penn Area 7 Superfund site, Montgomery County, Pennsylvania, was found to be contaminated with organic compounds, such as trichloroethylene (TCE), in 1979. At the time contamination was discovered, groundwater from the underlying fractured bedrock (shale) aquifer was the main source of supply for public drinking water and industrial use. As part of technical support to the U.S. Environmental Protection Agency (EPA) during the Remedial Investigation of the North Penn Area 7 Superfund site from 2000 to 2005, the U.S. Geological Survey (USGS) developed a model of regional groundwater flow to describe changes in groundwater flow and contaminant directions as a result of changes in pumping. Subsequently, large decreases in TCE concentrations (as much as 400 micrograms per liter) were measured in groundwater samples collected by the EPA from selected wells in 2010 compared to 2005‒06 concentrations.To provide insight on the fate of potentially contaminated groundwater during the period of generally decreasing pumping rates from 1990 to 2010, steady-state simulations were run using the previously developed groundwater-flow model for two conditions prior to extensive remediation, 1990 and 2000, two conditions subsequent to some remediation 2005 and 2010, and a No Pumping case, representing pre-development or cessation of pumping conditions. The model was used to (1) quantify the amount of recharge, including potentially contaminated recharge from sources near the land surface, that discharged to wells or streams and (2) delineate the areas contributing recharge that discharged to wells or streams for the five conditions.In all simulations, groundwater divides differed from surface-water divides, partly because of differences in stream elevations and because of geologic structure and pumping. In the 1990 and 2000 simulations, all recharge in and near the vicinity of North Penn Area 7 discharged to wells, but in the 2005 and 2010 simulations some recharge in this area discharged to streams, indicating possible discharge of contaminated groundwater from North Penn Area 7 sources to streams. As the amount of groundwater withdrawals by wells has declined since 1990, the area contributing recharge to wells in the vicinity of North Penn Area 7 has decreased.To determine the effect of changes in pumping on flow paths and possible flow-path-related contributions to the observed changes in spatial distribution of contaminants in groundwater from 2005 to 2010, the USGS conducted simulations using the previously developed regional groundwater-flow model using reported pumping and estimated recharge rates for 2005 and 2010. Flow paths from recharge at known contaminant source areas to discharge locations at wells or streams were simulated under steady-state conditions for the two periods. Simulated groundwater-flow paths shifted only slightly from 2005 to 2010 as a result of changes in pumping rates. These slight changes in groundwater-flow paths from known sources of contamination are not coincident with the spatial distribution of observed changes in TCE concentrations from 2005 to 2010, indicating that the decreases of TCE concentrations may be a result of other processes, such as source removal or degradation. Results of the simulations and the absence of increases in TCE-degradation-product concentrations indicate that the decreases of TCE concentrations observed in 2010 may be at least partly related to contaminant-source removal by soil excavation completed in 2005, although additional data would be needed to confirm this preliminary explanation.

Parameter Uncertainty on AGCM-simulated Tropical Cyclones

NASA Astrophysics Data System (ADS)

He, F.

2015-12-01

This work studies the parameter uncertainty on tropical cyclone (TC) simulations in Atmospheric General Circulation Models (AGCMs) using the Reed-Jablonowski TC test case, which is illustrated in Community Atmosphere Model (CAM). It examines the impact from 24 parameters across the physical parameterization schemes that represent the convection, turbulence, precipitation and cloud processes in AGCMs. The one-at-a-time (OAT) sensitivity analysis method first quantifies their relative importance on TC simulations and identifies the key parameters to the six different TC characteristics: intensity, precipitation, longwave cloud radiative forcing (LWCF), shortwave cloud radiative forcing (SWCF), cloud liquid water path (LWP) and ice water path (IWP). Then, 8 physical parameters are chosen and perturbed using the Latin-Hypercube Sampling (LHS) method. The comparison between OAT ensemble run and LHS ensemble run shows that the simulated TC intensity is mainly affected by the parcel fractional mass entrainment rate in Zhang-McFarlane (ZM) deep convection scheme. The nonlinear interactive effect among different physical parameters is negligible on simulated TC intensity. In contrast, this nonlinear interactive effect plays a significant role in other simulated tropical cyclone characteristics (precipitation, LWCF, SWCF, LWP and IWP) and greatly enlarge their simulated uncertainties. The statistical emulator Extended Multivariate Adaptive Regression Splines (EMARS) is applied to characterize the response functions for nonlinear effect. Last, we find that the intensity uncertainty caused by physical parameters is in a degree comparable to uncertainty caused by model structure (e.g. grid) and initial conditions (e.g. sea surface temperature, atmospheric moisture). These findings suggest the importance of using the perturbed physics ensemble (PPE) method to revisit tropical cyclone prediction under climate change scenario.

Energy consumption of ProTaper Next X1 after glide path with PathFiles and ProGlider.

PubMed

Berutti, Elio; Alovisi, Mario; Pastorelli, Michele Angelo; Chiandussi, Giorgio; Scotti, Nicola; Pasqualini, Damiano

2014-12-01

Instrument failure caused by excessive torsional stress can be controlled by creating a manual or mechanical glide path. The ProGlider single-file system (Dentsply Maillefer, Ballaigues, Switzerland) was recently introduced to perform a mechanical glide path. This study was designed to compare the effect of a glide path performed with PathFiles (Dentsply Maillefer) and ProGlider on torque, time, and pecking motion required for ProTaper Next X1 (Dentsply Maillefer) to reach the full working length in simulated root canals. Forty Endo Training Blocks (Dentsply Maillefer) were used. Twenty were prepared with a mechanical glide path using PathFiles 1 and 2 (the PathFile group), and 20 were prepared with a mechanical glide path using a ProGlider single file (the ProGlider group). All samples were shaped with ProTaper Next X1 driven by an endodontic motor connected to a digital wattmeter. The required torque for root canal instrumentation was analyzed by evaluating the electrical power consumption of the endodontic engine. Electric power consumption (mW/h), elapsed time (seconds), and number of pecking motions required to reach the full working length with ProTaper Next X1 were calculated. Differences among groups were analyzed with the parametric Student t test for independent data (P < .05). Elapsed time and electric power consumption were significantly different between groups (P = .0001 for both). ProGlider appears to perform more efficiently than PathFiles in decreasing electric power consumption of ProTaper Next X1 to reach the full working length. This study confirmed the ability of ProGlider to reduce stress in ProTaper Next X1 during shaping through a glide path and preliminary middle and coronal preflaring. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Variety Wins: Soccer-Playing Robots and Infant Walking.

PubMed

Ossmy, Ori; Hoch, Justine E; MacAlpine, Patrick; Hasan, Shohan; Stone, Peter; Adolph, Karen E

2018-01-01

Although both infancy and artificial intelligence (AI) researchers are interested in developing systems that produce adaptive, functional behavior, the two disciplines rarely capitalize on their complementary expertise. Here, we used soccer-playing robots to test a central question about the development of infant walking. During natural activity, infants' locomotor paths are immensely varied. They walk along curved, multi-directional paths with frequent starts and stops. Is the variability observed in spontaneous infant walking a "feature" or a "bug?" In other words, is variability beneficial for functional walking performance? To address this question, we trained soccer-playing robots on walking paths generated by infants during free play and tested them in simulated games of "RoboCup." In Tournament 1, we compared the functional performance of a simulated robot soccer team trained on infants' natural paths with teams trained on less varied, geometric paths-straight lines, circles, and squares. Across 1,000 head-to-head simulated soccer matches, the infant-trained team consistently beat all teams trained with less varied walking paths. In Tournament 2, we compared teams trained on different clusters of infant walking paths. The team trained with the most varied combination of path shape, step direction, number of steps, and number of starts and stops outperformed teams trained with less varied paths. This evidence indicates that variety is a crucial feature supporting functional walking performance. More generally, we propose that robotics provides a fruitful avenue for testing hypotheses about infant development; reciprocally, observations of infant behavior may inform research on artificial intelligence.

Hydrogen analysis depth calibration by CORTEO Monte-Carlo simulation

NASA Astrophysics Data System (ADS)

Moser, M.; Reichart, P.; Bergmaier, A.; Greubel, C.; Schiettekatte, F.; Dollinger, G.

2016-03-01

Hydrogen imaging with sub-μm lateral resolution and sub-ppm sensitivity has become possible with coincident proton-proton (pp) scattering analysis (Reichart et al., 2004). Depth information is evaluated from the energy sum signal with respect to energy loss of both protons on their path through the sample. In first order, there is no angular dependence due to elastic scattering. In second order, a path length effect due to different energy loss on the paths of the protons causes an angular dependence of the energy sum. Therefore, the energy sum signal has to be de-convoluted depending on the matrix composition, i.e. mainly the atomic number Z, in order to get a depth calibrated hydrogen profile. Although the path effect can be calculated analytically in first order, multiple scattering effects lead to significant deviations in the depth profile. Hence, in our new approach, we use the CORTEO Monte-Carlo code (Schiettekatte, 2008) in order to calculate the depth of a coincidence event depending on the scattering angle. The code takes individual detector geometry into account. In this paper we show, that the code correctly reproduces measured pp-scattering energy spectra with roughness effects considered. With more than 100 μm thick Mylar-sandwich targets (Si, Fe, Ge) we demonstrate the deconvolution of the energy spectra on our current multistrip detector at the microprobe SNAKE at the Munich tandem accelerator lab. As a result, hydrogen profiles can be evaluated with an accuracy in depth of about 1% of the sample thickness.

Simulation based optimized beam velocity in additive manufacturing

NASA Astrophysics Data System (ADS)

Vignat, Frédéric; Béraud, Nicolas; Villeneuve, François

2017-08-01

Manufacturing good parts with additive technologies rely on melt pool dimension and temperature and are controlled by manufacturing strategies often decided on machine side. Strategies are built on beam path and variable energy input. Beam path are often a mix of contour and hatching strategies filling the contours at each slice. Energy input depend on beam intensity and speed and is determined from simple thermal models to control melt pool dimensions and temperature and ensure porosity free material. These models take into account variation in thermal environment such as overhanging surfaces or back and forth hatching path. However not all the situations are correctly handled and precision is limited. This paper proposes new method to determine energy input from full built chamber 3D thermal simulation. Using the results of the simulation, energy is modified to keep melt pool temperature in a predetermined range. The paper present first an experimental method to determine the optimal range of temperature. In a second part the method to optimize the beam speed from the simulation results is presented. Finally, the optimized beam path is tested in the EBM machine and built part are compared with part built with ordinary beam path.

Measurement of tracer gas distributions using an open-path FTIR system coupled with computed tomography

NASA Astrophysics Data System (ADS)

Drescher, Anushka C.; Yost, Michael G.; Park, Doo Y.; Levine, Steven P.; Gadgil, Ashok J.; Fischer, Marc L.; Nazaroff, William W.

1995-05-01

Optical remote sensing and iterative computed tomography (CT) can be combined to measure the spatial distribution of gaseous pollutant concentrations in a plane. We have conducted chamber experiments to test this combination of techniques using an Open Path Fourier Transform Infrared Spectrometer (OP-FTIR) and a standard algebraic reconstruction technique (ART). ART was found to converge to solutions that showed excellent agreement with the ray integral concentrations measured by the FTIR but were inconsistent with simultaneously gathered point sample concentration measurements. A new CT method was developed based on (a) the superposition of bivariate Gaussians to model the concentration distribution and (b) a simulated annealing minimization routine to find the parameters of the Gaussians that resulted in the best fit to the ray integral concentration data. This new method, named smooth basis function minimization (SBFM) generated reconstructions that agreed well, both qualitatively and quantitatively, with the concentration profiles generated from point sampling. We present one set of illustrative experimental data to compare the performance of ART and SBFM.

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

PubMed

Varga, Matthew J; Schwartz, Steven D

2016-04-12

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

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

PubMed

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

2016-05-01

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

Simulated groundwater flow paths, travel time, and advective transport of nitrogen in the Kirkwood-Cohansey aquifer system, Barnegat Bay–Little Egg Harbor Watershed, New Jersey

USGS Publications Warehouse

Voronin, Lois M.; Cauller, Stephen J.

2017-07-31

Elevated concentrations of nitrogen in groundwater that discharges to surface-water bodies can degrade surface-water quality and habitats in the New Jersey Coastal Plain. An analysis of groundwater flow in the Kirkwood-Cohansey aquifer system and deeper confined aquifers that underlie the Barnegat Bay–Little Egg Harbor (BB-LEH) watershed and estuary was conducted by using groundwater-flow simulation, in conjunction with a particle-tracking routine, to provide estimates of groundwater flow paths and travel times to streams and the BB-LEH estuary.Water-quality data from the Ambient Groundwater Quality Monitoring Network, a long-term monitoring network of wells distributed throughout New Jersey, were used to estimate the initial nitrogen concentration in recharge for five different land-use classes—agricultural cropland or pasture, agricultural orchard or vineyard, urban non-residential, urban residential, and undeveloped. Land use at the point of recharge within the watershed was determined using a geographic information system (GIS). Flow path starting locations were plotted on land-use maps for 1930, 1973, 1986, 1997, and 2002. Information on the land use at the time and location of recharge, time of travel to the discharge location, and the point of discharge were determined for each simulated flow path. Particle-tracking analysis provided the link from the point of recharge, along the particle flow path, to the point of discharge, and the particle travel time. The travel time of each simulated particle established the recharge year. Land use during the year of recharge was used to define the nitrogen concentration associated with each flow path. The recharge-weighted average nitrogen concentration for all flow paths that discharge to the Toms River upstream from streamflow-gaging station 01408500 or to the BB-LEH estuary was calculated.Groundwater input into the Barnegat Bay–Little Egg Harbor estuary from two main sources— indirect discharge from base flow to streams that eventually flow into the bay and groundwater discharge directly into the estuary and adjoining coastal wetlands— is summarized by quantity, travel time, and estimated nitrogen concentration. Simulated average groundwater discharge to streams in the watershed that flow into the BB-LEH estuary is approximately 400 million gallons per day. Particle-tracking results indicate that the travel time of 56 percent of this discharge is less than 7 years. Fourteen percent of the groundwater discharge to the streams in the BB-LEH watershed has a travel time of less than 7 years and originates in urban land. Analysis of flow-path simulations indicate that approximately 13 percent of the total groundwater flow through the study area discharges directly to the estuary and adjoining coastal wetlands (approximately 64 million gallons per day). The travel time of 19 percent of this discharge is less than 7 years. Ten percent of this discharge (1 percent of the total groundwater flow through the study area) originates in urban areas and has a travel time of less than 7 years. Groundwater that discharges to the streams that flow into the BB-LEH, in general, has shorter travel times, and a higher percentage of it originates in urban areas than does direct groundwater discharge to the Barnegat Bay–Little Egg Harbor estuary.The simulated average nitrogen concentration in groundwater that discharges to the Toms River, upstream from streamflow-gaging station 01408500 was computed and compared to summary concentrations determined from analysis of multiple surface-water samples. The nitrogen concentration in groundwater that discharges directly to the estuary and adjoining coastal wetlands is a current data gap. The particle tracking methodology used in this study provides an estimate of this concentration."

