METHANOGENESIS AND SULFATE REDUCTION IN CHEMOSTATS: II. MODEL DEVELOPMENT AND VERIFICATION

EPA Science Inventory

A comprehensive dynamic model is presented that simulates methanogenesis and sulfate reduction in a continuously stirred tank reactor (CSTR). This model incorporates the complex chemistry of anaerobic systems. A salient feature of the model is its ability to predict the effluent ...

Langley test highlights, 1982

NASA Technical Reports Server (NTRS)

1983-01-01

A 20 ft vertical spin tunnel, a 30 by 60 ft tunnel, a 7 by 10 ft high speed tunnel, a 4 by 7 meter tunnel, an 8 ft transonic pressure tunnel, a transonic dynamics tunnel, a 16 ft transonic tunnel, a national transonic facility, a 0.3 meter transonic cryogenic tunnel, a unitary plan wind tunnel, a hypersonic facilities complex, an 8 ft high temperature tunnel, an aircraft noise reduction lab, an avionics integration research lab, a DC9 full workload simulator, a transport simulator, a general aviation simulator, an advanced concepts simulator, a mission oriented terminal area simulation (MOTAS), a differential maneuvering simulator, a visual/motion simulator, a vehicle antenna test facility, an impact dynamics research facility, and a flight research facility are all reviewed.

An evaluation of noise reduction algorithms for particle-based fluid simulations in multi-scale applications

NASA Astrophysics Data System (ADS)

Zimoń, M. J.; Prosser, R.; Emerson, D. R.; Borg, M. K.; Bray, D. J.; Grinberg, L.; Reese, J. M.

2016-11-01

Filtering of particle-based simulation data can lead to reduced computational costs and enable more efficient information transfer in multi-scale modelling. This paper compares the effectiveness of various signal processing methods to reduce numerical noise and capture the structures of nano-flow systems. In addition, a novel combination of these algorithms is introduced, showing the potential of hybrid strategies to improve further the de-noising performance for time-dependent measurements. The methods were tested on velocity and density fields, obtained from simulations performed with molecular dynamics and dissipative particle dynamics. Comparisons between the algorithms are given in terms of performance, quality of the results and sensitivity to the choice of input parameters. The results provide useful insights on strategies for the analysis of particle-based data and the reduction of computational costs in obtaining ensemble solutions.

On the precision of quasi steady state assumptions in stochastic dynamics

NASA Astrophysics Data System (ADS)

Agarwal, Animesh; Adams, Rhys; Castellani, Gastone C.; Shouval, Harel Z.

2012-07-01

Many biochemical networks have complex multidimensional dynamics and there is a long history of methods that have been used for dimensionality reduction for such reaction networks. Usually a deterministic mass action approach is used; however, in small volumes, there are significant fluctuations from the mean which the mass action approach cannot capture. In such cases stochastic simulation methods should be used. In this paper, we evaluate the applicability of one such dimensionality reduction method, the quasi-steady state approximation (QSSA) [L. Menten and M. Michaelis, "Die kinetik der invertinwirkung," Biochem. Z 49, 333369 (1913)] for dimensionality reduction in case of stochastic dynamics. First, the applicability of QSSA approach is evaluated for a canonical system of enzyme reactions. Application of QSSA to such a reaction system in a deterministic setting leads to Michaelis-Menten reduced kinetics which can be used to derive the equilibrium concentrations of the reaction species. In the case of stochastic simulations, however, the steady state is characterized by fluctuations around the mean equilibrium concentration. Our analysis shows that a QSSA based approach for dimensionality reduction captures well the mean of the distribution as obtained from a full dimensional simulation but fails to accurately capture the distribution around that mean. Moreover, the QSSA approximation is not unique. We have then extended the analysis to a simple bistable biochemical network model proposed to account for the stability of synaptic efficacies; the substrate of learning and memory [J. E. Lisman, "A mechanism of memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase," Proc. Natl. Acad. Sci. U.S.A. 82, 3055-3057 (1985)], 10.1073/pnas.82.9.3055. Our analysis shows that a QSSA based dimensionality reduction method results in errors as big as two orders of magnitude in predicting the residence times in the two stable states.

A new battery-charging method suggested by molecular dynamics simulations.

PubMed

Abou Hamad, Ibrahim; Novotny, M A; Wipf, D O; Rikvold, P A

2010-03-20

Based on large-scale molecular dynamics simulations, we propose a new charging method that should be capable of charging a lithium-ion battery in a fraction of the time needed when using traditional methods. This charging method uses an additional applied oscillatory electric field. Our simulation results show that this charging method offers a great reduction in the average intercalation time for Li(+) ions, which dominates the charging time. The oscillating field not only increases the diffusion rate of Li(+) ions in the electrolyte but, more importantly, also enhances intercalation by lowering the corresponding overall energy barrier.

Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks

NASA Astrophysics Data System (ADS)

Fahrenthold, Eric; Bass, Joseph

2015-06-01

Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.

Modeling and Simulation of Metallurgical Process Based on Hybrid Petri Net

NASA Astrophysics Data System (ADS)

Ren, Yujuan; Bao, Hong

2016-11-01

In order to achieve the goals of energy saving and emission reduction of iron and steel enterprises, an increasing number of modeling and simulation technologies are used to research and analyse metallurgical production process. In this paper, the basic principle of Hybrid Petri net is used to model and analyse the Metallurgical Process. Firstly, the definition of Hybrid Petri Net System of Metallurgical Process (MPHPNS) and its modeling theory are proposed. Secondly, the model of MPHPNS based on material flow is constructed. The dynamic flow of materials and the real-time change of each technological state in metallurgical process are simulated vividly by using this model. The simulation process can implement interaction between the continuous event dynamic system and the discrete event dynamic system at the same level, and play a positive role in the production decision.

Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.

PubMed Central

Soares, C M; Martel, P J; Mendes, J; Carrondo, M A

1998-01-01

The tetraheme cytochrome c3 from Desulfovibrio vulgaris Hildenborough is studied using molecular dynamics simulation studies in explicit solvent. The high heme content of the protein, which has its core almost entirely made up of c-type heme, presents specific problems in the simulation. Instability in the structure is observed in long simulations above 1 ns, something that does not occur in a monoheme cytochrome, suggesting problems in heme parametrization. Given these stability problems, a partially restrained model, which avoids destruction of the structure, was created with the objective of performing free energy calculations of heme reduction, studies that require long simulations. With this model, the free energy of reduction of each individual heme was calculated. A correction in the long-range electrostatic interactions of charge groups belonging to the redox centers had to be made in order to make the system physically meaningful. Correlation is obtained between the calculated free energies and the experimental data for three of four hemes. However, the relative scale of the calculated energies is different from the scale of the experimental free energies. Reasons for this are discussed. In addition to the free energy calculations, this model allows the study of conformational changes upon reduction. Even if the precise details of the structural changes that take place in this system upon individual heme reduction are probably out of the reach of this study, it appears that these structural changes are small, similarly to what is observed for other redox proteins. This does not mean that their effect is minor, and one example is the conformational change observed in propionate D from heme I when heme II becomes reduced. A motion of this kind could be the basis of the experimentally observed cooperativity effects between heme reduction, namely positive cooperativity. PMID:9545034

Novel mutant of Escherichia coli asparaginase II to reduction of the glutaminase activity in treatment of acute lymphocytic leukemia by molecular dynamics simulations and QM-MM studies.

PubMed

Ardalan, Noeman; Mirzaie, Sako; Sepahi, Abbas Akhavan; Khavari-Nejad, Ramazan Ali

2018-03-01

L-Asparaginases (ASNase) belong to a family of amidohydrolases, have both asparaginase and glutaminase activity. Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. Bacterial ASNase has been used for the treatment of ALL. Glutaminase activity of enzyme causes some side effect and it is not essential for anticancer activity. The aim of this study was engineering of Escherichia coli asparaginase II to find a mutant with reduced glutaminase activity by molecular docking, molecular dynamics (MD) and QM-MM (Quantum mechanics molecular dynamics) simulations. Residues with low free energy of binding to Asn and high free binding energy to Gln were chosen for mutagenesis. Then, a mutant with higher glutaminase free binding energy was selected for further studies. Additionally, the MD simulation and QM-MM computation of wild type (WT) were employed and the selected mutated ASNase were analyzed and discussed. Our data showed that V27T is a good candidate to reduction the glutaminase activity, while has no remarkable effect on asparaginase activity of the enzyme. The simulation analysis revealed that V27T mutant is more stable than WT and mutant simulation was successful completely. QM-MM results confirmed the successfulness of our mutagenesis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Chaos and simple determinism in reversed field pinch plasmas: Nonlinear analysis of numerical simulation and experimental data

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

Watts, Christopher A.