Global Qualitative Flow-Path Modeling for Local State Determination in Simulation and Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T. (Inventor); Fleming, Land D. (Inventor)

1998-01-01

For qualitative modeling and analysis, a general qualitative abstraction of power transmission variables (flow and effort) for elements of flow paths includes information on resistance, net flow, permissible directions of flow, and qualitative potential is discussed. Each type of component model has flow-related variables and an associated internal flow map, connected into an overall flow network of the system. For storage devices, the implicit power transfer to the environment is represented by "virtual" circuits that include an environmental junction. A heterogeneous aggregation method simplifies the path structure. A method determines global flow-path changes during dynamic simulation and analysis, and identifies corresponding local flow state changes that are effects of global configuration changes. Flow-path determination is triggered by any change in a flow-related device variable in a simulation or analysis. Components (path elements) that may be affected are identified, and flow-related attributes favoring flow in the two possible directions are collected for each of them. Next, flow-related attributes are determined for each affected path element, based on possibly conflicting indications of flow direction. Spurious qualitative ambiguities are minimized by using relative magnitudes and permissible directions of flow, and by favoring flow sources over effort sources when comparing flow tendencies. The results are output to local flow states of affected components.

Joint Use of ERT, Tracer, and Numerical Techniques to Image Preferential Flow Paths in a Fractured Granite Aquifer

NASA Astrophysics Data System (ADS)

Sanaga, S.; Vijay, S.; Kbvn, P.; Peddinti, S. R.; P S L, S.

2017-12-01

Fractured geologic media poses formidable challenges to hydrogeologists due of the strenuous mapping of fracture-matrix system and quantification of flow and transport processes. In this research, we demonstrated the efficacy of tracer-ERT studies coupled with numerical simulations to delineate preferential flow paths in a fractured granite aquifer of Deccan traps in India. A series of natural gradient saline tracer experiments were conducted from a depth window of 18 to 22 m in an injection well located inside the IIT Hyderabad campus. Tracer migration was monitored in a time-lapse mode using two cross-sectional surface ERT profiles placed in the direction of flow gradient. Dynamic changes in sub-surface electrical properties inferred via resistivity anomalies were used to highlight preferential flow paths of the study area. ERT-derived tracer breakthrough curves were in agreement with geochemical sample measurements (R2=0.74). Fracture geometry and hydraulic properties derived from ERT and pumping tests were then used to evaluate two mathematical conceptualizations that are relevant to fractured aquifers. Results of numerical analysis conclude that a dual continuum model that combines matrix and fracture systems through a flow exchange term has outperformed equivalent continuum model in reproducing tracer concentrations at the monitoring wells (evident by decrease in RMSE from 199 mg/l to 65 mg/l). A sensitivity analysis of the model parameters reveals that spatial variability in hydraulic conductivity, local-scale dispersion, and flow exchange at fracture-matrix interface have a profound effect on model simulations. Keywords: saline tracer, ERT, fractured granite, groundwater, preferential flow, numerical simulation

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

USGS Publications Warehouse

Otero, Cassi L.

2007-01-01

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

A theoretical framework to predict the most likely ion path in particle imaging.

PubMed

Collins-Fekete, Charles-Antoine; Volz, Lennart; Portillo, Stephen K N; Beaulieu, Luc; Seco, Joao

2017-03-07

In this work, a generic rigorous Bayesian formalism is introduced to predict the most likely path of any ion crossing a medium between two detection points. The path is predicted based on a combination of the particle scattering in the material and measurements of its initial and final position, direction and energy. The path estimate's precision is compared to the Monte Carlo simulated path. Every ion from hydrogen to carbon is simulated in two scenarios, (1) where the range is fixed and (2) where the initial velocity is fixed. In the scenario where the range is kept constant, the maximal root-mean-square error between the estimated path and the Monte Carlo path drops significantly between the proton path estimate (0.50 mm) and the helium path estimate (0.18 mm), but less so up to the carbon path estimate (0.09 mm). However, this scenario is identified as the configuration that maximizes the dose while minimizing the path resolution. In the scenario where the initial velocity is fixed, the maximal root-mean-square error between the estimated path and the Monte Carlo path drops significantly between the proton path estimate (0.29 mm) and the helium path estimate (0.09 mm) but increases for heavier ions up to carbon (0.12 mm). As a result, helium is found to be the particle with the most accurate path estimate for the lowest dose, potentially leading to tomographic images of higher spatial resolution.

Reentry Motion and Aerodynamics of the MUSES-C Sample Return Capsule

NASA Astrophysics Data System (ADS)

Ishii, Nobuaki; Yamada, Tetsuya; Hiraki, Koju; Inatani, Yoshifumi

The Hayabusa spacecraft (MUSES-C) carries a small capsule for bringing asteroid samples back to the earth. The initial spin rate of the reentry capsule together with the flight path angle of the reentry trajectory is a key parameter for the aerodynamic motion during the reentry flight. The initial spin rate is given by the spin-release mechanism attached between the capsule and the mother spacecraft, and the flight path angle can be modified by adjusting the earth approach orbit. To determine the desired values of both parameters, the attitude motion during atmospheric flight must be clarified, and angles of attack at the maximum dynamic pressure and the parachute deployment must be assessed. In previous studies, to characterize the aerodynamic effects of the reentry capsule, several wind-tunnel tests were conducted using the ISAS high-speed flow test facilities. In addition to the ground test data, the aerodynamic properties in hypersonic flows were analyzed numerically. Moreover, these data were made more accurate using the results of balloon drop tests. This paper summarized the aerodynamic properties of the reentry capsule and simulates the attitude motion of the full-configuration capsule during atmospheric flight in three dimensions with six degrees of freedom. The results show the best conditions for the initial spin rates and flight path angles of the reentry trajectory.

Accelerating Sequential Gaussian Simulation with a constant path

NASA Astrophysics Data System (ADS)

Nussbaumer, Raphaël; Mariethoz, Grégoire; Gravey, Mathieu; Gloaguen, Erwan; Holliger, Klaus

2018-03-01

Sequential Gaussian Simulation (SGS) is a stochastic simulation technique commonly employed for generating realizations of Gaussian random fields. Arguably, the main limitation of this technique is the high computational cost associated with determining the kriging weights. This problem is compounded by the fact that often many realizations are required to allow for an adequate uncertainty assessment. A seemingly simple way to address this problem is to keep the same simulation path for all realizations. This results in identical neighbourhood configurations and hence the kriging weights only need to be determined once and can then be re-used in all subsequent realizations. This approach is generally not recommended because it is expected to result in correlation between the realizations. Here, we challenge this common preconception and make the case for the use of a constant path approach in SGS by systematically evaluating the associated benefits and limitations. We present a detailed implementation, particularly regarding parallelization and memory requirements. Extensive numerical tests demonstrate that using a constant path allows for substantial computational gains with very limited loss of simulation accuracy. This is especially the case for a constant multi-grid path. The computational savings can be used to increase the neighbourhood size, thus allowing for a better reproduction of the spatial statistics. The outcome of this study is a recommendation for an optimal implementation of SGS that maximizes accurate reproduction of the covariance structure as well as computational efficiency.

Driven Langevin systems: fluctuation theorems and faithful dynamics

NASA Astrophysics Data System (ADS)

Sivak, David; Chodera, John; Crooks, Gavin

2014-03-01

Stochastic differential equations of motion (e.g., Langevin dynamics) provide a popular framework for simulating molecular systems. Any computational algorithm must discretize these equations, yet the resulting finite time step integration schemes suffer from several practical shortcomings. We show how any finite time step Langevin integrator can be thought of as a driven, nonequilibrium physical process. Amended by an appropriate work-like quantity (the shadow work), nonequilibrium fluctuation theorems can characterize or correct for the errors introduced by the use of finite time steps. We also quantify, for the first time, the magnitude of deviations between the sampled stationary distribution and the desired equilibrium distribution for equilibrium Langevin simulations of solvated systems of varying size. We further show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Group refractive index reconstruction with broadband interferometric confocal microscopy

PubMed Central

Marks, Daniel L.; Schlachter, Simon C.; Zysk, Adam M.; Boppart, Stephen A.

2010-01-01

We propose a novel method of measuring the group refractive index of biological tissues at the micrometer scale. The technique utilizes a broadband confocal microscope embedded into a Mach–Zehnder interferometer, with which spectral interferograms are measured as the sample is translated through the focus of the beam. The method does not require phase unwrapping and is insensitive to vibrations in the sample and reference arms. High measurement stability is achieved because a single spectral interferogram contains all the information necessary to compute the optical path delay of the beam transmitted through the sample. Included are a physical framework defining the forward problem, linear solutions to the inverse problem, and simulated images of biologically relevant phantoms. PMID:18451922

Optical modeling based on mean free path calculations for quantum dot phosphors applied to optoelectronic devices.

PubMed

Shin, Min-Ho; Kim, Hyo-Jun; Kim, Young-Joo

2017-02-20

We proposed an optical simulation model for the quantum dot (QD) nanophosphor based on the mean free path concept to understand precisely the optical performance of optoelectronic devices. A measurement methodology was also developed to get the desired optical characteristics such as the mean free path and absorption spectra for QD nanophosphors which are to be incorporated into the simulation. The simulation results for QD-based white LED and OLED displays show good agreement with the experimental values from the fabricated devices in terms of spectral power distribution, chromaticity coordinate, CCT, and CRI. The proposed simulation model and measurement methodology can be applied easily to the design of lots of optoelectronics devices using QD nanophosphors to obtain high efficiency and the desired color characteristics.

Cockpit simulation study of use of flight path angle for instrument approaches

NASA Technical Reports Server (NTRS)

Hanisch, B.; Ernst, H.; Johnston, R.

1981-01-01

The results of a piloted simulation experiment to evaluate the effect of integrating flight path angle information into a typical transport electronic attitude director indicator display format for flight director instrument landing system approaches are presented. Three electronic display formats are evaluated during 3 deg straight-in approaches with wind shear and turbulence conditions. Flight path tracking data and pilot subjective comments are analyzed with regard to the pilot's tracking performance and workload for all three display formats.

Design process for applying the nonlocal thermal transport iSNB model to a Polar-Drive ICF simulation

NASA Astrophysics Data System (ADS)

Cao, Duc; Moses, Gregory; Delettrez, Jacques; Collins, Timothy

2014-10-01

A design process is presented for the nonlocal thermal transport iSNB (implicit Schurtz, Nicolai, and Busquet) model to provide reliable nonlocal thermal transport in polar-drive ICF simulations. Results from the iSNB model are known to be sensitive to changes in the SNB ``mean free path'' formula, and the latter's original form required modification to obtain realistic preheat levels. In the presented design process, SNB mean free paths are first modified until the model can match temperatures from Goncharov's thermal transport model in 1D temperature relaxation simulations. Afterwards the same mean free paths are tested in a 1D polar-drive surrogate simulation to match adiabats from Goncharov's model. After passing the two previous steps, the model can then be run in a full 2D polar-drive simulation. This research is supported by the University of Rochester Laboratory for Laser Energetics.

When Affordances Climb into Your Mind: Advantages of Motor Simulation in a Memory Task Performed by Novice and Expert Rock Climbers

ERIC Educational Resources Information Center

Pezzulo, Giovanni; Barca, Laura; Bocconi, Alessandro Lamberti; Borghi, Anna M.

2010-01-01

Does the sight of multiple climbing holds laid along a path activate a motor simulation of climbing that path? One way of testing whether multiple affordances and their displacement influence the formation of a motor simulation is to study acquired motor skills. We used a behavioral task in which expert and novice rock climbers were shown three…

Bragg peak prediction from quantitative proton computed tomography using different path estimates

PubMed Central

Wang, Dongxu; Mackie, T Rockwell

2015-01-01

This paper characterizes the performance of the straight-line path (SLP) and cubic spline path (CSP) as path estimates used in reconstruction of proton computed tomography (pCT). The GEANT4 Monte Carlo simulation toolkit is employed to simulate the imaging phantom and proton projections. SLP, CSP and the most-probable path (MPP) are constructed based on the entrance and exit information of each proton. The physical deviations of SLP, CSP and MPP from the real path are calculated. Using a conditional proton path probability map, the relative probability of SLP, CSP and MPP are calculated and compared. The depth dose and Bragg peak are predicted on the pCT images reconstructed using SLP, CSP, and MPP and compared with the simulation result. The root-mean-square physical deviations and the cumulative distribution of the physical deviations show that the performance of CSP is comparable to MPP while SLP is slightly inferior. About 90% of the SLP pixels and 99% of the CSP pixels lie in the 99% relative probability envelope of the MPP. Even at an imaging dose of ~0.1 mGy the proton Bragg peak for a given incoming energy can be predicted on the pCT image reconstructed using SLP, CSP, or MPP with 1 mm accuracy. This study shows that SLP and CSP, like MPP, are adequate path estimates for pCT reconstruction, and therefore can be chosen as the path estimation method for pCT reconstruction, which can aid the treatment planning and range prediction of proton radiation therapy. PMID:21212472

Dependence of Internal Friction on Folding Mechanism

PubMed Central

2016-01-01

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

Dependence of internal friction on folding mechanism.