In this dissertation the possibility that chaos and simple determinism are governing the dynamics of reversed field pinch (RFP) plasmas is investigated. To properly assess this possibility, data from both numerical simulations and experiment are analyzed. A large repertoire of nonlinear analysis techniques is used to identify low dimensional chaos in the data. These tools include phase portraits and Poincare sections, correlation dimension, the spectrum of Lyapunov exponents and short term predictability. In addition, nonlinear noise reduction techniques are applied to the experimental data in an attempt to extract any underlying deterministic dynamics. Two model systems are used to simulatemore » the plasma dynamics. These are the DEBS code, which models global RFP dynamics, and the dissipative trapped electron mode (DTEM) model, which models drift wave turbulence. Data from both simulations show strong indications of low dimensional chaos and simple determinism. Experimental date were obtained from the Madison Symmetric Torus RFP and consist of a wide array of both global and local diagnostic signals. None of the signals shows any indication of low dimensional chaos or low simple determinism. Moreover, most of the analysis tools indicate the experimental system is very high dimensional with properties similar to noise. Nonlinear noise reduction is unsuccessful at extracting an underlying deterministic system.« less

Atmospheric Moisture Budget and Spatial Resolution Dependence of Precipitation Extremes in Aquaplanet Simulations

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

Yang, Qing; Leung, Lai-Yung R.; Rauscher, Sara

This study investigates the resolution dependency of precipitation extremes in an aqua-planet framework. Strong resolution dependency of precipitation extremes is seen over both tropics and extra-tropics, and the magnitude of this dependency also varies with dynamical cores. Moisture budget analyses based on aqua-planet simulations with the Community Atmosphere Model (CAM) using the Model for Prediction Across Scales (MPAS) and High Order Method Modeling Environment (HOMME) dynamical cores but the same physics parameterizations suggest that during precipitation extremes moisture supply for surface precipitation is mainly derived from advective moisture convergence. The resolution dependency of precipitation extremes mainly originates from advective moisturemore » transport in the vertical direction. At most vertical levels over the tropics and in the lower atmosphere over the subtropics, the vertical eddy transport of mean moisture field dominates the contribution to precipitation extremes and its resolution dependency. Over the subtropics, the source of moisture, its associated energy, and the resolution dependency during extremes are dominated by eddy transport of eddies moisture at the mid- and upper-troposphere. With both MPAS and HOMME dynamical cores, the resolution dependency of the vertical advective moisture convergence is mainly explained by dynamical changes (related to vertical velocity or omega), although the vertical gradients of moisture act like averaging kernels to determine the sensitivity of the overall resolution dependency to the changes in omega at different vertical levels. The natural reduction of variability with coarser resolution, represented by areal data averaging (aggregation) effect, largely explains the resolution dependency in omega. The thermodynamic changes, which likely result from non-linear feedback in response to the large dynamical changes, are small compared to the overall changes in dynamics (omega). However, after excluding the data aggregation effect in omega, thermodynamic changes become relatively significant in offsetting the effect of dynamics leading to reduce differences between the simulated and aggregated results. Compared to MPAS, the simulated stronger vertical motion with HOMME also results in larger resolution dependency. Compared to the simulation at fine resolution, the vertical motion during extremes is insufficiently resolved/parameterized at the coarser resolution even after accounting for the natural reduction in variability with coarser resolution, and this is more distinct in the simulation with HOMME. To reduce uncertainties in simulated precipitation extremes, future development in cloud parameterizations must address their sensitivity to spatial resolution as well as dynamical cores.« less

Calibration of Reduced Dynamic Models of Power Systems using Phasor Measurement Unit (PMU) Data

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

Zhou, Ning; Lu, Shuai; Singh, Ruchi

2011-09-23

Accuracy of a power system dynamic model is essential to the secure and efficient operation of the system. Lower confidence on model accuracy usually leads to conservative operation and lowers asset usage. To improve model accuracy, identification algorithms have been developed to calibrate parameters of individual components using measurement data from staged tests. To facilitate online dynamic studies for large power system interconnections, this paper proposes a model reduction and calibration approach using phasor measurement unit (PMU) data. First, a model reduction method is used to reduce the number of dynamic components. Then, a calibration algorithm is developed to estimatemore » parameters of the reduced model. This approach will help to maintain an accurate dynamic model suitable for online dynamic studies. The performance of the proposed method is verified through simulation studies.« less

Engine dynamic analysis with general nonlinear finite element codes

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1991-01-01

A general engine dynamic analysis as a standard design study computational tool is described for the prediction and understanding of complex engine dynamic behavior. Improved definition of engine dynamic response provides valuable information and insights leading to reduced maintenance and overhaul costs on existing engine configurations. Application of advanced engine dynamic simulation methods provides a considerable cost reduction in the development of new engine designs by eliminating some of the trial and error process done with engine hardware development.

Modelling and simulation of a heat exchanger

NASA Technical Reports Server (NTRS)

Xia, Lei; Deabreu-Garcia, J. Alex; Hartley, Tom T.

1991-01-01

Two models for two different control systems are developed for a parallel heat exchanger. First by spatially lumping a heat exchanger model, a good approximate model which has a high system order is produced. Model reduction techniques are applied to these to obtain low order models that are suitable for dynamic analysis and control design. The simulation method is discussed to ensure a valid simulation result.

Spatially explicit modeling of mixed-severity fire regimes and landscape dynamics

Treesearch

Michael C. Wimberly; Rebecca S.H. Kennedy

2008-01-01

Simulation models of disturbance and succession are being increasingly applied to characterize landscape composition and dynamics under natural fire regimes, and to evaluate alternative management strategies for ecological restoration and fire hazard reduction. However, we have a limited understanding of how landscapes respond to changes in fire frequency, and about...

An adaptive model order reduction by proper snapshot selection for nonlinear dynamical problems

NASA Astrophysics Data System (ADS)

Nigro, P. S. B.; Anndif, M.; Teixeira, Y.; Pimenta, P. M.; Wriggers, P.

2016-04-01

Model Order Reduction (MOR) methods are employed in many fields of Engineering in order to reduce the processing time of complex computational simulations. A usual approach to achieve this is the application of Galerkin projection to generate representative subspaces (reduced spaces). However, when strong nonlinearities in a dynamical system are present and this technique is employed several times along the simulation, it can be very inefficient. This work proposes a new adaptive strategy, which ensures low computational cost and small error to deal with this problem. This work also presents a new method to select snapshots named Proper Snapshot Selection (PSS). The objective of the PSS is to obtain a good balance between accuracy and computational cost by improving the adaptive strategy through a better snapshot selection in real time (online analysis). With this method, it is possible a substantial reduction of the subspace, keeping the quality of the model without the use of the Proper Orthogonal Decomposition (POD).

A dynamic model for assessing the effects of management strategies on the reduction of construction and demolition waste.

PubMed

Yuan, Hongping; Chini, Abdol R; Lu, Yujie; Shen, Liyin

2012-03-01

During the past few decades, construction and demolition (C&D) waste has received increasing attention from construction practitioners and researchers worldwide. A plethora of research regarding C&D waste management has been published in various academic journals. However, it has been determined that existing studies with respect to C&D waste reduction are mainly carried out from a static perspective, without considering the dynamic and interdependent nature of the whole waste reduction system. This might lead to misunderstanding about the actual effect of implementing any waste reduction strategies. Therefore, this research proposes a model that can serve as a decision support tool for projecting C&D waste reduction in line with the waste management situation of a given construction project, and more importantly, as a platform for simulating effects of various management strategies on C&D waste reduction. The research is conducted using system dynamics methodology, which is a systematic approach that deals with the complexity - interrelationships and dynamics - of any social, economic and managerial system. The dynamic model integrates major variables that affect C&D waste reduction. In this paper, seven causal loop diagrams that can deepen understanding about the feedback relationships underlying C&D waste reduction system are firstly presented. Then a stock-flow diagram is formulated by using software for system dynamics modeling. Finally, a case study is used to illustrate the validation and application of the proposed model. Results of the case study not only built confidence in the model so that it can be used for quantitative analysis, but also assessed and compared the effect of three designed policy scenarios on C&D waste reduction. One major contribution of this study is the development of a dynamic model for evaluating C&D waste reduction strategies under various scenarios, so that best management strategies could be identified before being implemented in practice. Copyright © 2011 Elsevier Ltd. All rights reserved.

WavePacket: A Matlab package for numerical quantum dynamics.II: Open quantum systems, optimal control, and model reduction

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard; Hartmann, Carsten

2018-07-01

WavePacket is an open-source program package for numeric simulations in quantum dynamics. It can solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows, e.g., to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semi-classical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. Being highly versatile and offering visualization of quantum dynamics 'on the fly', WavePacket is well suited for teaching or research projects in atomic, molecular and optical physics as well as in physical or theoretical chemistry. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] which dealt with closed quantum systems and discrete variable representations, the present Part II focuses on the dynamics of open quantum systems, with Lindblad operators modeling dissipation and dephasing. This part also describes the WavePacket function for optimal control of quantum dynamics, building on rapid monotonically convergent iteration methods. Furthermore, two different approaches to dimension reduction implemented in WavePacket are documented here. In the first one, a balancing transformation based on the concepts of controllability and observability Gramians is used to identify states that are neither well controllable nor well observable. Those states are either truncated or averaged out. In the other approach, the H2-error for a given reduced dimensionality is minimized by H2 optimal model reduction techniques, utilizing a bilinear iterative rational Krylov algorithm. The present work describes the MATLAB version of WavePacket 5.3.0 which is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous worked-out demonstration examples with animated graphics can be found.

Brownian Dynamics and Molecular Dynamics Study of the Association between Hydrogenase and Ferredoxin from Chlamydomonas reinhardtii

PubMed Central

Long, Hai; Chang, Christopher H.; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon

2008-01-01

The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer. PMID:18621810

Investigations on KONUS beam dynamics using the pre-stripper drift tube linac at GSI

NASA Astrophysics Data System (ADS)

Xiao, C.; Du, X. N.; Groening, L.

2018-04-01

Interdigital H-mode (IH) drift tube linacs (DTLs) based on KONUS beam dynamics are very sensitive to the rf-phases and voltages at the gaps between tubes. In order to design these DTLs, a deep understanding of the underlying longitudinal beam dynamics is mandatory. The report presents tracking simulations along an IH-DTL using the PARTRAN and BEAMPATH codes together with MATHCAD and CST. Simulation results illustrate that the beam dynamics design of the pre-stripper IH-DTL at GSI is sensitive to slight deviations of rf-phase and gap voltages with impact to the mean beam energy at the DTL exit. Applying the existing geometrical design, rf-voltages, and rf-phases of the DTL were re-adjusted. In simulations this re-optimized design can provide for more than 90% of transmission of an intense 15 emA beam keeping the reduction of beam brilliance below 25%.

Simulation gravity modeling to spacecraft-tracking data - Analysis and application

NASA Technical Reports Server (NTRS)

Phillips, R. J.; Sjogren, W. L.; Abbott, E. A.; Zisk, S. H.

1978-01-01

It is proposed that line-of-sight gravity measurements derived from spacecraft-tracking data can be used for quantitative subsurface density modeling by suitable orbit simulation procedures. Such an approach avoids complex dynamic reductions and is analogous to the modeling of conventional surface gravity data. This procedure utilizes the vector calculations of a given gravity model in a simplified trajectory integration program that simulates the line-of-sight gravity. Solutions from an orbit simulation inversion and a dynamic inversion on Doppler observables compare well (within 1% in mass and size), and the error sources in the simulation approximation are shown to be quite small. An application of this technique is made to lunar crater gravity anomalies by simulating the complete Bouguer correction to several large young lunar craters. It is shown that the craters all have negative Bouguer anomalies.

Benchmarking nitrogen removal suspended-carrier biofilm systems using dynamic simulation.

PubMed

Vanhooren, H; Yuan, Z; Vanrolleghem, P A

2002-01-01

We are witnessing an enormous growth in biological nitrogen removal from wastewater. It presents specific challenges beyond traditional COD (carbon) removal. A possibility for optimised process design is the use of biomass-supporting media. In this paper, attached growth processes (AGP) are evaluated using dynamic simulations. The advantages of these systems that were qualitatively described elsewhere, are validated quantitatively based on a simulation benchmark for activated sludge treatment systems. This simulation benchmark is extended with a biofilm model that allows for fast and accurate simulation of the conversion of different substrates in a biofilm. The economic feasibility of this system is evaluated using the data generated with the benchmark simulations. Capital savings due to volume reduction and reduced sludge production are weighed out against increased aeration costs. In this evaluation, effluent quality is integrated as well.

Dynamic evaluation of the CMAQv5.0 modeling system: Assessing the model’s ability to simulate ozone changes due to NOx emission reductions

EPA Science Inventory

Regional air quality models are frequently used for regulatory applications to predict changes in air quality due to changes in emissions or changes in meteorology. Dynamic model evaluation is thus an important step in establishing credibility in the model predicted pollutant re...

“Overview and Evaluation of AQMEII Phase 2 Coupled ...

EPA Pesticide Factsheets

This presentation provides an overview of the second phase of the Air Quality Model Evaluation International Initative (AQMEII). Activities in this phase are focused on the application and evaluation of coupled meteorology-chemistry models to assess how well these models can simulate the observed spatio-temporal variability in the optical and radiative characteristics of atmospheric aerosols and associated feedbacks among aerosols, radiation, clouds, and precipitation. To this end, these modeling systems are being applied for annual simulations over both North America and Europe using common emissions and boundary conditions for all modeling groups. We present an overview of these common input datasets, observational datasets for model evaluation, and case studies for diagnostic evaluation. In addition to this overview, we also present results from AQMEII Phase 2 WRF/CMAQ simulations over North America for both 2006 and 2010. The time period between 2006 and 2010 was characterized by a 35% reduction in U.S. SO2 emissions and 20% reduction in U.S. NOx emissions, providing an opportunity for dynamic model evaluation by investigating the impact of emission reductions on ambient concentrations as well as aerosol/radiation feedback effects. We present results of this dynamic evaluation. We also present a brief overview of initial results from WRF-Chem and GEM-MACH simulations performed for the same time period and domain as part of AQMEII Phase 2. The National Exposu

Numerical simulation of the geometrical-optics reduction of CE2 and comparisons to quasilinear dynamics

NASA Astrophysics Data System (ADS)

Parker, Jeffrey B.

2018-05-01

Zonal flows have been observed to appear spontaneously from turbulence in a number of physical settings. A complete theory for their behavior is still lacking. Recently, a number of studies have investigated the dynamics of zonal flows using quasilinear (QL) theories and the statistical framework of a second-order cumulant expansion (CE2). A geometrical-optics (GO) reduction of CE2, derived under an assumption of separation of scales between the fluctuations and the zonal flow, is studied here numerically. The reduced model, CE2-GO, has a similar phase-space mathematical structure to the traditional wave-kinetic equation, but that wave-kinetic equation has been shown to fail to preserve enstrophy conservation and to exhibit an ultraviolet catastrophe. CE2-GO, in contrast, preserves nonlinear conservation of both energy and enstrophy. We show here how to retain these conservation properties in a pseudospectral simulation of CE2-GO. We then present nonlinear simulations of CE2-GO and compare with direct simulations of quasilinear (QL) dynamics. We find that CE2-GO retains some similarities to QL. The partitioning of energy that resides in the zonal flow is in good quantitative agreement between CE2-GO and QL. On the other hand, the length scale of the zonal flow does not follow the same qualitative trend in the two models. Overall, these simulations indicate that CE2-GO provides a simpler and more tractable statistical paradigm than CE2, but CE2-GO is missing important physics.

Simulated root dynamics of a 160-year-old sugar maple (Acer saccharum Marsh.) tree with and without ozone exposure using the TREGRO model.

PubMed

Retzlaff, W. A.; Weinstein, D. A.; Laurence, J. A.; Gollands, B.

1996-01-01

Because of difficulties in directly assessing root responses of mature forest trees exposed to atmospheric pollutants, we have used the model TREGRO to analyze the effects of a 3- and a 10-year exposure to ozone (O(3)) on root dynamics of a simulated 160-year-old sugar maple (Acer saccharum Marsh.) tree. We used existing phenological, allometric, and growth data to parameterize TREGRO to produce a simulated 160-year-old tree. Simulations were based on literature values for sugar maple fine root production and senescence and the photosynthetic responses of sugar maple seedlings exposed to O(3) in open-top chambers. In the simulated 3-year exposure to O(3), 2 x ambient atmospheric O(3) concentrations reduced net carbon (C) gain of the 160-year-old tree. This reduction occurred in the C storage pools (total nonstructural carbohydrate, TNC), with most of the reduction occurring in coarse (woody) roots. Total fine root production and senescence were unaffected by the simulated 3-year exposure to O(3). However, extending the simulated O(3) exposure period to 10 years depleted the TNC pools of the coarse roots and reduced total fine root production. Similar reductions in TNC pools have been observed in forest-grown sugar maple trees exhibiting symptoms of stress. We conclude that modeling can aid in evaluating the belowground response of mature forest trees to atmospheric pollution stress and could indicate the potential for gradual deterioration of tree health under conditions of long-term stress, a situation similar to that underlying the decline of sugar maple trees.

Examination of Wave Speed in Rotating Detonation Engines Using Simplified Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Paxson, Daniel E.

2018-01-01

A simplified, two-dimensional, computational fluid dynamic (CFD) simulation, with a reactive Euler solver is used to examine possible causes for the low detonation wave propagation speeds that are consistently observed in air breathing rotating detonation engine (RDE) experiments. Intense, small-scale turbulence is proposed as the primary mechanism. While the solver cannot model this turbulence, it can be used to examine the most likely, and profound effect of turbulence. That is a substantial enlargement of the reaction zone, or equivalently, an effective reduction in the chemical reaction rate. It is demonstrated that in the unique flowfield of the RDE, a reduction in reaction rate leads to a reduction in the detonation speed. A subsequent test of reduced reaction rate in a purely one-dimensional pulsed detonation engine (PDE) flowfield yields no reduction in wave speed. The reasons for this are explained. The impact of reduced wave speed on RDE performance is then examined, and found to be minimal. Two other potential mechanisms are briefly examined. These are heat transfer, and reactive mixture non-uniformity. In the context of the simulation used for this study, both mechanisms are shown to have negligible effect on either wave speed or performance.

Oxygen reduction on a Pt(111) catalyst in HT-PEM fuel cells by density functional theory

NASA Astrophysics Data System (ADS)

Sun, Hong; Li, Jie; Almheiri, Saif; Xiao, Jianyu

2017-08-01

The oxygen reduction reaction plays an important role in the performance of high-temperature proton exchange membrane (HT-PEM) fuel cells. In this study, a molecular dynamics model, which is based on the density functional theory and couples the system's energy, the exchange-correlation energy functional, the charge density distribution function, and the simplified Kohn-Sham equation, was developed to simulate the oxygen reduction reaction on a Pt(111) surface. Additionally, an electrochemical reaction system on the basis of a four-electron reaction mechanism was also developed for this simulation. The reaction path of the oxygen reduction reaction, the product structure of each reaction step and the system's energy were simulated. It is found that the first step reaction of the first hydrogen ion with the oxygen molecule is the controlling step of the overall reaction. Increasing the operating temperature speeds up the first step reaction rate and slightly decreases its reaction energy barrier. Our results provide insight into the working principles of HT-PEM fuel cells.