PubMed

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

2015-03-11

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

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

PubMed Central

Liu, Qixin; Cai, Zhiyong

2014-01-01

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

Remote sensing data with the conditional latin hypercube sampling and geostatistical approach to delineate landscape changes induced by large chronological physical disturbances.

PubMed

Lin, Yu-Pin; Chu, Hone-Jay; Wang, Cheng-Long; Yu, Hsiao-Hsuan; Wang, Yung-Chieh

2009-01-01

This study applies variogram analyses of normalized difference vegetation index (NDVI) images derived from SPOT HRV images obtained before and after the ChiChi earthquake in the Chenyulan watershed, Taiwan, as well as images after four large typhoons, to delineate the spatial patterns, spatial structures and spatial variability of landscapes caused by these large disturbances. The conditional Latin hypercube sampling approach was applied to select samples from multiple NDVI images. Kriging and sequential Gaussian simulation with sufficient samples were then used to generate maps of NDVI images. The variography of NDVI image results demonstrate that spatial patterns of disturbed landscapes were successfully delineated by variogram analysis in study areas. The high-magnitude Chi-Chi earthquake created spatial landscape variations in the study area. After the earthquake, the cumulative impacts of typhoons on landscape patterns depended on the magnitudes and paths of typhoons, but were not always evident in the spatiotemporal variability of landscapes in the study area. The statistics and spatial structures of multiple NDVI images were captured by 3,000 samples from 62,500 grids in the NDVI images. Kriging and sequential Gaussian simulation with the 3,000 samples effectively reproduced spatial patterns of NDVI images. However, the proposed approach, which integrates the conditional Latin hypercube sampling approach, variogram, kriging and sequential Gaussian simulation in remotely sensed images, efficiently monitors, samples and maps the effects of large chronological disturbances on spatial characteristics of landscape changes including spatial variability and heterogeneity.

Acceleration of Monte Carlo SPECT simulation using convolution-based forced detection

NASA Astrophysics Data System (ADS)

de Jong, H. W. A. M.; Slijpen, E. T. P.; Beekman, F. J.

2001-02-01

Monte Carlo (MC) simulation is an established tool to calculate photon transport through tissue in Emission Computed Tomography (ECT). Since the first appearance of MC a large variety of variance reduction techniques (VRT) have been introduced to speed up these notoriously slow simulations. One example of a very effective and established VRT is known as forced detection (FD). In standard FD the path from the photon's scatter position to the camera is chosen stochastically from the appropriate probability density function (PDF), modeling the distance-dependent detector response. In order to speed up MC the authors propose a convolution-based FD (CFD) which involves replacing the sampling of the PDF by a convolution with a kernel which depends on the position of the scatter event. The authors validated CFD for parallel-hole Single Photon Emission Computed Tomography (SPECT) using a digital thorax phantom. Comparison of projections estimated with CFD and standard FD shows that both estimates converge to practically identical projections (maximum bias 0.9% of peak projection value), despite the slightly different photon paths used in CFD and standard FD. Projections generated with CFD converge, however, to a noise-free projection up to one or two orders of magnitude faster, which is extremely useful in many applications such as model-based image reconstruction.

Earth Model with Laser Beam Simulating Seismic Ray Paths.

ERIC Educational Resources Information Center

Ryan, John Arthur; Handzus, Thomas Jay, Jr.

1988-01-01

Described is a simple device, that uses a laser beam to simulate P waves. It allows students to follow ray paths, reflections and refractions within the earth. Included is a set of exercises that lead students through the steps by which the presence of the outer and inner cores can be recognized. (Author/CW)

Heads-Up Display with Virtual Precision Approach Path Indicator as Implemented in a Real-Time Piloted Lifting-Body Simulation

NASA Technical Reports Server (NTRS)

Neuhaus, Jason R.

2018-01-01

This document describes the heads-up display (HUD) used in a piloted lifting-body entry, approach and landing simulation developed for the simulator facilities of the Simulation Development and Analysis Branch (SDAB) at NASA Langley Research Center. The HUD symbology originated with the piloted simulation evaluations of the HL-20 lifting body concept conducted in 1989 at NASA Langley. The original symbology was roughly based on Shuttle HUD symbology, as interpreted by Langley researchers. This document focuses on the addition of the precision approach path indicator (PAPI) lights to the HUD overlay.

Thermal conductivity of nanocrystalline silicon: importance of grain size and frequency-dependent mean free paths.

PubMed

Wang, Zhaojie; Alaniz, Joseph E; Jang, Wanyoung; Garay, Javier E; Dames, Chris

2011-06-08

The thermal conductivity reduction due to grain boundary scattering is widely interpreted using a scattering length assumed equal to the grain size and independent of the phonon frequency (gray). To assess these assumptions and decouple the contributions of porosity and grain size, five samples of undoped nanocrystalline silicon have been measured with average grain sizes ranging from 550 to 64 nm and porosities from 17% to less than 1%, at temperatures from 310 to 16 K. The samples were prepared using current activated, pressure assisted densification (CAPAD). At low temperature the thermal conductivities of all samples show a T(2) dependence which cannot be explained by any traditional gray model. The measurements are explained over the entire temperature range by a new frequency-dependent model in which the mean free path for grain boundary scattering is inversely proportional to the phonon frequency, which is shown to be consistent with asymptotic analysis of atomistic simulations from the literature. In all cases the recommended boundary scattering length is smaller than the average grain size. These results should prove useful for the integration of nanocrystalline materials in devices such as advanced thermoelectrics.

QM/MM free energy simulations: recent progress and challenges

PubMed Central

Lu, Xiya; Fang, Dong; Ito, Shingo; Okamoto, Yuko; Ovchinnikov, Victor

2016-01-01

Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections. PMID:27563170

Inclusion of trial functions in the Langevin equation path integral ground state method: Application to parahydrogen clusters and their isotopologues

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

Schmidt, Matthew; Constable, Steve; Ing, Christopher

2014-06-21

We developed and studied the implementation of trial wavefunctions in the newly proposed Langevin equation Path Integral Ground State (LePIGS) method [S. Constable, M. Schmidt, C. Ing, T. Zeng, and P.-N. Roy, J. Phys. Chem. A 117, 7461 (2013)]. The LePIGS method is based on the Path Integral Ground State (PIGS) formalism combined with Path Integral Molecular Dynamics sampling using a Langevin equation based sampling of the canonical distribution. This LePIGS method originally incorporated a trivial trial wavefunction, ψ{sub T}, equal to unity. The present paper assesses the effectiveness of three different trial wavefunctions on three isotopes of hydrogen formore » cluster sizes N = 4, 8, and 13. The trial wavefunctions of interest are the unity trial wavefunction used in the original LePIGS work, a Jastrow trial wavefunction that includes correlations due to hard-core repulsions, and a normal mode trial wavefunction that includes information on the equilibrium geometry. Based on this analysis, we opt for the Jastrow wavefunction to calculate energetic and structural properties for parahydrogen, orthodeuterium, and paratritium clusters of size N = 4 − 19, 33. Energetic and structural properties are obtained and compared to earlier work based on Monte Carlo PIGS simulations to study the accuracy of the proposed approach. The new results for paratritium clusters will serve as benchmark for future studies. This paper provides a detailed, yet general method for optimizing the necessary parameters required for the study of the ground state of a large variety of systems.« less

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

PubMed

Chen, Changjun; Huang, Yanzhao; Xiao, Yi

2013-01-01

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

Simulation in production of open rotor propellers: from optimal surface geometry to automated control of mechanical treatment

NASA Astrophysics Data System (ADS)

Grinyok, A.; Boychuk, I.; Perelygin, D.; Dantsevich, I.

2018-03-01

A complex method of the simulation and production design of open rotor propellers was studied. An end-to-end diagram was proposed for the evaluating, designing and experimental testing the optimal geometry of the propeller surface, for the machine control path generation as well as for simulating the cutting zone force condition and its relationship with the treatment accuracy which was defined by the propeller elastic deformation. The simulation data provided the realization of the combined automated path control of the cutting tool.

Simulation of path delay multiplexing-based Fourier transform spectrometer for fiber Bragg grating interrogation.

PubMed

Chelliah, Pandian; Sahoo, Trilochan; Singh, Sheela; Sujatha, Annie

2015-10-20

A Fourier transform spectrometer (FTS) used for interrogating a fiber Bragg grating (FBG) consists of a scanning-type interferometer. The FTS has a broad wavelength range of operation and good multiplexing capability. However, it has poor wavelength resolution and interrogation speed. We propose a modification to the FTS using path delay multiplexing to improve the same. Using this method, spatial resolution and interrogation time can be improved by n times by using n path delays. In this paper, simulation results for n=2, 5 are shown.

Path integral pricing of Wasabi option in the Black-Scholes model

NASA Astrophysics Data System (ADS)

Cassagnes, Aurelien; Chen, Yu; Ohashi, Hirotada

2014-11-01

In this paper, using path integral techniques, we derive a formula for a propagator arising in the study of occupation time derivatives. Using this result we derive a fair price for the case of the cumulative Parisian option. After confirming the validity of the derived result using Monte Carlo simulation, a new type of heavily path dependent derivative product is investigated. We derive an approximation for our so-called Wasabi option fair price and check the accuracy of our result with a Monte Carlo simulation.

Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method.

PubMed

Chen, Changjun

2016-03-31

The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.

UAV path planning using artificial potential field method updated by optimal control theory

NASA Astrophysics Data System (ADS)

Chen, Yong-bo; Luo, Guan-chen; Mei, Yue-song; Yu, Jian-qiao; Su, Xiao-long

2016-04-01

The unmanned aerial vehicle (UAV) path planning problem is an important assignment in the UAV mission planning. Based on the artificial potential field (APF) UAV path planning method, it is reconstructed into the constrained optimisation problem by introducing an additional control force. The constrained optimisation problem is translated into the unconstrained optimisation problem with the help of slack variables in this paper. The functional optimisation method is applied to reform this problem into an optimal control problem. The whole transformation process is deduced in detail, based on a discrete UAV dynamic model. Then, the path planning problem is solved with the help of the optimal control method. The path following process based on the six degrees of freedom simulation model of the quadrotor helicopters is introduced to verify the practicability of this method. Finally, the simulation results show that the improved method is more effective in planning path. In the planning space, the length of the calculated path is shorter and smoother than that using traditional APF method. In addition, the improved method can solve the dead point problem effectively.

Variety Wins: Soccer-Playing Robots and Infant Walking

PubMed Central

Ossmy, Ori; Hoch, Justine E.; MacAlpine, Patrick; Hasan, Shohan; Stone, Peter; Adolph, Karen E.

2018-01-01

Although both infancy and artificial intelligence (AI) researchers are interested in developing systems that produce adaptive, functional behavior, the two disciplines rarely capitalize on their complementary expertise. Here, we used soccer-playing robots to test a central question about the development of infant walking. During natural activity, infants' locomotor paths are immensely varied. They walk along curved, multi-directional paths with frequent starts and stops. Is the variability observed in spontaneous infant walking a “feature” or a “bug?” In other words, is variability beneficial for functional walking performance? To address this question, we trained soccer-playing robots on walking paths generated by infants during free play and tested them in simulated games of “RoboCup.” In Tournament 1, we compared the functional performance of a simulated robot soccer team trained on infants' natural paths with teams trained on less varied, geometric paths—straight lines, circles, and squares. Across 1,000 head-to-head simulated soccer matches, the infant-trained team consistently beat all teams trained with less varied walking paths. In Tournament 2, we compared teams trained on different clusters of infant walking paths. The team trained with the most varied combination of path shape, step direction, number of steps, and number of starts and stops outperformed teams trained with less varied paths. This evidence indicates that variety is a crucial feature supporting functional walking performance. More generally, we propose that robotics provides a fruitful avenue for testing hypotheses about infant development; reciprocally, observations of infant behavior may inform research on artificial intelligence. PMID:29867427

Transition path time distributions for Lévy flights

NASA Astrophysics Data System (ADS)

Janakiraman, Deepika

2018-07-01

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

Fast exploration of an optimal path on the multidimensional free energy surface

PubMed Central

Chen, Changjun

2017-01-01

In a reaction, determination of an optimal path with a high reaction rate (or a low free energy barrier) is important for the study of the reaction mechanism. This is a complicated problem that involves lots of degrees of freedom. For simple models, one can build an initial path in the collective variable space by the interpolation method first and then update the whole path constantly in the optimization. However, such interpolation method could be risky in the high dimensional space for large molecules. On the path, steric clashes between neighboring atoms could cause extremely high energy barriers and thus fail the optimization. Moreover, performing simulations for all the snapshots on the path is also time-consuming. In this paper, we build and optimize the path by a growing method on the free energy surface. The method grows a path from the reactant and extends its length in the collective variable space step by step. The growing direction is determined by both the free energy gradient at the end of the path and the direction vector pointing at the product. With fewer snapshots on the path, this strategy can let the path avoid the high energy states in the growing process and save the precious simulation time at each iteration step. Applications show that the presented method is efficient enough to produce optimal paths on either the two-dimensional or the twelve-dimensional free energy surfaces of different small molecules. PMID:28542475

Results of a simulator test comparing two display concepts for piloted flight-path-angle control

NASA Technical Reports Server (NTRS)

Kelley, W. W.