Molecular dynamics simulations of the effect of waviness and agglomeration of CNTs on interface strength of thermoset nanocomposites.

PubMed

Alian, A R; Meguid, S A

2017-02-08

Most existing molecular dynamics simulations in nanoreinforced composites assume carbon nanotubes (CNTs) to be straight and uniformly dispersed within thermoplastics. In reality, however, CNTs are typically curved, agglomerated and aggregated as a result of van der Waal interactions and electrostatic forces. In this paper, we account for both curvature and agglomeration of CNTs in extensive molecular dynamic (MD) simulations. The purpose of these simulations is to evaluate the influence of waviness and agglomeration of these curved and agglomerated CNTs on the interfacial strength of thermoset nanocomposite and upon their load transfer capability. Two aspects of the work were accordingly examined. In the first, realistic carbon nanotubes (CNTs) of the same length but varied curvatures were embedded in thermoset polymer composites and simulations of pull-out tests were conducted to evaluate the corresponding interfacial shear strength (ISS). In the second, the effect of the agglomerate size upon the ISS was determined using bundles of CNTs of different diameters. The results of our MD simulations revealed the following. The pull-out force of the curved CNTs is significantly higher than its straight counterpart and increases further with the increase in the waviness of the CNTs. This is attributed to the added pull-out energy dissipated in straightening the CNTs during the pull-out process. It also reveals that agglomeration of CNTs leads to a reduction in the ISS and poor load transferability, and that this reduction is governed by the size of the agglomerate. The simulation results were also used to develop a generalized relation for the ISS that takes into consideration the effect of waviness and agglomeration of CNTs of CNT-polymer composites.

Solvent as electron donor: Donor/acceptor electronic coupling is a dynamical variable

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

Castner, E.W. Jr.; Kennedy, D.; Cave, R.J.

2000-04-06

The authors combine analysis of measurements by femtosecond optical spectroscopy, computer simulations, and the generalized Mulliken-Hush (GMH) theory in the study of electron-transfer reactions and electron donor-acceptor interactions. The study focus is on ultrafast photoinduced electron-transfer reactions from aromatic amine solvent donors to excited-state acceptors. The experimental results from femtosecond dynamical measurements fall into three categories: six coumarin acceptors reductively quenched by N,N-dimethylaniline (DMA), eight electron-donating amine solvents reductively quenching coumarin 152 (7-(dimethylamino)-4-(trifluoromethyl)-coumarin), and reductive quenching dynamics of two coumarins by DMA as a function of dilution in the nonreactive solvents toluene and chlorobenzene. Applying a combination of molecular dynamicsmore » trajectories, semiempirical quantum mechanical calculations (of the relevant adiabatic electronic states), and GMH theory to the C152/DMA photoreaction, the authors calculate the electron donor/acceptor interaction parameter H{sub DA} at various time frames, H{sub DA} is strongly modulated by both inner-sphere and outer-sphere nuclear dynamics, leading us to conclude that H{sub DA} must be considered as a dynamical variable.« less

Hierarchical optimization for neutron scattering problems

DOE PAGES

Bao, Feng; Archibald, Rick; Bansal, Dipanshu; ...

2016-03-14

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Hierarchical optimization for neutron scattering problems

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

Bao, Feng; Archibald, Rick; Bansal, Dipanshu

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Graphene production by laser shot on graphene oxide: An ab initio prediction

NASA Astrophysics Data System (ADS)

Zhang, Hong; Miyamoto, Yoshiyuki

2012-01-01

By performing the first-principles simulation of electron-ion dynamics based on the time-dependent density-functional theory, we propose a way to produce graphene from graphene oxides by means of the laser-induced reduction without using chemical species. Epoxy and hydroxyl groups on graphene sheets can be completely removed upon irradiation with femtosecond laser without damaging the graphene sheet. By comparing the simulated results with different pulse shapes and intensities, optimum conditions of the femtosecond laser for reduction of graphene oxide were determined. The current works will be useful for further experimental researches.

Blood flow in intracranial aneurysms treated with Pipeline embolization devices: computational simulation and verification with Doppler ultrasonography on phantom models

PubMed Central

2015-01-01

Purpose: The aim of this study was to validate a computational fluid dynamics (CFD) simulation of flow-diverter treatment through Doppler ultrasonography measurements in patient-specific models of intracranial bifurcation and side-wall aneurysms. Methods: Computational and physical models of patient-specific bifurcation and sidewall aneurysms were constructed from computed tomography angiography with use of stereolithography, a three-dimensional printing technology. Flow dynamics parameters before and after flow-diverter treatment were measured with pulse-wave and color Doppler ultrasonography, and then compared with CFD simulations. Results: CFD simulations showed drastic flow reduction after flow-diverter treatment in both aneurysms. The mean volume flow rate decreased by 90% and 85% for the bifurcation aneurysm and the side-wall aneurysm, respectively. Velocity contour plots from computer simulations before and after flow diversion closely resembled the patterns obtained by color Doppler ultrasonography. Conclusion: The CFD estimation of flow reduction in aneurysms treated with a flow-diverting stent was verified by Doppler ultrasonography in patient-specific phantom models of bifurcation and side-wall aneurysms. The combination of CFD and ultrasonography may constitute a feasible and reliable technique in studying the treatment of intracranial aneurysms with flow-diverting stents. PMID:25754367

Thickened boundary layer theory for air film drag reduction on a van body surface

NASA Astrophysics Data System (ADS)

Xie, Xiaopeng; Cao, Lifeng; Huang, Heng

2018-05-01

To elucidate drag reduction mechanism on a van body surface under air film condition, a thickened boundary layer theory was proposed and a frictional resistance calculation model of the van body surface was established. The frictional resistance on the van body surface was calculated with different parameters of air film thickness. In addition, the frictional resistance of the van body surface under the air film condition was analyzed by computational fluid dynamics (CFD) simulation and different air film states that influenced the friction resistance on the van body surface were discussed. As supported by the CFD simulation results, the thickened boundary layer theory may provide reference for practical application of air film drag reduction on a van body surface.

The Dornier 328 Acoustic Test Cell (ATC) for interior noise tests and selected test results

NASA Technical Reports Server (NTRS)

Hackstein, H. Josef; Borchers, Ingo U.; Renger, Klaus; Vogt, Konrad

1992-01-01

To perform acoustic studies for achieving low noise levels for the Dornier 328, an acoustic test cell (ATC) of the Dornier 328 has been built. The ATC consists of a fuselage section, a realistic fuselage suspension system, and three exterior noise simulation rings. A complex digital 60 channel computer/amplifier noise generation system as well as multichannel digital data acquisition and evaluation system have been used. The noise control tests started with vibration measurements for supporting acoustic data interpretation. In addition, experiments have been carried out on dynamic vibration absorbers, the most important passive noise reduction measure for low frequency propeller noise. The design and arrangement of the current ATC are presented. Furthermore, exterior noise simulation as well as data acquisition are explained. The most promising results show noise reduction due to synchrophasing and dynamic vibration absorbers.

Collective Langevin dynamics of conformational motions in proteins

NASA Astrophysics Data System (ADS)

Lange, Oliver F.; Grubmüller, Helmut

2006-06-01

Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. The accumulated influence of these fluctuations is crucial for a correct treatment of the conformational dynamics; however, their details can be considered irrelevant for most purposes. To accurately describe long time protein dynamics we here propose a reduced dimension approach, collective Langevin dynamics (CLD), which evolves the dynamics of the system within a small subspace of relevant collective degrees of freedom. The dynamics within the low-dimensional conformational subspace is evolved via a generalized Langevin equation which accounts for memory effects via memory kernels also extracted from short explicit MD simulations. To determine the memory kernel with differing levels of regularization, we propose and evaluate two methods. As a first test, CLD is applied to describe the conformational motion of the peptide neurotensin. A drastic dimension reduction is achieved by considering one single curved conformational coordinate. CLD yielded accurate thermodynamical and dynamical behaviors. In particular, the rate of transitions between two conformational states agreed well with a rate obtained from a 150ns reference molecular dynamics simulation, despite the fact that the time scale of the transition (˜50ns) was much longer than the 1ns molecular dynamics simulation from which the memory kernel was extracted.

Dynamic Data-Driven Reduced-Order Models of Macroscale Quantities for the Prediction of Equilibrium System State for Multiphase Porous Medium Systems

NASA Astrophysics Data System (ADS)

Talbot, C.; McClure, J. E.; Armstrong, R. T.; Mostaghimi, P.; Hu, Y.; Miller, C. T.

2017-12-01

Microscale simulation of multiphase flow in realistic, highly-resolved porous medium systems of a sufficient size to support macroscale evaluation is computationally demanding. Such approaches can, however, reveal the dynamic, steady, and equilibrium states of a system. We evaluate methods to utilize dynamic data to reduce the cost associated with modeling a steady or equilibrium state. We construct data-driven models using extensions to dynamic mode decomposition (DMD) and its connections to Koopman Operator Theory. DMD and its variants comprise a class of equation-free methods for dimensionality reduction of time-dependent nonlinear dynamical systems. DMD furnishes an explicit reduced representation of system states in terms of spatiotemporally varying modes with time-dependent oscillation frequencies and amplitudes. We use DMD to predict the steady and equilibrium macroscale state of a realistic two-fluid porous medium system imaged using micro-computed tomography (µCT) and simulated using the lattice Boltzmann method (LBM). We apply Koopman DMD to direct numerical simulation data resulting from simulations of multiphase fluid flow through a 1440x1440x4320 section of a full 1600x1600x5280 realization of imaged sandstone. We determine a representative set of system observables via dimensionality reduction techniques including linear and kernel principal component analysis. We demonstrate how this subset of macroscale quantities furnishes a representation of the time-evolution of the system in terms of dynamic modes, and discuss the selection of a subset of DMD modes yielding the optimal reduced model, as well as the time-dependence of the error in the predicted equilibrium value of each macroscale quantity. Finally, we describe how the above procedure, modified to incorporate methods from compressed sensing and random projection techniques, may be used in an online fashion to facilitate adaptive time-stepping and parsimonious storage of system states over time.

Drag reduction and the dynamics of turbulence in simple and complex fluidsa)

NASA Astrophysics Data System (ADS)

Graham, Michael D.

2014-10-01

Addition of a small amount of very large polymer molecules or micelle-forming surfactants to a liquid can dramatically reduce the energy dissipation it exhibits in the turbulent flow regime. This rheological drag reduction phenomenon is widely used, for example, in the Alaska pipeline, but it is not well-understood, and no comparable technology exists to reduce turbulent energy consumption in flows of gases, in which polymers or surfactants cannot be dissolved. The most striking feature of this phenomenon is the existence of a so-called maximum drag reduction (MDR) asymptote: for a given geometry and driving force, there is a maximum level of drag reduction that can be achieved through addition of polymers. Changing the concentration, molecular weight or even the chemical structure of the additives has little to no effect on this asymptotic value. This universality is the major puzzle of drag reduction. We describe direct numerical simulations of turbulent minimal channel flow of Newtonian fluids and viscoelastic polymer solutions. Even in the absence of polymers, we show that there are intervals of "hibernating" turbulence that display very low drag as well as many other features of the MDR asymptote observed in polymer solutions. As Weissenberg number increases to moderate values the frequency of these intervals also increases, and a simple theory captures key features of the intermittent dynamics observed in the simulations. At higher Weissenberg number, these intervals are altered - for example, their duration becomes substantially longer and the instantaneous Reynolds shear stress during them becomes very small. Additionally, simulations of "edge states," dynamical trajectories that lie on the boundary between turbulent and laminar flow, display characteristics that are similar to those of hibernating turbulence and thus to the MDR asymptote, again even in the absence of polymer additives. Based on these observations, we propose a tentative unified description of rheological drag reduction. The existence of MDR-like intervals even in the absence of additives sheds light on the observed universality of MDR and may ultimately lead to new flow control approaches for improving energy efficiency in a wide range of processes.

Modeling hydrologic controls on sulfur processes in sulfate-impacted wetland and stream sediments

NASA Astrophysics Data System (ADS)

Ng, G.-H. C.; Yourd, A. R.; Johnson, N. W.; Myrbo, A. E.

2017-09-01

Recent studies show sulfur redox processes in terrestrial settings are more important than previously considered, but much remains uncertain about how these processes respond to dynamic hydrologic conditions in natural field settings. We used field observations from a sulfate-impacted wetland and stream in the mining region of Minnesota (USA) to calibrate a reactive transport model and evaluate sulfur and coupled geochemical processes under contrasting hydrogeochemical scenarios. Simulations of different hydrological conditions showed that flux and chemistry differences between surface water and deeper groundwater strongly control hyporheic zone geochemical profiles. However, model results for the stream channel versus wetlands indicate sediment organic carbon content to be the more important driver of sulfate reduction rates. A complex nonlinear relationship between sulfate reduction rates and geochemical conditions is apparent from the model's higher sensitivity to sulfate concentrations in settings with higher organic content. Across all scenarios, simulated e- balance results unexpectedly showed that sulfate reduction dominates iron reduction, which is contrary to the traditional thermodynamic ladder but corroborates recent experimental findings by Hansel et al. (2015) that "cryptic" sulfur cycling could drive sulfate reduction in preference over iron reduction. Following the thermodynamic ladder, our models shows that high surface water sulfate slows methanogenesis in shallow sediments, but field observations suggest that sulfate reduction may not entirely suppress methane. Overall, our results show that sulfate reduction may serve as a major component making up and influencing terrestrial redox processes, with dynamic hyporheic fluxes controlling sulfate concentrations and reaction rates, especially in high organic content settings.

The Simulation of Magnetorheological Elastomers Adaptive Tuned Dynamic Vibration Absorber for Automobile Engine Vibration Control

NASA Astrophysics Data System (ADS)

Zhang, X. C.; Zhang, X. Z.; Li, W. H.; Liu, B.; Gong, X. L.; Zhang, P. Q.

The aim of this article is to investigate the use of a Dynamic Vibration Absorber to control vibration of engine by using simulation. Traditional means of vibration control have involved the use of passive and more recently, active methods. This study is different in that it involves an adaptive component in the design of vibration absorber using magnetorheological elastomers (MREs) as the adaptive spring. MREs are kind of novel smart material whose shear modulus can be controlled by applied magnetic field. In this paper, the vibration mode of a simple model of automobile engine is simulated by Finite Element Method (FEM) analysis. Based on the analysis, the MREs Adaptive Tuned Dynamic Vibration Absorber (ATDVA) is presented to reduce the vibration of the engine. Simulation result indicate that the control frequency of ATDVA can be changed by modifing the shear modulus of MREs and the vibraion reduction efficiency of ATDVA are also evaluated by FEM analysis.

Equilibrium responses of global net primary production and carbon storage to doubled atmospheric carbon dioxide: Sensitivity to changes in vegetation nitrogen concentration

USGS Publications Warehouse

McGuire, David A.; Melillo, J.M.; Kicklighter, D.W.; Pan, Y.; Xiao, X.; Helfrich, J.; Moore, B.; Vorosmarty, C.J.; Schloss, A.L.

1997-01-01

We ran the terrestrial ecosystem model (TEM) for the globe at 0.5?? resolution for atmospheric CO2 concentrations of 340 and 680 parts per million by volume (ppmv) to evaluate global and regional responses of net primary production (NPP) and carbon storage to elevated CO2 for their sensitivity to changes in vegetation nitrogen concentration. At 340 ppmv, TEM estimated global NPP of 49.0 1015 g (Pg) C yr-1 and global total carbon storage of 1701.8 Pg C; the estimate of total carbon storage does not include the carbon content of inert soil organic matter. For the reference simulation in which doubled atmospheric CO2 was accompanied with no change in vegetation nitrogen concentration, global NPP increased 4.1 Pg C yr-1 (8.3%), and global total carbon storage increased 114.2 Pg C. To examine sensitivity in the global responses of NPP and carbon storage to decreases in the nitrogen concentration of vegetation, we compared doubled CO2 responses of the reference TEM to simulations in which the vegetation nitrogen concentration was reduced without influencing decomposition dynamics ("lower N" simulations) and to simulations in which reductions in vegetation nitrogen concentration influence decomposition dynamics ("lower N+D" simulations). We conducted three lower N simulations and three lower N+D simulations in which we reduced the nitrogen concentration of vegetation by 7,5, 15.0, and 22.5%. In the lower N simulations, the response of global NPP to doubled atmospheric CO2 increased approximately 2 Pg C yr-1 for each incremental 7.5% reduction in vegetation nitrogen concentration, and vegetation carbon increased approximately an additional 40 Pg C, and soil carbon increased an additional 30 Pg C, for a total carbon storage increase of approximately 70 Pg C. In the lower N+D simulations, the responses of NPP and vegetation carbon storage were relatively insensitive to differences in the reduction of nitrogen concentration, but soil carbon storage showed a large change. The insensitivity of NPP in the N+D simulations occurred because potential enhancements in NPP associated with reduced vegetation nitrogen concentration were approximately offset by lower nitrogen availability associated with the decomposition dynamics of reduced litter nitrogen concentration. For each 7.5% reduction in vegetation nitrogen concentration, soil carbon increased approximately an additional 60 Pg C, while vegetation carbon storage increased by only approximately 5 Pg C. As the reduction in vegetation nitrogen concentration gets greater in the lower N+D simulations, more of the additional carbon storage tends to become concentrated in the north temperateboreal region in comparison to the tropics. Other studies with TEM show that elevated CO2 more than offsets the effects of climate change to cause increased carbon storage. The results of this study indicate that carbon storage would be enhanced by the influence of changes in plant nitrogen concentration on carbon assimilation and decomposition rates. Thus changes in vegetation nitrogen concentration may have important implications for the ability of the terrestrial biosphere to mitigate increases in the atmospheric concentration of CO2 and climate changes associated with the increases.