1978-01-01

Results of a simulator experiment which was conducted in order to compare pilot gamma-control performance using two display formats are reported. Pilots flew a variable flight path angle tracking task in the landing configuration. Pilot and airplane performance parameters were recorded and pilot comments noted for each case.

Path integration of head direction: updating a packet of neural activity at the correct speed using axonal conduction delays.

PubMed

Walters, Daniel; Stringer, Simon; Rolls, Edmund

2013-01-01

The head direction cell system is capable of accurately updating its current representation of head direction in the absence of visual input. This is known as the path integration of head direction. An important question is how the head direction cell system learns to perform accurate path integration of head direction. In this paper we propose a model of velocity path integration of head direction in which the natural time delay of axonal transmission between a linked continuous attractor network and competitive network acts as a timing mechanism to facilitate the correct speed of path integration. The model effectively learns a "look-up" table for the correct speed of path integration. In simulation, we show that the model is able to successfully learn two different speeds of path integration across two different axonal conduction delays, and without the need to alter any other model parameters. An implication of this model is that, by learning look-up tables for each speed of path integration, the model should exhibit a degree of robustness to damage. In simulations, we show that the speed of path integration is not significantly affected by degrading the network through removing a proportion of the cells that signal rotational velocity.

Path Integration of Head Direction: Updating a Packet of Neural Activity at the Correct Speed Using Axonal Conduction Delays

PubMed Central

Walters, Daniel; Stringer, Simon; Rolls, Edmund

2013-01-01

The head direction cell system is capable of accurately updating its current representation of head direction in the absence of visual input. This is known as the path integration of head direction. An important question is how the head direction cell system learns to perform accurate path integration of head direction. In this paper we propose a model of velocity path integration of head direction in which the natural time delay of axonal transmission between a linked continuous attractor network and competitive network acts as a timing mechanism to facilitate the correct speed of path integration. The model effectively learns a “look-up” table for the correct speed of path integration. In simulation, we show that the model is able to successfully learn two different speeds of path integration across two different axonal conduction delays, and without the need to alter any other model parameters. An implication of this model is that, by learning look-up tables for each speed of path integration, the model should exhibit a degree of robustness to damage. In simulations, we show that the speed of path integration is not significantly affected by degrading the network through removing a proportion of the cells that signal rotational velocity. PMID:23526976

A hyperbolastic type-I diffusion process: Parameter estimation by means of the firefly algorithm.

PubMed

Barrera, Antonio; Román-Román, Patricia; Torres-Ruiz, Francisco

2018-01-01

A stochastic diffusion process, whose mean function is a hyperbolastic curve of type I, is presented. The main characteristics of the process are studied and the problem of maximum likelihood estimation for the parameters of the process is considered. To this end, the firefly metaheuristic optimization algorithm is applied after bounding the parametric space by a stagewise procedure. Some examples based on simulated sample paths and real data illustrate this development. Copyright © 2017 Elsevier B.V. All rights reserved.

The United States Army Medical Department Journal. July - September 2011

DTIC Science & Technology

2011-09-01

compliance. Figure 1. Functional schematic of the flow path and treatment stages of the water treatment plant. Basin 5  Basin  4  Basin  3  Basin 2...that hindered optimal performance of the WTP. They were the flocculation treatment process and flow distribution through the WTP. Flocculation...designed to simulate the WTP at a flow of 1.5 MGD (the flow through the WTP at the time of jar testing). Jar test samples were collected after

Procedure Enabling Simulation and In-Depth Analysis of Optical Effects in Camera-Based Time-Of Sensors

NASA Astrophysics Data System (ADS)

Baumgart, M.; Druml, N.; Consani, M.

2018-05-01

This paper presents a simulation approach for Time-of-Flight cameras to estimate sensor performance and accuracy, as well as to help understanding experimentally discovered effects. The main scope is the detailed simulation of the optical signals. We use a raytracing-based approach and use the optical path length as the master parameter for depth calculations. The procedure is described in detail with references to our implementation in Zemax OpticStudio and Python. Our simulation approach supports multiple and extended light sources and allows accounting for all effects within the geometrical optics model. Especially multi-object reflection/scattering ray-paths, translucent objects, and aberration effects (e.g. distortion caused by the ToF lens) are supported. The optical path length approach also enables the implementation of different ToF senor types and transient imaging evaluations. The main features are demonstrated on a simple 3D test scene.

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

PubMed Central

Xayaphoummine, A.; Bucher, T.; Isambert, H.

2005-01-01

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at . PMID:15980546

High-density amorphous ice: A path-integral simulation

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.; Ramírez, Rafael

2012-09-01

Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Quantum nuclear motion is found to affect several observable properties of the amorphous solid. At low temperature (T = 50 K) the molar volume of HDA ice is found to increase by 6%, and the intramolecular O-H distance rises by 1.4% due to quantum motion. Peaks in the radial distribution function of HDA ice are broadened with respect to their classical expectancy. The bulk modulus, B, is found to rise linearly with the pressure, with a slope ∂B/∂P = 7.1. Our results are compared with those derived earlier from classical and path-integral simulations of HDA ice. We discuss similarities and discrepancies with those earlier simulations.

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

PubMed

Tiwari, Ambuj; Ensing, Bernd

2016-12-22

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

Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase.

PubMed

Engel, Hamutal; Doron, Dvir; Kohen, Amnon; Major, Dan Thomas

2012-04-10

The inclusion of nuclear quantum effects such as zero-point energy and tunneling is of great importance in studying condensed phase chemical reactions involving the transfer of protons, hydrogen atoms, and hydride ions. In the current work, we derive an efficient quantum simulation approach for the computation of the momentum distribution in condensed phase chemical reactions. The method is based on a quantum-classical approach wherein quantum and classical simulations are performed separately. The classical simulations use standard sampling techniques, whereas the quantum simulations employ an open polymer chain path integral formulation which is computed using an efficient Monte Carlo staging algorithm. The approach is validated by applying it to a one-dimensional harmonic oscillator and symmetric double-well potential. Subsequently, the method is applied to the dihydrofolate reductase (DHFR) catalyzed reduction of 7,8-dihydrofolate by nicotinamide adenine dinucleotide phosphate hydride (NADPH) to yield S-5,6,7,8-tetrahydrofolate and NADP(+). The key chemical step in the catalytic cycle of DHFR involves a stereospecific hydride transfer. In order to estimate the amount of quantum delocalization, we compute the position and momentum distributions for the transferring hydride ion in the reactant state (RS) and transition state (TS) using a recently developed hybrid semiempirical quantum mechanics-molecular mechanics potential energy surface. Additionally, we examine the effect of compression of the donor-acceptor distance (DAD) in the TS on the momentum distribution. The present results suggest differential quantum delocalization in the RS and TS, as well as reduced tunneling upon DAD compression.

Mathematical model for path selection by ants between nest and food source.

PubMed

Bodnar, Marek; Okińczyc, Natalia; Vela-Pérez, M

2017-03-01

Several models have been proposed to describe the behavior of ants when moving from nest to food sources. Most of these studies where based on numerical simulations with no mathematical justification. In this paper, we propose a mechanism for the formation of paths of minimal length between two points by a collection of individuals undergoing reinforced random walks taking into account not only the lengths of the paths but also the angles (connected to the preference of ants to move along straight lines). Our model involves reinforcement (pheromone accumulation), persistence (tendency to preferably follow straight directions in absence of any external effect) and takes into account the bifurcation angles of each edge (represented by a probability of willingness of choosing the path with the smallest angle). We describe analytically the results for 2 ants and different path lengths and numerical simulations for several ants. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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

2016-07-14

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

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

Spatial connectivity in a highly heterogeneous aquifer: From cores to preferential flow paths

USGS Publications Warehouse

Bianchi, M.; Zheng, C.; Wilson, C.; Tick, G.R.; Liu, Gaisheng; Gorelick, S.M.

2011-01-01

This study investigates connectivity in a small portion of the extremely heterogeneous aquifer at the Macrodispersion Experiment (MADE) site in Columbus, Mississippi. A total of 19 fully penetrating soil cores were collected from a rectangular grid of 4 m by 4 m. Detailed grain size analysis was performed on 5 cm segments of each core, yielding 1740 hydraulic conductivity (K) estimates. Three different geostatistical simulation methods were used to generate 3-D conditional realizations of the K field for the sampled block. Particle tracking calculations showed that the fastest particles, as represented by the first 5% to arrive, converge along preferential flow paths and exit the model domain within preferred areas. These 5% fastest flow paths accounted for about 40% of the flow. The distribution of preferential flow paths and particle exit locations is clearly influenced by the occurrence of clusters formed by interconnected cells with K equal to or greater than the 0.9 decile of the data distribution (10% of the volume). The fraction of particle paths within the high-K clusters ranges from 43% to 69%. In variogram-based K fields, some of the fastest paths are through media with lower K values, suggesting that transport connectivity may not require fully connected zones of relatively homogenous K. The high degree of flow and transport connectivity was confirmed by the values of two groups of connectivity indicators. In particular, the ratio between effective and geometric mean K (on average, about 2) and the ratio between the average arrival time and the arrival time of the fastest particles (on average, about 9) are consistent with flow and advective transport behavior characterized by channeling along preferential flow paths. ?? 2011 by the American Geophysical Union.

Low cost label-free live cell imaging for biological samples

NASA Astrophysics Data System (ADS)

Seniya, C.; Towers, C. E.; Towers, D. P.

2017-02-01

This paper reports the progress to develop a practical phase measuring microscope offering new capabilities in terms of phase measurement accuracy and quantification of cell:cell interactions over the longer term. A novel, low cost phase interference microscope for imaging live cells (label-free) is described. The method combines the Zernike phase contrast approach with a dual mirror design to enable phase modulation between the scattered and un-scattered optical fields. Two designs are proposed and demonstrated, one of which retains the common path nature of Zernike's original microscopy concept. In both setups the phase shift is simple to control via a piezoelectric driven mirror in the back focal plane of the imaging system. The approach is significantly cheaper to implement than those based on spatial light modulators (SLM) at approximately 20% of the cost. A quantitative assessment of the performance of a set of phase shifting algorithms is also presented, specifically with regard to broad bandwidth illumination in phase contrast microscopy. The simulation results show that the phase measurement accuracy is strongly dependent on the algorithm selected and the optical path difference in the sample.

Feller processes: the next generation in modeling. Brownian motion, Lévy processes and beyond.

PubMed

Böttcher, Björn

2010-12-03

We present a simple construction method for Feller processes and a framework for the generation of sample paths of Feller processes. The construction is based on state space dependent mixing of Lévy processes. Brownian Motion is one of the most frequently used continuous time Markov processes in applications. In recent years also Lévy processes, of which Brownian Motion is a special case, have become increasingly popular. Lévy processes are spatially homogeneous, but empirical data often suggest the use of spatially inhomogeneous processes. Thus it seems necessary to go to the next level of generalization: Feller processes. These include Lévy processes and in particular brownian motion as special cases but allow spatial inhomogeneities. Many properties of Feller processes are known, but proving the very existence is, in general, very technical. Moreover, an applicable framework for the generation of sample paths of a Feller process was missing. We explain, with practitioners in mind, how to overcome both of these obstacles. In particular our simulation technique allows to apply Monte Carlo methods to Feller processes.

Feller Processes: The Next Generation in Modeling. Brownian Motion, Lévy Processes and Beyond

PubMed Central

Böttcher, Björn

2010-01-01

We present a simple construction method for Feller processes and a framework for the generation of sample paths of Feller processes. The construction is based on state space dependent mixing of Lévy processes. Brownian Motion is one of the most frequently used continuous time Markov processes in applications. In recent years also Lévy processes, of which Brownian Motion is a special case, have become increasingly popular. Lévy processes are spatially homogeneous, but empirical data often suggest the use of spatially inhomogeneous processes. Thus it seems necessary to go to the next level of generalization: Feller processes. These include Lévy processes and in particular Brownian motion as special cases but allow spatial inhomogeneities. Many properties of Feller processes are known, but proving the very existence is, in general, very technical. Moreover, an applicable framework for the generation of sample paths of a Feller process was missing. We explain, with practitioners in mind, how to overcome both of these obstacles. In particular our simulation technique allows to apply Monte Carlo methods to Feller processes. PMID:21151931

Development of a detector in order to investigate (n,γ)-cross sections by ToF method with a very short flight path

NASA Astrophysics Data System (ADS)

Wolf, C.; Glorius, J.; Reifarth, R.; Weigand, M.

2018-01-01

The determination of neutron capture cross sections of some radioactive isotopes like 85Kr is very important to improve the knowledge about the s process. Based on its own radioactive decay these isotopes can only be used in small samples inside a TOF facility, which is why the neutron flux of these facilities has to be very high. Unfortunately the neutron flux of the FRANZ setup at Goethe University Frankfurt, which will offer the highest neutron flux in astrophysical energy regions (keV region) [1], is still to low to investigate isotopes like 85Kr. Therefore a new setup called NAUTILUS is under development, which will reduce the flight path from 80 cm to a few centimeter to enhance the angular coverage of the sample and therefore increase the neutron flux by a factor of nearly 100. This implies a higher intensity of the γ-flash energy inside the detector and the neutron induced background. Hence the geometry, the scintillator material and the moderator were optimized by GEANT3 simulations.

Simulations and Experiments of Dynamic Granular Compaction in Non-ideal Geometries

NASA Astrophysics Data System (ADS)

Homel, Michael; Herbold, Eric; Lind, John; Crum, Ryan; Hurley, Ryan; Akin, Minta; Pagan, Darren; LLNL Team

2017-06-01

Accurately describing the dynamic compaction of granular materials is a persistent challenge in computational mechanics. Using a synchrotron x-ray source we have obtained detailed imaging of the evolving compaction front in synthetic olivine powder impacted at 300 - 600 m / s . To facilitate imaging, a non-traditional sample geometry is used, producing multiple load paths within the sample. We demonstrate that (i) commonly used models for porous compaction may produce inaccurate results for complex loading, even if the 1 - D , uniaxial-strain compaction response is reasonable, and (ii) the experimental results can be used along with simulations to determine parameters for sophisticated constitutive models that more accurately describe the strength, softening, bulking, and poroelastic response. Effects of experimental geometry and alternative configurations are discussed. Our understanding of the material response is further enhanced using mesoscale simulations that allow us to relate the mechanisms of grain fracture, contact, and comminution to the macroscale continuum response. Numerical considerations in both continuum and mesoscale simulations are described. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LDRD#16-ERD-010. LLNL-ABS-725113.