Numerical Simulation of Multiphase Magnetohydrodynamic Flow and Deformation of Electrolyte-Metal Interface in Aluminum Electrolysis Cells

NASA Astrophysics Data System (ADS)

Hua, Jinsong; Rudshaug, Magne; Droste, Christian; Jorgensen, Robert; Giskeodegard, Nils-Haavard

2018-06-01

A computational fluid dynamics based multiphase magnetohydrodynamic (MHD) flow model for simulating the melt flow and bath-metal interface deformation in realistic aluminum reduction cells is presented. The model accounts for the complex physics of the MHD problem in aluminum reduction cells by coupling two immiscible fluids, electromagnetic field, Lorentz force, flow turbulence, and complex cell geometry with large length scale. Especially, the deformation of bath-metal interface is tracked directly in the simulation, and the condition of constant anode-cathode distance (ACD) is maintained by moving anode bottom dynamically with the deforming bath-metal interface. The metal pad deformation and melt flow predicted by the current model are compared to the predictions using a simplified model where the bath-metal interface is assumed flat. The effects of the induced electric current due to fluid flow and the magnetic field due to the interior cell current on the metal pad deformation and melt flow are investigated. The presented model extends the conventional simplified box model by including detailed cell geometry such as the ledge profile and all channels (side, central, and cross-channels). The simulations show the model sensitivity to different side ledge profiles and the cross-channel width by comparing the predicted melt flow and metal pad heaving. In addition, the model dependencies upon the reduction cell operation conditions such as ACD, current distribution on cathode surface and open/closed channel top, are discussed.

The research of hourglass worm dynamic balancing simulation based on SolidWorks motion

NASA Astrophysics Data System (ADS)

Wang, Zhuangzhuang; Yang, Jie; Liu, Pingyi; Zhao, Junpeng

2018-02-01

Hourglass worm is extensively used in industry due to its characteristic of heavy-load and a large reduction ratio. Varying sizes of unbalanced mass distribution appeared in the design of a single head worm. With machines developing towards higher speed and precision, the vibration and shock caused by the unbalanced mass distribution of rotating parts must be considered. Therefore, the balance grade of these parts must meet higher requirements. A method based on theoretical analysis and SolidWorks motion software simulation is presented in this paper; the virtual dynamic balance simulation test of the hourglass worm was carried out during the design of the product, so as to ensure that the hourglass worm meet the requirements of dynamic balance in the design process. This can effectively support the structural design of the hourglass worm and provide a way of thinking and designing the same type of products.

Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations.

PubMed

Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas

2015-11-10

Data mining techniques depend strongly on how the data are represented and how distance between samples is measured. High-dimensional data often contain a large number of irrelevant dimensions (features) for a given query. These features act as noise and obfuscate relevant information. Unsupervised approaches to mine such data require distance measures that can account for feature relevance. Molecular dynamics simulations produce high-dimensional data sets describing molecules observed in time. Here, we propose to globally or locally weight simulation features based on effective rates. This emphasizes, in a data-driven manner, slow degrees of freedom that often report on the metastable states sampled by the molecular system. We couple this idea to several unsupervised learning protocols. Our approach unmasks slow side chain dynamics within the native state of a miniprotein and reveals additional metastable conformations of a protein. The approach can be combined with most algorithms for clustering or dimensionality reduction.

Influence of an Internally-Generated QBO on Modeled Stratospheric Dynamics and Ozone

NASA Technical Reports Server (NTRS)

Hurwitz, M. M.; Newman, P. A.; Song, I. S.

2011-01-01

A GEOS V2 CCM simulation with an internally generated quasi-biennial oscillation (QBO) signal is compared to an otherwise identical simulation without a QBO. In a present-day climate, inclusion of the modeled QBO makes a significant difference to stratospheric dynamics and ozone throughout the year. The QBO enhances variability in the tropics, as expected, but also in the polar stratosphere in some seasons. The modeled QBO also affects the mean stratospheric climate. Because tropical zonal winds in the baseline simulation are generally easterly, there is a relative increase in zonal wind magnitudes in tropical lower and middle stratosphere in the QBO simulation. Extra-tropical differences between the QBO and 'no QBO' simulations thus reflect a bias toward the westerly phase of the QBO: a relative strengthening and poleward shifting the polar stratospheric jets, and a reduction in Arctic lower stratospheric ozone.

Real-time dynamic simulation of the Cassini spacecraft using DARTS. Part 2: Parallel/vectorized real-time implementation

NASA Technical Reports Server (NTRS)

Fijany, A.; Roberts, J. A.; Jain, A.; Man, G. K.

1993-01-01

Part 1 of this paper presented the requirements for the real-time simulation of Cassini spacecraft along with some discussion of the DARTS algorithm. Here, in Part 2 we discuss the development and implementation of parallel/vectorized DARTS algorithm and architecture for real-time simulation. Development of the fast algorithms and architecture for real-time hardware-in-the-loop simulation of spacecraft dynamics is motivated by the fact that it represents a hard real-time problem, in the sense that the correctness of the simulation depends on both the numerical accuracy and the exact timing of the computation. For a given model fidelity, the computation should be computed within a predefined time period. Further reduction in computation time allows increasing the fidelity of the model (i.e., inclusion of more flexible modes) and the integration routine.

Cycle-averaged dynamics of a periodically driven, closed-loop circulation model

NASA Technical Reports Server (NTRS)

Heldt, T.; Chang, J. L.; Chen, J. J. S.; Verghese, G. C.; Mark, R. G.

2005-01-01

Time-varying elastance models have been used extensively in the past to simulate the pulsatile nature of cardiovascular waveforms. Frequently, however, one is interested in dynamics that occur over longer time scales, in which case a detailed simulation of each cardiac contraction becomes computationally burdensome. In this paper, we apply circuit-averaging techniques to a periodically driven, closed-loop, three-compartment recirculation model. The resultant cycle-averaged model is linear and time invariant, and greatly reduces the computational burden. It is also amenable to systematic order reduction methods that lead to further efficiencies. Despite its simplicity, the averaged model captures the dynamics relevant to the representation of a range of cardiovascular reflex mechanisms. c2004 Elsevier Ltd. All rights reserved.

Modeling the electrophoretic separation of short biological molecules in nanofluidic devices

NASA Astrophysics Data System (ADS)

Fayad, Ghassan; Hadjiconstantinou, Nicolas

2010-11-01

Via comparisons with Brownian Dynamics simulations of the worm-like-chain and rigid-rod models, and the experimental results of Fu et al. [Phys. Rev. Lett., 97, 018103 (2006)], we demonstrate that, for the purposes of low-to-medium field electrophoretic separation in periodic nanofilter arrays, sufficiently short biomolecules can be modeled as point particles, with their orientational degrees of freedom accounted for using partition coefficients. This observation is used in the present work to build a particularly simple and efficient Brownian Dynamics simulation method. Particular attention is paid to the model's ability to quantitatively capture experimental results using realistic values of all physical parameters. A variance-reduction method is developed for efficiently simulating arbitrarily small forcing electric fields.

Low thermal conductivity in ultrathin carbon nanotube (2, 1)

PubMed Central

Zhu, Liyan; Li, Baowen

2014-01-01

Molecular dynamic simulations reveal that the ultrathin carbon nanotube (CNT) (2, 1) with a reconstructed structure exhibits a surprisingly low thermal conductivity, which is only ~16–30% of those in regular CNTs, e.g. CNT (2, 2) and (5, 5). Detailed lattice dynamic calculations suggest that the acoustic phonon modes greatly soften in CNT (2, 1) as compared to regular CNTs. Moreover, both phonon group velocities and phonon lifetimes strikingly decrease in CNT (2, 1), which result in the remarkable reduction of thermal conductivity. Besides, isotope doping and chemical functionalization enable the further reduction of thermal conductivity in CNT (2, 1). PMID:24815003

Dynamic, mechanistic, molecular-level modelling of cyanobacteria: Anabaena and nitrogen interaction.

PubMed

Hellweger, Ferdi L; Fredrick, Neil D; McCarthy, Mark J; Gardner, Wayne S; Wilhelm, Steven W; Paerl, Hans W

2016-09-01

Phytoplankton (eutrophication, biogeochemical) models are important tools for ecosystem research and management, but they generally have not been updated to include modern biology. Here, we present a dynamic, mechanistic, molecular-level (i.e. gene, transcript, protein, metabolite) model of Anabaena - nitrogen interaction. The model was developed using the pattern-oriented approach to model definition and parameterization of complex agent-based models. It simulates individual filaments, each with individual cells, each with genes that are expressed to yield transcripts and proteins. Cells metabolize various forms of N, grow and divide, and differentiate heterocysts when fixed N is depleted. The model is informed by observations from 269 laboratory experiments from 55 papers published from 1942 to 2014. Within this database, we identified 331 emerging patterns, and, excluding inconsistencies in observations, the model reproduces 94% of them. To explore a practical application, we used the model to simulate nutrient reduction scenarios for a hypothetical lake. For a 50% N only loading reduction, the model predicts that N fixation increases, but this fixed N does not compensate for the loading reduction, and the chlorophyll a concentration decreases substantially (by 33%). When N is reduced along with P, the model predicts an additional 8% reduction (compared to P only). © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Network visualization of conformational sampling during molecular dynamics simulation.