Defending Tor from Network Adversaries: A Case Study of Network Path Prediction

DTIC Science & Technology

2015-01-01

independence in Tor. 5.1 Vanilla Tor All of our Tor simulations run over the week of January 19– 25, 2014. When producing and analyzing these simulations, we...selection using path simula- tion and our traceroute data, similar to how they were used in Section 5.1 to explore vanilla Tor security. As a byproduct

Elucidating the electron transport in semiconductors via Monte Carlo simulations: an inquiry-driven learning path for engineering undergraduates

NASA Astrophysics Data System (ADS)

Persano Adorno, Dominique; Pizzolato, Nicola; Fazio, Claudio

2015-09-01

Within the context of higher education for science or engineering undergraduates, we present an inquiry-driven learning path aimed at developing a more meaningful conceptual understanding of the electron dynamics in semiconductors in the presence of applied electric fields. The electron transport in a nondegenerate n-type indium phosphide bulk semiconductor is modelled using a multivalley Monte Carlo approach. The main characteristics of the electron dynamics are explored under different values of the driving electric field, lattice temperature and impurity density. Simulation results are presented by following a question-driven path of exploration, starting from the validation of the model and moving up to reasoned inquiries about the observed characteristics of electron dynamics. Our inquiry-driven learning path, based on numerical simulations, represents a viable example of how to integrate a traditional lecture-based teaching approach with effective learning strategies, providing science or engineering undergraduates with practical opportunities to enhance their comprehension of the physics governing the electron dynamics in semiconductors. Finally, we present a general discussion about the advantages and disadvantages of using an inquiry-based teaching approach within a learning environment based on semiconductor simulations.

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

Improved graphite furnace atomizer

DOEpatents

Siemer, D.D.

1983-05-18

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

Interactive cutting path analysis programs

NASA Technical Reports Server (NTRS)

Weiner, J. M.; Williams, D. S.; Colley, S. R.

1975-01-01

The operation of numerically controlled machine tools is interactively simulated. Four programs were developed to graphically display the cutting paths for a Monarch lathe, Cintimatic mill, Strippit sheet metal punch, and the wiring path for a Standard wire wrap machine. These programs are run on a IMLAC PDS-ID graphic display system under the DOS-3 disk operating system. The cutting path analysis programs accept input via both paper tape and disk file.

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

PubMed

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

2017-01-01

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

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

PubMed

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

2008-01-01

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

An integrated biomechanical modeling approach to the ergonomic evaluation of drywall installation.

PubMed

Yuan, Lu; Buchholz, Bryan; Punnett, Laura; Kriebel, David

2016-03-01

Three different methodologies: work sampling, computer simulation and biomechanical modeling, were integrated to study the physical demands of drywall installation. PATH (Posture, Activity, Tools, and Handling), a work-sampling based method, was used to quantify the percent of time that the drywall installers were conducting different activities with different body segment (trunk, arm, and leg) postures. Utilizing Monte-Carlo simulation to convert the categorical PATH data into continuous variables as inputs for the biomechanical models, the required muscle contraction forces and joint reaction forces at the low back (L4/L5) and shoulder (glenohumeral and sternoclavicular joints) were estimated for a typical eight-hour workday. To demonstrate the robustness of this modeling approach, a sensitivity analysis was conducted to examine the impact of some quantitative assumptions that have been made to facilitate the modeling approach. The results indicated that the modeling approach seemed to be the most sensitive to both the distribution of work cycles for a typical eight-hour workday and the distribution and values of Euler angles that are used to determine the "shoulder rhythm." Other assumptions including the distribution of trunk postures did not appear to have a significant impact on the model outputs. It was concluded that the integrated approach might provide an applicable examination of physical loads during the non-routine construction work, especially for those operations/tasks that have certain patterns/sequences for the workers to follow. Copyright © 2015 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Coupled Long-Term Simulation of Reach-Scale Water and Heat Fluxes Across the River-Groundwater Interface for Retrieving Hyporheic Residence Times and Temperature Dynamics

NASA Astrophysics Data System (ADS)

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

2017-11-01

Flow patterns in conjunction with seasonal and diurnal temperature variations control ecological and biogeochemical conditions in hyporheic sediments. In particular, hyporheic temperatures have a great impact on many temperature-sensitive microbial processes. In this study, we used 3-D coupled water flow and heat transport simulations applying the HydroGeoSphere code in combination with high-resolution observations of hydraulic heads and temperatures to quantify reach-scale water and heat flux across the river-groundwater interface and hyporheic temperature dynamics of a lowland gravel bed river. The model was calibrated in order to constrain estimates of the most sensitive model parameters. The magnitude and variations of the simulated temperatures matched the observed ones, with an average mean absolute error of 0.7°C and an average Nash Sutcliffe efficiency of 0.87. Our results indicate that nonsubmerged streambed structures such as gravel bars cause substantial thermal heterogeneity within the saturated sediment at the reach scale. Individual hyporheic flow path temperatures strongly depend on the flow path residence time, flow path depth, river, and groundwater temperature. Variations in individual hyporheic flow path temperatures were up to 7.9°C, significantly higher than the daily average (2.8°C), but still lower than the average seasonal hyporheic temperature difference (19.2°C). The distribution between flow path temperatures and residence times follows a power law relationship with exponent of about 0.37. Based on this empirical relation, we further estimated the influence of hyporheic flow path residence time and temperature on oxygen consumption which was found to partly increase by up to 29% in simulations.

Numerically robust and efficient nonlocal electron transport in 2D DRACO simulations

NASA Astrophysics Data System (ADS)

Cao, Duc; Chenhall, Jeff; Moses, Greg; Delettrez, Jacques; Collins, Tim

2013-10-01

An improved implicit algorithm based on Schurtz, Nicolai and Busquet (SNB) algorithm for nonlocal electron transport is presented. Validation with direct drive shock timing experiments and verification with the Goncharov nonlocal model in 1D LILAC simulations demonstrate the viability of this efficient algorithm for producing 2D lagrangian radiation hydrodynamics direct drive simulations. Additionally, simulations provide strong incentive to further modify key parameters within the SNB theory, namely the ``mean free path.'' An example 2D polar drive simulation to study 2D effects of the nonlocal flux as well as mean free path modifications will also be presented. This research was supported by the University of Rochester Laboratory for Laser Energetics.

Periscopic Spine Surgery

DTIC Science & Technology

2005-03-01

Guided Technologies, Boulder, CO; motion path built from three orthogonal sinusoidal paths is Optotrak , Northern Digital, Waterloo, ON) optical tracking...Hopkins University using an Optotrak to evaluate the simulated motions. The Optotrak (Northern Digital, Inc.) is an optical high- precision 3-D motion...verify the accuracy of the RMS, tests were carried out using the Optotrak , which was placed about 2 m from the simulator. For each test, two sets of data

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

Computing the total atmospheric refraction for real-time optical imaging sensor simulation

NASA Astrophysics Data System (ADS)

Olson, Richard F.

2015-05-01

Fast and accurate computation of light path deviation due to atmospheric refraction is an important requirement for real-time simulation of optical imaging sensor systems. A large body of existing literature covers various methods for application of Snell's Law to the light path ray tracing problem. This paper provides a discussion of the adaptation to real time simulation of atmospheric refraction ray tracing techniques used in mid-1980's LOWTRAN releases. The refraction ray trace algorithm published in a LOWTRAN-6 technical report by Kneizys (et. al.) has been coded in MATLAB for development, and in C-language for simulation use. To this published algorithm we have added tuning parameters for variable path segment lengths, and extensions for Earth grazing and exoatmospheric "near Earth" ray paths. Model atmosphere properties used to exercise the refraction algorithm were obtained from tables published in another LOWTRAN-6 related report. The LOWTRAN-6 based refraction model is applicable to atmospheric propagation at wavelengths in the IR and visible bands of the electromagnetic spectrum. It has been used during the past two years by engineers at the U.S. Army Aviation and Missile Research, Development and Engineering Center (AMRDEC) in support of several advanced imaging sensor simulations. Recently, a faster (but sufficiently accurate) method using Gauss-Chebyshev Quadrature integration for evaluating the refraction integral was adopted.

Quadcopter Path Following Control Design Using Output Feedback with Command Generator Tracker LOS Based At Square Path

NASA Astrophysics Data System (ADS)

Nugraha, A. T.; Agustinah, T.

2018-01-01

Quadcopter an unstable system, underactuated and nonlinear in quadcopter control research developments become an important focus of attention. In this study, following the path control method for position on the X and Y axis, used structure-Generator Tracker Command (CGT) is tested. Attitude control and position feedback quadcopter is compared using the optimal output. The addition of the H∞ performance optimal output feedback control is used to maintain the stability and robustness of quadcopter. Iterative numerical techniques Linear Matrix Inequality (LMI) is used to find the gain controller. The following path control problems is solved using the method of LQ regulators with output feedback. Simulations show that the control system can follow the paths that have been defined in the form of a reference signal square shape. The result of the simulation suggest that the method which used can bring the yaw angle at the expected value algorithm. Quadcopter can do automatically following path with cross track error mean X=0.5 m and Y=0.2 m.

Monte Carlo simulation for coherent backscattering with diverging illumination (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wu, Wenli; Radosevich, Andrew J.; Eshein, Adam; Nguyen, The-Quyen; Backman, Vadim

2016-03-01

Diverging beam illumination is widely used in many optical techniques especially in fiber optic applications and coherence phenomenon is one of the most important properties to consider for these applications. Until now, people have used Monte Carlo simulations to study the backscattering coherence phenomenon in collimated beam illumination only. We are the first one to study the coherence phenomenon under the exact diverging beam geometry by taking into account the impossibility of the existence for the exact time-reversed path pairs of photons, which is the main contribution to the backscattering coherence pattern in collimated beam. In this work, we present a Monte Carlo simulation that considers the influence of the illumination numerical aperture. The simulation tracks the electric field for the unique paths of forward path and reverse path in time-reversed pairs of photons as well as the same path shared by them. With this approach, we can model the coherence pattern formed between the pairs by considering their phase difference at the collection plane directly. To validate this model, we use the Low-coherence Enhanced Backscattering Spectroscopy, one of the instruments looking at the coherence pattern using diverging beam illumination, as the benchmark to compare with. In the end, we show how this diverging configuration would significantly change the coherent pattern under coherent light source and incoherent light source. This Monte Carlo model we developed can be used to study the backscattering phenomenon in both coherence and non-coherence situation with both collimated beam and diverging beam setups.

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

PubMed

Tims, Maria; Akkermans, Jos

2017-01-01

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

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

PubMed Central

Akkermans, Jos

2017-01-01

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

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

Zhang, Yuxuan; Bilheux, Jean -Christophe

ImagingReso is an open-source Python library that simulates the neutron resonance signal for neutron imaging measurements. By defining the sample information such as density, thickness in the neutron path, and isotopic ratios of the elemental composition of the material, this package plots the expected resonance peaks for a selected neutron energy range. Various sample types such as layers of single elements (Ag, Co, etc. in solid form), chemical compounds (UO 3, Gd 2O 3, etc.), or even multiple layers of both types can be plotted with this package. As a result, major plotting features include display of the transmission/attenuation inmore » wavelength, energy, and time scale, and show/hide elemental and isotopic contributions in the total resonance signal.« less

Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures

NASA Astrophysics Data System (ADS)

Bishop, Kevin P.; Roy, Pierre-Nicholas

2018-03-01

Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures.

PubMed

Bishop, Kevin P; Roy, Pierre-Nicholas

2018-03-14

Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

A comparative study of inelastic scattering models at energy levels ranging from 0.5 keV to 10 keV

NASA Astrophysics Data System (ADS)

Hu, Chia-Yu; Lin, Chun-Hung

2017-03-01

Six models, including a single-scattering model, four hybrid models, and one dielectric function model, were evaluated using Monte Carlo simulations for aluminum and copper at incident beam energies ranging from 0.5 keV to 10 keV. The inelastic mean free path, mean energy loss per unit path length, and backscattering coefficients obtained by these models are compared and discussed to understand the merits of the various models. ANOVA (analysis of variance) statistical models were used to quantify the effects of inelastic cross section and energy loss models on the basis of the simulated results deviation from the experimental data for the inelastic mean free path, the mean energy loss per unit path length, and the backscattering coefficient, as well as their correlations. This work in this study is believed to be the first application of ANOVA models towards evaluating inelastic electron beam scattering models. This approach is an improvement over the traditional approach which involves only visual estimation of the difference between the experimental data and simulated results. The data suggests that the optimization of the effective electron number per atom, binding energy, and cut-off energy of an inelastic model for different materials at different beam energies is more important than the selection of inelastic models for Monte Carlo electron scattering simulation. During the simulations, parameters in the equations should be tuned according to different materials for different beam energies rather than merely employing default parameters for an arbitrary material. Energy loss models and cross-section formulas are not the main factors influencing energy loss. Comparison of the deviation of the simulated results from the experimental data shows a significant correlation (p < 0.05) between the backscattering coefficient and energy loss per unit path length. The inclusion of backscattering electrons generated by both primary and secondary electrons for backscattering coefficient simulation is recommended for elements with high atomic numbers. In hybrid models, introducing the inner shell ionization model improves the accuracy of simulated results.

Path Integral Metadynamics.

PubMed

Quhe, Ruge; Nava, Marco; Tiwary, Pratyush; Parrinello, Michele

2015-04-14

We develop a new efficient approach for the simulation of static properties of quantum systems using path integral molecular dynamics in combination with metadynamics. We use the isomorphism between a quantum system and a classical one in which a quantum particle is mapped into a ring polymer. A history dependent biasing potential is built as a function of the elastic energy of the isomorphic polymer. This enhances fluctuations in the shape and size of the necklace in a controllable manner and allows escaping deep energy minima in a limited computer time. In this way, we are able to sample high free energy regions and cross barriers, which would otherwise be insurmountable with unbiased methods. This substantially improves the ability of finding the global free energy minimum as well as exploring other metastable states. The performance of the new technique is demonstrated by illustrative applications on model potentials of varying complexity.

Adaptive Conditioning of Multiple-Point Geostatistical Facies Simulation to Flow Data with Facies Probability Maps

NASA Astrophysics Data System (ADS)

Khodabakhshi, M.; Jafarpour, B.

2013-12-01

Characterization of complex geologic patterns that create preferential flow paths in certain reservoir systems requires higher-order geostatistical modeling techniques. Multipoint statistics (MPS) provides a flexible grid-based approach for simulating such complex geologic patterns from a conceptual prior model known as a training image (TI). In this approach, a stationary TI that encodes the higher-order spatial statistics of the expected geologic patterns is used to represent the shape and connectivity of the underlying lithofacies. While MPS is quite powerful for describing complex geologic facies connectivity, the nonlinear and complex relation between the flow data and facies distribution makes flow data conditioning quite challenging. We propose an adaptive technique for conditioning facies simulation from a prior TI to nonlinear flow data. Non-adaptive strategies for conditioning facies simulation to flow data can involves many forward flow model solutions that can be computationally very demanding. To improve the conditioning efficiency, we develop an adaptive sampling approach through a data feedback mechanism based on the sampling history. In this approach, after a short period of sampling burn-in time where unconditional samples are generated and passed through an acceptance/rejection test, an ensemble of accepted samples is identified and used to generate a facies probability map. This facies probability map contains the common features of the accepted samples and provides conditioning information about facies occurrence in each grid block, which is used to guide the conditional facies simulation process. As the sampling progresses, the initial probability map is updated according to the collective information about the facies distribution in the chain of accepted samples to increase the acceptance rate and efficiency of the conditioning. This conditioning process can be viewed as an optimization approach where each new sample is proposed based on the sampling history to improve the data mismatch objective function. We extend the application of this adaptive conditioning approach to the case where multiple training images are proposed to describe the geologic scenario in a given formation. We discuss the advantages and limitations of the proposed adaptive conditioning scheme and use numerical experiments from fluvial channel formations to demonstrate its applicability and performance compared to non-adaptive conditioning techniques.

Turbulent Flow Simulation at the Exascale: Opportunities and Challenges Workshop: August 4-5, 2015, Washington, D.C.

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

Sprague, Michael A.; Boldyrev, Stanislav; Fischer, Paul

This report details the impact exascale will bring to turbulent-flow simulations in applied science and technology. The need for accurate simulation of turbulent flows is evident across the DOE applied-science and engineering portfolios, including combustion, plasma physics, nuclear-reactor physics, wind energy, and atmospheric science. The workshop brought together experts in turbulent-flow simulation, computational mathematics, and high-performance computing. Building upon previous ASCR workshops on exascale computing, participants defined a research agenda and path forward that will enable scientists and engineers to continually leverage, engage, and direct advances in computational systems on the path to exascale computing.

A new method for photon transport in Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Sato, T.; Ogawa, K.

1999-12-01

Monte Carlo methods are used to evaluate data methods such as scatter and attenuation compensation in single photon emission CT (SPECT), treatment planning in radiation therapy, and in many industrial applications. In Monte Carlo simulation, photon transport requires calculating the distance from the location of the emitted photon to the nearest boundary of each uniform attenuating medium along its path of travel, and comparing this distance with the length of its path generated at emission. Here, the authors propose a new method that omits the calculation of the location of the exit point of the photon from each voxel and of the distance between the exit point and the original position. The method only checks the medium of each voxel along the photon's path. If the medium differs from that in the voxel from which the photon was emitted, the authors calculate the location of the entry point in the voxel, and the length of the path is compared with the mean free path length generated by a random number. Simulations using the MCAT phantom show that the ratios of the calculation time were 1.0 for the voxel-based method, and 0.51 for the proposed method with a 256/spl times/256/spl times/256 matrix image, thereby confirming the effectiveness of the algorithm.

A True Eddy Accumulation - Eddy Covariance hybrid for measurements of turbulent trace gas fluxes

NASA Astrophysics Data System (ADS)

Siebicke, Lukas

2016-04-01

Eddy covariance (EC) is state-of-the-art in directly and continuously measuring turbulent fluxes of carbon dioxide and water vapor. However, low signal-to-noise ratios, high flow rates and missing or complex gas analyzers limit it's application to few scalars. True eddy accumulation, based on conditional sampling ideas by Desjardins in 1972, requires no fast response analyzers and is therefore potentially applicable to a wider range of scalars. Recently we showed possibly the first successful implementation of True Eddy Accumulation (TEA) measuring net ecosystem exchange of carbon dioxide of a grassland. However, most accumulation systems share the complexity of having to store discrete air samples in physical containers representing entire flux averaging intervals. The current study investigates merging principles of eddy accumulation and eddy covariance, which we here refer to as "true eddy accumulation in transient mode" (TEA-TM). This direct flux method TEA-TM combines true eddy accumulation with continuous sampling. The TEA-TM setup is simpler than discrete accumulation methods while avoiding the need for fast response gas analyzers and high flow rates required for EC. We implemented the proposed TEA-TM method and measured fluxes of carbon dioxide (CO2), methane (CH4) and water vapor (H2O) above a mixed beech forest at the Hainich Fluxnet and ICOS site, Germany, using a G2301 laser spectrometer (Picarro Inc., USA). We further simulated a TEA-TM sampling system using measured high frequency CO2 time series from an open-path gas analyzer. We operated TEA-TM side-by-side with open-, enclosed- and closed-path EC flux systems for CO2, H2O and CH4 (LI-7500, LI-7200, LI-6262, LI-7700, Licor, USA, and FGGA LGR, USA). First results show that TEA-TM CO2 fluxes were similar to EC fluxes. Remaining differences were similar to those between the three eddy covariance setups (open-, enclosed- and closed-path gas analyzers). Measured TEA-TM CO2 fluxes from our physical sampling system closely reproduced dynamics of simulated TEA-TM fluxes. In conclusion this study introduces a new approach to trace gas flux measurements using transient-mode true eddy accumulation. First TEA-TM CO2 fluxes compared favorably with side-by-side EC fluxes, in agreement with our previous experiments comparing discrete TEA to EC. True eddy accumulation has thus potential for measuring turbulent fluxes of a range of atmospheric tracers using slow response analyzers.

Reflectivity retrieval in a networked radar environment

NASA Astrophysics Data System (ADS)

Lim, Sanghun

Monitoring of precipitation using a high-frequency radar system such as X-band is becoming increasingly popular due to its lower cost compared to its counterpart at S-band. Networks of meteorological radar systems at higher frequencies are being pursued for targeted applications such as coverage over a city or a small basin. However, at higher frequencies, the impact of attenuation due to precipitation needs to be resolved for successful implementation. In this research, new attenuation correction algorithms are introduced to compensate the attenuation impact due to rain medium. In order to design X-band radar systems as well as evaluate algorithm development, it is useful to have simultaneous X-band observation with and without the impact of path attenuation. One way to obtain that data set is through theoretical models. Methodologies for generating realistic range profiles of radar variables at attenuating frequencies such as X-band for rain medium are presented here. Fundamental microphysical properties of precipitation, namely size and shape distribution information, are used to generate realistic profiles of X-band starting with S-band observations. Conditioning the simulation from S-band radar measurements maintains the natural distribution of microphysical parameters associated with rainfall. In this research, data taken by the CSU-CHILL radar and the National Center for Atmospheric Research S-POL radar are used to simulate X-band radar variables. Three procedures to simulate the radar variables at X-band and sample applications are presented. A new attenuation correction algorithm based on profiles of reflectivity, differential reflectivity, and differential propagation phase shift is presented. A solution for specific attenuation retrieval in rain medium is proposed that solves the integral equations for reflectivity and differential reflectivity with cumulative differential propagation phase shift constraint. The conventional rain profiling algorithms that connect reflectivity and specific attenuation can retrieve specific attenuation values along the radar path assuming a constant intercept parameter of the normalized drop size distribution. However, in convective storms, the drop size distribution parameters can have significant variation along the path. In this research, a dual-polarization rain profiling algorithm for horizontal-looking radars incorporating reflectivity as well as differential reflectivity profiles is developed. The dual-polarization rain profiling algorithm has been evaluated with X-band radar observations simulated from drop size distribution derived from high-resolution S-band measurements collected by the CSU-CHILL radar. The analysis shows that the dual-polarization rain profiling algorithm provides significant improvement over the current algorithms. A methodology for reflectivity and attenuation retrieval for rain medium in a networked radar environment is described. Electromagnetic waves backscattered from a common volume in networked radar systems are attenuated differently along the different paths. A solution for the specific attenuation distribution is proposed by solving the integral equation for reflectivity. The set of governing integral equations describing the backscatter and propagation of common resolution volume are solved simultaneously with constraints on total path attenuation. The proposed algorithm is evaluated based on simulated X-band radar observations synthesized from S-band measurements collected by the CSU-CHILL radar. Retrieved reflectivity and specific attenuation using the proposed method show good agreement with simulated reflectivity and specific attenuation.

Mobile robot dynamic path planning based on improved genetic algorithm

NASA Astrophysics Data System (ADS)

Wang, Yong; Zhou, Heng; Wang, Ying

2017-08-01

In dynamic unknown environment, the dynamic path planning of mobile robots is a difficult problem. In this paper, a dynamic path planning method based on genetic algorithm is proposed, and a reward value model is designed to estimate the probability of dynamic obstacles on the path, and the reward value function is applied to the genetic algorithm. Unique coding techniques reduce the computational complexity of the algorithm. The fitness function of the genetic algorithm fully considers three factors: the security of the path, the shortest distance of the path and the reward value of the path. The simulation results show that the proposed genetic algorithm is efficient in all kinds of complex dynamic environments.

A path planning method used in fluid jet polishing eliminating lightweight mirror imprinting effect

NASA Astrophysics Data System (ADS)

Li, Wenzong; Fan, Bin; Shi, Chunyan; Wang, Jia; Zhuo, Bin

2014-08-01

With the development of space technology, the design of optical system tends to large aperture lightweight mirror with high dimension-thickness ratio. However, when the lightweight mirror PV value is less than λ/10 , the surface will show wavy imprinting effect obviously. Imprinting effect introduced by head-tool pressure has become a technological barrier in high-precision lightweight mirror manufacturing. Fluid jet polishing can exclude outside pressure. Presently, machining tracks often used are grating type path, screw type path and pseudo-random path. On the edge of imprinting error, the speed of adjacent path points changes too fast, which causes the machine hard to reflect quickly, brings about new path error, and increases the polishing time due to superfluous path. This paper presents a new planning path method to eliminate imprinting effect. Simulation results show that the path of the improved grating path can better eliminate imprinting effect compared to the general path.

Simulation based optimization on automated fibre placement process

NASA Astrophysics Data System (ADS)

Lei, Shi

2018-02-01

In this paper, a software simulation (Autodesk TruPlan & TruFiber) based method is proposed to optimize the automate fibre placement (AFP) process. Different types of manufacturability analysis are introduced to predict potential defects. Advanced fibre path generation algorithms are compared with respect to geometrically different parts. Major manufacturing data have been taken into consideration prior to the tool paths generation to achieve high success rate of manufacturing.

Data-Driven Correlation Analysis Between Observed 3D Fatigue-Crack Path and Computed Fields from High-Fidelity, Crystal-Plasticity, Finite-Element Simulations

NASA Astrophysics Data System (ADS)

Pierson, Kyle D.; Hochhalter, Jacob D.; Spear, Ashley D.

2018-05-01

Systematic correlation analysis was performed between simulated micromechanical fields in an uncracked polycrystal and the known path of an eventual fatigue-crack surface based on experimental observation. Concurrent multiscale finite-element simulation of cyclic loading was performed using a high-fidelity representation of grain structure obtained from near-field high-energy x-ray diffraction microscopy measurements. An algorithm was developed to parameterize and systematically correlate the three-dimensional (3D) micromechanical fields from simulation with the 3D fatigue-failure surface from experiment. For comparison, correlation coefficients were also computed between the micromechanical fields and hypothetical, alternative surfaces. The correlation of the fields with hypothetical surfaces was found to be consistently weaker than that with the known crack surface, suggesting that the micromechanical fields of the cyclically loaded, uncracked microstructure might provide some degree of predictiveness for microstructurally small fatigue-crack paths, although the extent of such predictiveness remains to be tested. In general, gradients of the field variables exhibit stronger correlations with crack path than the field variables themselves. Results from the data-driven approach implemented here can be leveraged in future model development for prediction of fatigue-failure surfaces (for example, to facilitate univariate feature selection required by convolution-based models).

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

PubMed

Hopkins, Carl

2011-05-01

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

Flight testing and simulation of an F-15 airplane using throttles for flight control

NASA Technical Reports Server (NTRS)

Burcham, Frank W., Jr.; Maine, Trindel; Wolf, Thomas

1992-01-01

Flight tests and simulation studies using the throttles of an F-15 airplane for emergency flight control have been conducted at the NASA Dryden Flight Research Facility. The airplane and the simulation are capable of extended up-and-away flight, using only throttles for flight path control. Initial simulation results showed that runway landings using manual throttles-only control were difficult, but possible with practice. Manual approaches flown in the airplane were much more difficult, indicating a significant discrepancy between flight and simulation. Analysis of flight data and development of improved simulation models that resolve the discrepancy are discussed. An augmented throttle-only control system that controls bank angle and flight path with appropriate feedback parameters has also been developed, evaluated in simulations, and is planned for flight in the F-15.