PubMed

Ahlstrom, Logan S; Baker, Joseph Lee; Ehrlich, Kent; Campbell, Zachary T; Patel, Sunita; Vorontsov, Ivan I; Tama, Florence; Miyashita, Osamu

2013-11-01

Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions. Copyright © 2013 Elsevier Inc. All rights reserved.

A continuum model for dynamic analysis of the Space Station

NASA Technical Reports Server (NTRS)

Thomas, Segun

1989-01-01

Dynamic analysis of the International Space Station using MSC/NASTRAN had 1312 rod elements, 62 beam elements, 489 nodes and 1473 dynamic degrees of freedom. A realtime, man-in-the-loop simulation of such a model is impractical. This paper discusses the mathematical model for realtime dynamic simulation of the Space Station. Several key questions in structures and structural dynamics are addressed. First, to achieve a significant reduction in the number of dynamic degrees of freedom, a continuum equivalent representation of the Space Station truss structure which accounted for the unsymmetry of the basic configuration and resulted in the coupling of extensional and transverse deformation, is developed. Next, dynamic equations for the continuum equivalent of the Space Station truss structure are formulated using a matrix version of Kane's dynamical equations. Flexibility is accounted for by using a theory that accommodates extension, bending in two principal planes and shear displacement. Finally, constraint equations suitable for dynamic analysis of flexible bodies with closed loop configuration are developed and solution of the resulting system of equations is based on the zero eigenvalue theorem.

Magnetohydrodynamic Modeling of Solar Coronal Dynamics with an Initial Non-force-free Magnetic Field

NASA Astrophysics Data System (ADS)

Prasad, A.; Bhattacharyya, R.; Kumar, Sanjay

2017-05-01

The magnetic fields in the solar corona are generally neither force-free nor axisymmetric and have complex dynamics that are difficult to characterize. Here we simulate the topological evolution of solar coronal magnetic field lines (MFLs) using a magnetohydrodynamic model. The simulation is initialized with a non-axisymmetric non-force-free magnetic field that best correlates with the observed vector magnetograms of solar active regions (ARs). To focus on these ideas, simulations are performed for the flaring AR 11283 noted for its complexity and well-documented dynamics. The simulated dynamics develops as the initial Lorentz force pushes the plasma and facilitates successive magnetic reconnections at the two X-type null lines present in the initial field. Importantly, the simulation allows for the spontaneous development of mass flow, unique among contemporary works, that preferentially reconnects field lines at one of the X-type null lines. Consequently, a flux rope consisting of low-lying twisted MFLs, which approximately traces the major polarity inversion line, undergoes an asymmetric monotonic rise. The rise is attributed to a reduction in the magnetic tension force at the region overlying the rope, resulting from the reconnection. A monotonic rise of the rope is in conformity with the standard scenario of flares. Importantly, the simulated dynamics leads to bifurcations of the flux rope, which, being akin to the observed filament bifurcation in AR 11283, establishes the appropriateness of the initial field in describing ARs.

Magnetohydrodynamic Modeling of Solar Coronal Dynamics with an Initial Non-force-free Magnetic Field

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

Prasad, A.; Bhattacharyya, R.; Kumar, Sanjay

The magnetic fields in the solar corona are generally neither force-free nor axisymmetric and have complex dynamics that are difficult to characterize. Here we simulate the topological evolution of solar coronal magnetic field lines (MFLs) using a magnetohydrodynamic model. The simulation is initialized with a non-axisymmetric non-force-free magnetic field that best correlates with the observed vector magnetograms of solar active regions (ARs). To focus on these ideas, simulations are performed for the flaring AR 11283 noted for its complexity and well-documented dynamics. The simulated dynamics develops as the initial Lorentz force pushes the plasma and facilitates successive magnetic reconnections atmore » the two X-type null lines present in the initial field. Importantly, the simulation allows for the spontaneous development of mass flow, unique among contemporary works, that preferentially reconnects field lines at one of the X-type null lines. Consequently, a flux rope consisting of low-lying twisted MFLs, which approximately traces the major polarity inversion line, undergoes an asymmetric monotonic rise. The rise is attributed to a reduction in the magnetic tension force at the region overlying the rope, resulting from the reconnection. A monotonic rise of the rope is in conformity with the standard scenario of flares. Importantly, the simulated dynamics leads to bifurcations of the flux rope, which, being akin to the observed filament bifurcation in AR 11283, establishes the appropriateness of the initial field in describing ARs.« less

Numerical Investigation of the Dynamic Properties of Intermittent Jointed Rock Models Subjected to Cyclic Uniaxial Compression

NASA Astrophysics Data System (ADS)

Liu, Yi; Dai, Feng; Zhao, Tao; Xu, Nu-wen

2017-01-01

Intermittent jointed rocks, which exist in a myriad of engineering projects, are extraordinarily susceptible to cyclic loadings. Understanding the dynamic fatigue properties of jointed rocks is necessary for evaluating the stability of rock engineering structures. This study numerically investigated the influences of cyclic loading conditions (i.e., frequency, maximum stress and amplitude) and joint geometric configurations (i.e., dip angle, persistency and interspace) on the dynamic fatigue mechanisms of jointed rock models. A reduction model of stiffness and strength was first proposed, and then, sixteen cyclic uniaxial loading tests with distinct loading parameters and joint geometries were simulated. Our results indicate that the reduction model can effectively reproduce the hysteresis loops and the accumulative plastic deformation of jointed rocks in the cyclic process. Both the loading parameters and the joint geometries significantly affect the dynamic properties, including the irreversible strain, damage evolution, dynamic residual strength and fatigue life. Three failure modes of jointed rocks, which are principally controlled by joint geometries, occur in the simulations: splitting failure through the entire rock sample, sliding failure along joint planes and mixed failure, which are principally controlled by joint geometries. Furthermore, the progressive failure processes of the jointed rock samples are numerically observed, and the different loading stages can be distinguished by the relationship between the number of broken bonds and the axial stress.

TREDI: A self consistent three-dimensional integration scheme for RF-gun dynamics based on the Lienard-Wiechert potentials formalism

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

Giannessi, Luca; Quattromini, Marcello

1997-06-01

We describe the model for the simulation of charged beam dynamics in radiofrequency injectors used in the three dimensional code TREDI, where the inclusion of space charge fields is obtained by means of the Lienard-Wiechert retarded potentials. The problem of charge screening is analyzed in covariant form and some general recipes for charge assignment and noise reduction are given.

Wind speed reductions by large-scale wind turbine deployments lower turbine efficiencies and set low generation limits.

PubMed

Miller, Lee M; Kleidon, Axel

2016-11-29

Wind turbines generate electricity by removing kinetic energy from the atmosphere. Large numbers of wind turbines are likely to reduce wind speeds, which lowers estimates of electricity generation from what would be presumed from unaffected conditions. Here, we test how well wind power limits that account for this effect can be estimated without explicitly simulating atmospheric dynamics. We first use simulations with an atmospheric general circulation model (GCM) that explicitly simulates the effects of wind turbines to derive wind power limits (GCM estimate), and compare them to a simple approach derived from the climatological conditions without turbines [vertical kinetic energy (VKE) estimate]. On land, we find strong agreement between the VKE and GCM estimates with respect to electricity generation rates (0.32 and 0.37 W e m -2 ) and wind speed reductions by 42 and 44%. Over ocean, the GCM estimate is about twice the VKE estimate (0.59 and 0.29 W e m -2 ) and yet with comparable wind speed reductions (50 and 42%). We then show that this bias can be corrected by modifying the downward momentum flux to the surface. Thus, large-scale limits to wind power use can be derived from climatological conditions without explicitly simulating atmospheric dynamics. Consistent with the GCM simulations, the approach estimates that only comparatively few land areas are suitable to generate more than 1 W e m -2 of electricity and that larger deployment scales are likely to reduce the expected electricity generation rate of each turbine. We conclude that these atmospheric effects are relevant for planning the future expansion of wind power.

Wind speed reductions by large-scale wind turbine deployments lower turbine efficiencies and set low generation limits

PubMed Central

Miller, Lee M.; Kleidon, Axel

2016-01-01

Wind turbines generate electricity by removing kinetic energy from the atmosphere. Large numbers of wind turbines are likely to reduce wind speeds, which lowers estimates of electricity generation from what would be presumed from unaffected conditions. Here, we test how well wind power limits that account for this effect can be estimated without explicitly simulating atmospheric dynamics. We first use simulations with an atmospheric general circulation model (GCM) that explicitly simulates the effects of wind turbines to derive wind power limits (GCM estimate), and compare them to a simple approach derived from the climatological conditions without turbines [vertical kinetic energy (VKE) estimate]. On land, we find strong agreement between the VKE and GCM estimates with respect to electricity generation rates (0.32 and 0.37 We m−2) and wind speed reductions by 42 and 44%. Over ocean, the GCM estimate is about twice the VKE estimate (0.59 and 0.29 We m−2) and yet with comparable wind speed reductions (50 and 42%). We then show that this bias can be corrected by modifying the downward momentum flux to the surface. Thus, large-scale limits to wind power use can be derived from climatological conditions without explicitly simulating atmospheric dynamics. Consistent with the GCM simulations, the approach estimates that only comparatively few land areas are suitable to generate more than 1 We m−2 of electricity and that larger deployment scales are likely to reduce the expected electricity generation rate of each turbine. We conclude that these atmospheric effects are relevant for planning the future expansion of wind power. PMID:27849587

Reconfigurable Control with Neural Network Augmentation for a Modified F-15 Aircraft

NASA Technical Reports Server (NTRS)

Burken, John J.; Williams-Hayes, Peggy; Kaneshige, John T.; Stachowiak, Susan J.