SIMRAND I- SIMULATION OF RESEARCH AND DEVELOPMENT PROJECTS

NASA Technical Reports Server (NTRS)

Miles, R. F.

1994-01-01

The Simulation of Research and Development Projects program (SIMRAND) aids in the optimal allocation of R&D resources needed to achieve project goals. SIMRAND models the system subsets or project tasks as various network paths to a final goal. Each path is described in terms of task variables such as cost per hour, cost per unit, availability of resources, etc. Uncertainty is incorporated by treating task variables as probabilistic random variables. SIMRAND calculates the measure of preference for each alternative network. The networks yielding the highest utility function (or certainty equivalence) are then ranked as the optimal network paths. SIMRAND has been used in several economic potential studies at NASA's Jet Propulsion Laboratory involving solar dish power systems and photovoltaic array construction. However, any project having tasks which can be reduced to equations and related by measures of preference can be modeled. SIMRAND analysis consists of three phases: reduction, simulation, and evaluation. In the reduction phase, analytical techniques from probability theory and simulation techniques are used to reduce the complexity of the alternative networks. In the simulation phase, a Monte Carlo simulation is used to derive statistics on the variables of interest for each alternative network path. In the evaluation phase, the simulation statistics are compared and the networks are ranked in preference by a selected decision rule. The user must supply project subsystems in terms of equations based on variables (for example, parallel and series assembly line tasks in terms of number of items, cost factors, time limits, etc). The associated cumulative distribution functions and utility functions for each variable must also be provided (allowable upper and lower limits, group decision factors, etc). SIMRAND is written in Microsoft FORTRAN 77 for batch execution and has been implemented on an IBM PC series computer operating under DOS.

Regression-based model of skin diffuse reflectance for skin color analysis

NASA Astrophysics Data System (ADS)

Tsumura, Norimichi; Kawazoe, Daisuke; Nakaguchi, Toshiya; Ojima, Nobutoshi; Miyake, Yoichi

2008-11-01

A simple regression-based model of skin diffuse reflectance is developed based on reflectance samples calculated by Monte Carlo simulation of light transport in a two-layered skin model. This reflectance model includes the values of spectral reflectance in the visible spectra for Japanese women. The modified Lambert Beer law holds in the proposed model with a modified mean free path length in non-linear density space. The averaged RMS and maximum errors of the proposed model were 1.1 and 3.1%, respectively, in the above range.

R2 effect-size measures for mediation analysis

PubMed Central

Fairchild, Amanda J.; MacKinnon, David P.; Taborga, Marcia P.; Taylor, Aaron B.

2010-01-01

R2 effect-size measures are presented to assess variance accounted for in mediation models. The measures offer a means to evaluate both component paths and the overall mediated effect in mediation models. Statistical simulation results indicate acceptable bias across varying parameter and sample-size combinations. The measures are applied to a real-world example using data from a team-based health promotion program to improve the nutrition and exercise habits of firefighters. SAS and SPSS computer code are also provided for researchers to compute the measures in their own data. PMID:19363189

R2 effect-size measures for mediation analysis.

PubMed

Fairchild, Amanda J; Mackinnon, David P; Taborga, Marcia P; Taylor, Aaron B

2009-05-01

R(2) effect-size measures are presented to assess variance accounted for in mediation models. The measures offer a means to evaluate both component paths and the overall mediated effect in mediation models. Statistical simulation results indicate acceptable bias across varying parameter and sample-size combinations. The measures are applied to a real-world example using data from a team-based health promotion program to improve the nutrition and exercise habits of firefighters. SAS and SPSS computer code are also provided for researchers to compute the measures in their own data.

EVA Suit Microbial Leakage Investigation Project

NASA Technical Reports Server (NTRS)

Falker, Jay; Baker, Christopher; Clayton, Ronald; Rucker, Michelle

2016-01-01

The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during simulated planetary exploration activities. Data will be released to the planetary protection and science communities, and advanced EVA system designers. In the best case scenario, we will discover that very little microbial contamination leaks from our current or prototype suit designs, in the worst case scenario, we will identify leak paths, learn more about what affects leakage--and we'll have a new, flight-certified swab tool for our EVA toolbox.

Dissolution-induced preferential flow in a limestone fracture.

PubMed

Liu, Jishan; Polak, Amir; Elsworth, Derek; Grader, Avrami

2005-06-01

Flow in a rock fracture is surprisingly sensitive to the evolution of flow paths that develop as a result of dissolution. Net dissolution may either increase or decrease permeability uniformly within the fracture, or may form a preferential flow path through which most of the injected fluid flows, depending on the prevailing ambient mechanical and chemical conditions. A flow-through test was completed on an artificial fracture in limestone at room temperature under ambient confining stress of 3.5 MPa. The sample was sequentially circulated by water of two different compositions through the 1500 h duration of the experiment; the first 935 h by tap groundwater, followed by 555 h of distilled water. Measurements of differential pressures between the inlet and the outlet, fluid and dissolved mass fluxes, and concurrent X-ray CT imaging and sectioning were used to characterize the evolution of flow paths within the limestone fracture. During the initial circulation of groundwater, the differential pressure increased almost threefold, and was interpreted as a net reduction in permeability as the contacting asperities across the fracture are removed, and the fracture closes. With the circulation of distilled water, permeability initially reduces threefold, and ultimately increases by two orders of magnitude. This spontaneous switch from net decrease in permeability, to net increase occurred with no change in flow rate or applied effective stress, and is attributed to the evolving localization of flow path as evidenced by CT images. Based on the X-ray CT characterizations, a flow path-dependent flow model was developed to simulate the evolution of flow paths within the fracture and its influence on the overall flow behaviors of the injected fluid in the fracture.

Simulation of the Load-Unload Paths Experienced by Rock in the Vicinity of Buried Explosions.

DTIC Science & Technology

1977-12-01

Y99QAXSB04903 H2590D. 19. KEY WORDS (Continue on revere. aide if necessary end Identify by block number) Kayenta Sandstone Strain and Stress Paths Buried...These calculations are used to define loading and unloading paths in static laboratory tests on Kayenta sandstone. The data presented hsreithus...spherical explosions in an infinite medium. The material tested in the experimental program is Kayenta sandstone. 5 STRESS PATH DETERMINATION FROM FINITE

Use of 3H/3He Ages to evaluate and improve groundwater flow models in a complex buried-valley aquifer

USGS Publications Warehouse

Sheets, Rodney A.; Bair, E. Scott; Rowe, Gary L.

1998-01-01

Combined use of the tritium/helium 3 (3H/3He) dating technique and particle-tracking analysis can improve flow-model calibration. As shown at two sites in the Great Miami buried-valley aquifer in southwestern Ohio, the combined use of 3H/3He age dating and particle tracking led to a lower mean absolute error between measured heads and simulated heads than in the original calibrated models and/or between simulated travel times and 3H/3He ages. Apparent groundwater ages were obtained for water samples collected from 44 wells at two locations where previously constructed finite difference models of groundwater flow were available (Mound Plant and Wright-Patterson Air Force Base (WPAFB)). The two-layer Mound Plant model covers 11 km2 within the buried-valley aquifer. The WPAFB model has three layers and covers 262 km2 within the buried-valley aquifer and adjacent bedrock uplands. Sampled wells were chosen along flow paths determined from potentiometric maps or particle-tracking analyses. Water samples were collected at various depths within the aquifer. In the Mound Plant area, samples used for comparison of 3H/3He ages with simulated travel times were from wells completed in the uppermost model layer. Simulated travel times agreed well with 3H/3He ages. The mean absolute error (MAE) was 3.5 years. Agreement in ages at WPAFB decreased with increasing depth in the system. The MAEs were 1.63, 17.2, and 255 years for model layers 1, 2, and 3, respectively. Discrepancies between the simulated travel times and 3H/3He ages were assumed to be due to improper conceptualization or incorrect parameterization of the flow models. Selected conceptual and parameter modifications to the models resulted in improved agreement between 3H/3He ages and simulated travel times and between measured and simulated heads and flows.

Systems and methods for analyzing liquids under vacuum

DOEpatents

Yu, Xiao-Ying; Yang, Li; Cowin, James P.; Iedema, Martin J.; Zhu, Zihua

2013-10-15

Systems and methods for supporting a liquid against a vacuum pressure in a chamber can enable analysis of the liquid surface using vacuum-based chemical analysis instruments. No electrical or fluid connections are required to pass through the chamber walls. The systems can include a reservoir, a pump, and a liquid flow path. The reservoir contains a liquid-phase sample. The pump drives flow of the sample from the reservoir, through the liquid flow path, and back to the reservoir. The flow of the sample is not substantially driven by a differential between pressures inside and outside of the liquid flow path. An aperture in the liquid flow path exposes a stable portion of the liquid-phase sample to the vacuum pressure within the chamber. The radius, or size, of the aperture is less than or equal to a critical value required to support a meniscus of the liquid-phase sample by surface tension.

Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia.

PubMed

Miklós, István; Darling, Aaron E

2009-06-22

Inversions are among the most common mutations acting on the order and orientation of genes in a genome, and polynomial-time algorithms exist to obtain a minimal length series of inversions that transform one genome arrangement to another. However, the minimum length series of inversions (the optimal sorting path) is often not unique as many such optimal sorting paths exist. If we assume that all optimal sorting paths are equally likely, then statistical inference on genome arrangement history must account for all such sorting paths and not just a single estimate. No deterministic polynomial algorithm is known to count the number of optimal sorting paths nor sample from the uniform distribution of optimal sorting paths. Here, we propose a stochastic method that uniformly samples the set of all optimal sorting paths. Our method uses a novel formulation of parallel Markov chain Monte Carlo. In practice, our method can quickly estimate the total number of optimal sorting paths. We introduce a variant of our approach in which short inversions are modeled to be more likely, and we show how the method can be used to estimate the distribution of inversion lengths and breakpoint usage in pathogenic Yersinia pestis. The proposed method has been implemented in a program called "MC4Inversion." We draw comparison of MC4Inversion to the sampler implemented in BADGER and a previously described importance sampling (IS) technique. We find that on high-divergence data sets, MC4Inversion finds more optimal sorting paths per second than BADGER and the IS technique and simultaneously avoids bias inherent in the IS technique.

Analysis of water flow paths: methodology and example calculations for a potential geological repository in Sweden.

PubMed

Werner, Kent; Bosson, Emma; Berglund, Sten

2006-12-01

Safety assessment related to the siting of a geological repository for spent nuclear fuel deep in the bedrock requires identification of potential flow paths and the associated travel times for radionuclides originating at repository depth. Using the Laxemar candidate site in Sweden as a case study, this paper describes modeling methodology, data integration, and the resulting water flow models, focusing on the Quaternary deposits and the upper 150 m of the bedrock. Example simulations identify flow paths to groundwater discharge areas and flow paths in the surface system. The majority of the simulated groundwater flow paths end up in the main surface waters and along the coastline, even though the particles used to trace the flow paths are introduced with a uniform spatial distribution at a relatively shallow depth. The calculated groundwater travel time, determining the time available for decay and retention of radionuclides, is on average longer to the coastal bays than to other biosphere objects at the site. Further, it is demonstrated how GIS-based modeling can be used to limit the number of surface flow paths that need to be characterized for safety assessment. Based on the results, the paper discusses an approach for coupling the present models to a model for groundwater flow in the deep bedrock.

Bidirectional amplifier

DOEpatents

Wright, James T.

1986-01-01

A bilateral circuit is operable for transmitting signals in two directions without generation of ringing due to feedback caused by the insertion of the circuit. The circuit may include gain for each of the signals to provide a bidirectional amplifier. The signals are passed through two separate paths, with a unidirectional amplifier in each path. A controlled sampling device is provided in each path for sampling the two signals. Any feedback loop between the two signals is disrupted by providing a phase displacement between the control signals for the two sampling devices.

Bidirectional amplifier

DOEpatents

Wright, J.T.

1984-02-02

A bilateral circuit is operable for transmitting signals in two directions without generation of ringing due to feedback caused by the insertion of the circuit. The circuit may include gain for each of the signals to provide a bidirectional amplifier. The signals are passed through two separate paths, with a unidirectional amplifier in each path. A controlled sampling device is provided in each path for sampling the two signals. Any feedback loop between the two signals is disrupted by providing a phase displacement between the control signals for the two sampling devices.

Simulation of photon attenuation coefficients for high effective shielding material Lead-Boron Polyethyene

NASA Astrophysics Data System (ADS)

Zhang, L.; Jia, M. C.; Gong, J. J.; Xia, W. M.

2017-12-01

The mass attenuation coefficient of various Lead-Boron Polyethylene samples which can be used as the photon shielding materials in marine reactor, have been simulated using the MCNP-5 code, and compared with the theoretical values at the photon energy range 0.001MeV—20MeV. A good agreement has been observed. The variations of mass attenuation coefficient, linear attenuation coefficient and mean free path with photon energy between 0.001MeV to 100MeV have been plotted. The result shows that all the coefficients strongly depends on the photon energy, material atomic composition and density. The dose transmission factors for source Cesium-137 and Cobalt-60 have been worked out and their variations with the thickness of various sample materials have also been plotted. The variations show that with the increase of materials thickness the dose transmission factors decrease continuously. The results of this paper can provide some reference for the use of the high effective shielding material Lead-Boron Polyethyene.

Computerized X-ray Microtomography Observations and Fluid Flow Measurements of the Effect of Effective Stress on Fractured Reservoir Seal Shale

NASA Astrophysics Data System (ADS)

Welch, N.; Crawshaw, J.; Boek, E.

2014-12-01

The successful storage of carbon dioxide in geologic formations requires an in-depth understanding of all reservoir characteristics and morphologies. An intact and substantial seal formation above a storage reservoir is required for a significant portion of the initial sealing mechanisms believed to occur during carbon dioxide storage operations. Shales are a common seal formation rock types found above numerous hydrocarbon reservoirs, as well as potential saline aquifer storage locations. Shales commonly have very low permeability, however they also have the tendency to be quite fissile, and the formation of fractures within these seals can have a significant detrimental effect on the sealing potential of a reservoir and amount to large areas of high permeability and low capillary pressures compared to the surrounding intact rock. Fractured shales also have an increased current interest due to the increasing development of shale gas reservoirs using hydraulic fracturing techniques. This work shows the observed changes that occur within fractured pieces of reservoir seal shale samples, along with quarry analogues, using an in-situ micro-CT fluid flow imaging apparatus with a Hassler type core holder. Changes within the preferential flow path under different stress regimes as well as physical changes to the fracture geometry are reported. Lattice Boltzmann flow simulations were then performed on the extracted flow paths and compared to experiment permeability measurements. The preferential flow path of carbon dioxide through the fracture network is also observed and compared to the results two-phase Lattice Boltzmann fluid flow simulations.

System and method for measuring residual stress

DOEpatents

Prime, Michael B.

2002-01-01

The present invention is a method and system for determining the residual stress within an elastic object. In the method, an elastic object is cut along a path having a known configuration. The cut creates a portion of the object having a new free surface. The free surface then deforms to a contour which is different from the path. Next, the contour is measured to determine how much deformation has occurred across the new free surface. Points defining the contour are collected in an empirical data set. The portion of the object is then modeled in a computer simulator. The points in the empirical data set are entered into the computer simulator. The computer simulator then calculates the residual stress along the path which caused the points within the object to move to the positions measured in the empirical data set. The calculated residual stress is then presented in a useful format to an analyst.

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

PubMed Central

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

2017-01-01

Background: The Norwegian Cervical Cancer Screening Program recommends screening every 3 years for women between 25 and 69 years of age. There is a large difference in the percentage of unsatisfactory samples between laboratories that use different brands of liquid-based cytology. We wished to examine if inadequate ThinPrep samples could be satisfactory by processing them with the SurePath protocol. Materials and Methods: A total of 187 inadequate ThinPrep specimens from the Department of Clinical Pathology at University Hospital of North Norway were sent to Akershus University Hospital for conversion to SurePath medium. Ninety-one (48.7%) were processed through the automated “gynecologic” application for cervix cytology samples, and 96 (51.3%) were processed with the “nongynecological” automatic program. Results: Out of 187 samples that had been unsatisfactory by ThinPrep, 93 (49.7%) were satisfactory after being converted to SurePath. The rate of satisfactory cytology was 36.6% and 62.5% for samples run through the “gynecology” program and “nongynecology” program, respectively. Of the 93 samples that became satisfactory after conversion from ThinPrep to SurePath, 80 (86.0%) were screened as normal while 13 samples (14.0%) were given an abnormal diagnosis, which included 5 atypical squamous cells of undetermined significance, 5 low-grade squamous intraepithelial lesion, 2 atypical glandular cells not otherwise specified, and 1 atypical squamous cells cannot exclude high-grade squamous intraepithelial lesion. A total of 2.1% (4/187) of the women got a diagnosis of cervical intraepithelial neoplasia 2 or higher at a later follow-up. Conclusions: Converting cytology samples from ThinPrep to SurePath processing can reduce the number of unsatisfactory samples. The samples should be run through the “nongynecology” program to ensure an adequate number of cells. PMID:28900466

An Extended Trajectory Mechanics Approach for Calculating the Path of a Pressure Transient: Derivation and Illustration

NASA Astrophysics Data System (ADS)

Vasco, D. W.

2018-04-01

Following an approach used in quantum dynamics, an exponential representation of the hydraulic head transforms the diffusion equation governing pressure propagation into an equivalent set of ordinary differential equations. Using a reservoir simulator to determine one set of dependent variables leaves a reduced set of equations for the path of a pressure transient. Unlike the current approach for computing the path of a transient, based on a high-frequency asymptotic solution, the trajectories resulting from this new formulation are valid for arbitrary spatial variations in aquifer properties. For a medium containing interfaces and layers with sharp boundaries, the trajectory mechanics approach produces paths that are compatible with travel time fields produced by a numerical simulator, while the asymptotic solution produces paths that bend too strongly into high permeability regions. The breakdown of the conventional asymptotic solution, due to the presence of sharp boundaries, has implications for model parameter sensitivity calculations and the solution of the inverse problem. For example, near an abrupt boundary, trajectories based on the asymptotic approach deviate significantly from regions of high sensitivity observed in numerical computations. In contrast, paths based on the new trajectory mechanics approach coincide with regions of maximum sensitivity to permeability changes.

Simulation of car movement along circular path

NASA Astrophysics Data System (ADS)

Fedotov, A. I.; Tikhov-Tinnikov, D. A.; Ovchinnikova, N. I.; Lysenko, A. V.

2017-10-01

Under operating conditions, suspension system performance changes which negatively affects vehicle stability and handling. The paper aims to simulate the impact of changes in suspension system performance on vehicle stability and handling. Methods. The paper describes monitoring of suspension system performance, testing of vehicle stability and handling, analyzes methods of suspension system performance monitoring under operating conditions. The mathematical model of a car movement along a circular path was developed. Mathematical tools describing a circular movement of a vehicle along a horizontal road were developed. Turning car movements were simulated. Calculation and experiment results were compared. Simulation proves the applicability of a mathematical model for assessment of the impact of suspension system performance on vehicle stability and handling.

A dynamic Brownian bridge movement model to estimate utilization distributions for heterogeneous animal movement.

PubMed

Kranstauber, Bart; Kays, Roland; Lapoint, Scott D; Wikelski, Martin; Safi, Kamran

2012-07-01

1. The recently developed Brownian bridge movement model (BBMM) has advantages over traditional methods because it quantifies the utilization distribution of an animal based on its movement path rather than individual points and accounts for temporal autocorrelation and high data volumes. However, the BBMM assumes unrealistic homogeneous movement behaviour across all data. 2. Accurate quantification of the utilization distribution is important for identifying the way animals use the landscape. 3. We improve the BBMM by allowing for changes in behaviour, using likelihood statistics to determine change points along the animal's movement path. 4. This novel extension, outperforms the current BBMM as indicated by simulations and examples of a territorial mammal and a migratory bird. The unique ability of our model to work with tracks that are not sampled regularly is especially important for GPS tags that have frequent failed fixes or dynamic sampling schedules. Moreover, our model extension provides a useful one-dimensional measure of behavioural change along animal tracks. 5. This new method provides a more accurate utilization distribution that better describes the space use of realistic, behaviourally heterogeneous tracks. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Water evaporation: a transition path sampling study.

PubMed

Varilly, Patrick; Chandler, David

2013-02-07

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

Mission Planning and Decision Support for Underwater Glider Networks: A Sampling on-Demand Approach

PubMed Central

Ferri, Gabriele; Cococcioni, Marco; Alvarez, Alberto

2015-01-01

This paper describes an optimal sampling approach to support glider fleet operators and marine scientists during the complex task of planning the missions of fleets of underwater gliders. Optimal sampling, which has gained considerable attention in the last decade, consists in planning the paths of gliders to minimize a specific criterion pertinent to the phenomenon under investigation. Different criteria (e.g., A, G, or E optimality), used in geosciences to obtain an optimum design, lead to different sampling strategies. In particular, the A criterion produces paths for the gliders that minimize the overall level of uncertainty over the area of interest. However, there are commonly operative situations in which the marine scientists may prefer not to minimize the overall uncertainty of a certain area, but instead they may be interested in achieving an acceptable uncertainty sufficient for the scientific or operational needs of the mission. We propose and discuss here an approach named sampling on-demand that explicitly addresses this need. In our approach the user provides an objective map, setting both the amount and the geographic distribution of the uncertainty to be achieved after assimilating the information gathered by the fleet. A novel optimality criterion, called Aη, is proposed and the resulting minimization problem is solved by using a Simulated Annealing based optimizer that takes into account the constraints imposed by the glider navigation features, the desired geometry of the paths and the problems of reachability caused by ocean currents. This planning strategy has been implemented in a Matlab toolbox called SoDDS (Sampling on-Demand and Decision Support). The tool is able to automatically download the ocean fields data from MyOcean repository and also provides graphical user interfaces to ease the input process of mission parameters and targets. The results obtained by running SoDDS on three different scenarios are provided and show that SoDDS, which is currently used at NATO STO Centre for Maritime Research and Experimentation (CMRE), can represent a step forward towards a systematic mission planning of glider fleets, dramatically reducing the efforts of glider operators. PMID:26712763

Mission Planning and Decision Support for Underwater Glider Networks: A Sampling on-Demand Approach.

PubMed

Ferri, Gabriele; Cococcioni, Marco; Alvarez, Alberto

2015-12-26

This paper describes an optimal sampling approach to support glider fleet operators and marine scientists during the complex task of planning the missions of fleets of underwater gliders. Optimal sampling, which has gained considerable attention in the last decade, consists in planning the paths of gliders to minimize a specific criterion pertinent to the phenomenon under investigation. Different criteria (e.g., A, G, or E optimality), used in geosciences to obtain an optimum design, lead to different sampling strategies. In particular, the A criterion produces paths for the gliders that minimize the overall level of uncertainty over the area of interest. However, there are commonly operative situations in which the marine scientists may prefer not to minimize the overall uncertainty of a certain area, but instead they may be interested in achieving an acceptable uncertainty sufficient for the scientific or operational needs of the mission. We propose and discuss here an approach named sampling on-demand that explicitly addresses this need. In our approach the user provides an objective map, setting both the amount and the geographic distribution of the uncertainty to be achieved after assimilating the information gathered by the fleet. A novel optimality criterion, called A η , is proposed and the resulting minimization problem is solved by using a Simulated Annealing based optimizer that takes into account the constraints imposed by the glider navigation features, the desired geometry of the paths and the problems of reachability caused by ocean currents. This planning strategy has been implemented in a Matlab toolbox called SoDDS (Sampling on-Demand and Decision Support). The tool is able to automatically download the ocean fields data from MyOcean repository and also provides graphical user interfaces to ease the input process of mission parameters and targets. The results obtained by running SoDDS on three different scenarios are provided and show that SoDDS, which is currently used at NATO STO Centre for Maritime Research and Experimentation (CMRE), can represent a step forward towards a systematic mission planning of glider fleets, dramatically reducing the efforts of glider operators.

Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase:Barstar.

PubMed

Spaar, Alexander; Helms, Volkhard

2005-07-01

Over the past years Brownian dynamics (BD) simulations have been proven to be a suitable tool for the analysis of protein-protein association. The computed rates and relative trends for protein mutants and different ionic strength are generally in good agreement with experimental results, e.g. see ref 1. By design, BD simulations correspond to an intensive sampling over energetically favorable states, rather than to a systematic sampling over all possible states which is feasible only at rather low resolution. On the example of barnase and barstar, a well characterized model system of electrostatically steered diffusional encounter, we report here the computation of the 6-dimensional free energy landscape for the encounter process of two proteins by a novel, careful analysis of the trajectories from BD simulations. The aim of these studies was the clarification of the encounter state. Along the trajectories, the individual positions and orientations of one protein (relative to the other) are recorded and stored in so-called occupancy maps. Since the number of simulated trajectories is sufficiently high, these occupancy maps can be interpreted as a probability distribution which allows the calculation of the entropy landscape by the use of a locally defined entropy function. Additionally, the configuration dependent electrostatic and desolvation energies are recorded in separate maps. The free energy landscape of protein-protein encounter is finally obtained by summing the energy and entropy contributions. In the free energy profile along the reaction path, which is defined as the path along the minima in the free energy landscape, a minimum shows up suggesting this to be used as the definition of the encounter state. This minimum describes a state of reduced diffusion velocity where the electrostatic attraction is compensated by the repulsion due to the unfavorable desolvation of the charged residues and the entropy loss due to the increasing restriction of the motional freedom. In the simulations the orientational degrees of freedom at the encounter state are found to be less restricted than the translational degrees of freedom. Therefore, the orientational alignment of the two binding partners seems to take place beyond this free energy minimum. The free energy profiles along the reaction pathway are compared for different ionic strength and temperature. This novel analysis technique facilitates mechanistic interpretation of protein-protein encounter pathways which should be useful for interpretation of experimental results as well.

Verification of target motion effects on SAR imagery using the Gotcha GMTI challenge dataset

NASA Astrophysics Data System (ADS)

Hack, Dan E.; Saville, Michael A.

2010-04-01

This paper investigates the relationship between a ground moving target's kinematic state and its SAR image. While effects such as cross-range offset, defocus, and smearing appear well understood, their derivations in the literature typically employ simplifications of the radar/target geometry and assume point scattering targets. This study adopts a geometrical model for understanding target motion effects in SAR imagery, termed the target migration path, and focuses on experimental verification of predicted motion effects using both simulated and empirical datasets based on the Gotcha GMTI challenge dataset. Specifically, moving target imagery is generated from three data sources: first, simulated phase history for a moving point target; second, simulated phase history for a moving vehicle derived from a simulated Mazda MPV X-band signature; and third, empirical phase history from the Gotcha GMTI challenge dataset. Both simulated target trajectories match the truth GPS target position history from the Gotcha GMTI challenge dataset, allowing direct comparison between all three imagery sets and the predicted target migration path. This paper concludes with a discussion of the parallels between the target migration path and the measurement model within a Kalman filtering framework, followed by conclusions.

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

NASA Astrophysics Data System (ADS)

McGibbon, J.; Bretherton, C. S.

2017-06-01

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