2006-01-01

Description of the performance of a simplified dynamic inversion controller with neural network augmentation follows. Simulation studies focus on the results with and without neural network adaptation through the use of an F-15 aircraft simulator that has been modified to include canards. Simulated control law performance with a surface failure, in addition to an aerodynamic failure, is presented. The aircraft, with adaptation, attempts to minimize the inertial cross-coupling effect of the failure (a control derivative anomaly associated with a jammed control surface). The dynamic inversion controller calculates necessary surface commands to achieve desired rates. The dynamic inversion controller uses approximate short period and roll axis dynamics. The yaw axis controller is a sideslip rate command system. Methods are described to reduce the cross-coupling effect and maintain adequate tracking errors for control surface failures. The aerodynamic failure destabilizes the pitching moment due to angle of attack. The results show that control of the aircraft with the neural networks is easier (more damped) than without the neural networks. Simulation results show neural network augmentation of the controller improves performance with aerodynamic and control surface failures in terms of tracking error and cross-coupling reduction.

Adaptive Control Using Neural Network Augmentation for a Modified F-15 Aircraft

NASA Technical Reports Server (NTRS)

Burken, John J.; Williams-Hayes, Peggy; Karneshige, J. T.; Stachowiak, Susan J.

2006-01-01

Description of the performance of a simplified dynamic inversion controller with neural network augmentation follows. Simulation studies focus on the results with and without neural network adaptation through the use of an F-15 aircraft simulator that has been modified to include canards. Simulated control law performance with a surface failure, in addition to an aerodynamic failure, is presented. The aircraft, with adaptation, attempts to minimize the inertial cross-coupling effect of the failure (a control derivative anomaly associated with a jammed control surface). The dynamic inversion controller calculates necessary surface commands to achieve desired rates. The dynamic inversion controller uses approximate short period and roll axis dynamics. The yaw axis controller is a sideslip rate command system. Methods are described to reduce the cross-coupling effect and maintain adequate tracking errors for control surface failures. The aerodynamic failure destabilizes the pitching moment due to angle of attack. The results show that control of the aircraft with the neural networks is easier (more damped) than without the neural networks. Simulation results show neural network augmentation of the controller improves performance with aerodynamic and control surface failures in terms of tracking error and cross-coupling reduction.

Dynamics Modeling and Simulation of Large Transport Airplanes in Upset Conditions

NASA Technical Reports Server (NTRS)

Foster, John V.; Cunningham, Kevin; Fremaux, Charles M.; Shah, Gautam H.; Stewart, Eric C.; Rivers, Robert A.; Wilborn, James E.; Gato, William

2005-01-01

As part of NASA's Aviation Safety and Security Program, research has been in progress to develop aerodynamic modeling methods for simulations that accurately predict the flight dynamics characteristics of large transport airplanes in upset conditions. The motivation for this research stems from the recognition that simulation is a vital tool for addressing loss-of-control accidents, including applications to pilot training, accident reconstruction, and advanced control system analysis. The ultimate goal of this effort is to contribute to the reduction of the fatal accident rate due to loss-of-control. Research activities have involved accident analyses, wind tunnel testing, and piloted simulation. Results have shown that significant improvements in simulation fidelity for upset conditions, compared to current training simulations, can be achieved using state-of-the-art wind tunnel testing and aerodynamic modeling methods. This paper provides a summary of research completed to date and includes discussion on key technical results, lessons learned, and future research needs.

Optimal design of wind barriers using 3D computational fluid dynamics simulations

NASA Astrophysics Data System (ADS)

Fang, H.; Wu, X.; Yang, X.

2017-12-01

Desertification is a significant global environmental and ecological problem that requires human-regulated control and management. Wind barriers are commonly used to reduce wind velocity or trap drifting sand in arid or semi-arid areas. Therefore, optimal design of wind barriers becomes critical in Aeolian engineering. In the current study, we perform 3D computational fluid dynamics (CFD) simulations for flow passing through wind barriers with different structural parameters. To validate the simulation results, we first inter-compare the simulated flow field results with those from both wind-tunnel experiments and field measurements. Quantitative analyses of the shelter effect are then conducted based on a series of simulations with different structural parameters (such as wind barrier porosity, row numbers, inter-row spacing and belt schemes). The results show that wind barriers with porosity of 0.35 could provide the longest shelter distance (i.e., where the wind velocity reduction is more than 50%) thus are recommended in engineering designs. To determine the optimal row number and belt scheme, we introduce a cost function that takes both wind-velocity reduction effects and economical expense into account. The calculated cost function show that a 3-row-belt scheme with inter-row spacing of 6h (h as the height of wind barriers) and inter-belt spacing of 12h is the most effective.

NASA aerodynamics program

NASA Technical Reports Server (NTRS)

Holmes, Bruce J.; Schairer, Edward; Hicks, Gary; Wander, Stephen; Blankson, Isiaiah; Rose, Raymond; Olson, Lawrence; Unger, George

1990-01-01

Presented here is a comprehensive review of the following aerodynamics elements: computational methods and applications, computational fluid dynamics (CFD) validation, transition and turbulence physics, numerical aerodynamic simulation, drag reduction, test techniques and instrumentation, configuration aerodynamics, aeroacoustics, aerothermodynamics, hypersonics, subsonic transport/commuter aviation, fighter/attack aircraft and rotorcraft.

Ionic liquid induced dehydration and domain closure in lysozyme: FCS and MD simulation

NASA Astrophysics Data System (ADS)

Ghosh, Shirsendu; Parui, Sridip; Jana, Biman; Bhattacharyya, Kankan

2015-09-01

Effect of a room temperature ionic liquid (RTIL, [pmim][Br]) on the structure and dynamics of the protein, lysozyme, is investigated by fluorescence correlation spectroscopy (FCS) and molecular dynamic (MD) simulation. The FCS data indicate that addition of the RTIL ([pmim][Br]) leads to reduction in size and faster conformational dynamics of the protein. The hydrodynamic radius (rH) of lysozyme decreases from 18 Å in 0 M [pmim][Br] to 11 Å in 1.5 M [pmim][Br] while the conformational relaxation time decreases from 65 μs to 5 μs. Molecular origin of the collapse (size reduction) of lysozyme in aqueous RTIL is analyzed by MD simulation. The radial distribution function of water, RTIL cation, and RTIL anion from protein clearly indicates that addition of RTIL causes replacement of interfacial water by RTIL cation ([pmim]+) from the first solvation layer of the protein providing a comparatively dehydrated environment. This preferential solvation of the protein by the RTIL cation extends up to ˜30 Å from the protein surface giving rise to a nanoscopic cage of overall radius 42 Å. In the nanoscopic cage of the RTIL (42 Å), volume fraction of the protein (radius 12 Å) is only about 2%. RTIL anion does not show any preferential solvation near protein surface. Comparison of effective radius obtained from simulation and from FCS data suggests that the "dry" protein (radius 12 Å) alone diffuses in a nanoscopic cage of RTIL (radius 42 Å). MD simulation further reveals a decrease in distance ("domain closure") between the two domains (alpha and beta) of the protein leading to a more compact structure compared to that in the native state.

Ionic liquid induced dehydration and domain closure in lysozyme: FCS and MD simulation.

PubMed

Ghosh, Shirsendu; Parui, Sridip; Jana, Biman; Bhattacharyya, Kankan

2015-09-28

Effect of a room temperature ionic liquid (RTIL, [pmim][Br]) on the structure and dynamics of the protein, lysozyme, is investigated by fluorescence correlation spectroscopy (FCS) and molecular dynamic (MD) simulation. The FCS data indicate that addition of the RTIL ([pmim][Br]) leads to reduction in size and faster conformational dynamics of the protein. The hydrodynamic radius (rH) of lysozyme decreases from 18 Å in 0 M [pmim][Br] to 11 Å in 1.5 M [pmim][Br] while the conformational relaxation time decreases from 65 μs to 5 μs. Molecular origin of the collapse (size reduction) of lysozyme in aqueous RTIL is analyzed by MD simulation. The radial distribution function of water, RTIL cation, and RTIL anion from protein clearly indicates that addition of RTIL causes replacement of interfacial water by RTIL cation ([pmim](+)) from the first solvation layer of the protein providing a comparatively dehydrated environment. This preferential solvation of the protein by the RTIL cation extends up to ∼30 Å from the protein surface giving rise to a nanoscopic cage of overall radius 42 Å. In the nanoscopic cage of the RTIL (42 Å), volume fraction of the protein (radius 12 Å) is only about 2%. RTIL anion does not show any preferential solvation near protein surface. Comparison of effective radius obtained from simulation and from FCS data suggests that the "dry" protein (radius 12 Å) alone diffuses in a nanoscopic cage of RTIL (radius 42 Å). MD simulation further reveals a decrease in distance ("domain closure") between the two domains (alpha and beta) of the protein leading to a more compact structure compared to that in the native state.

Novel models and algorithms of load balancing for variable-structured collaborative simulation under HLA/RTI

NASA Astrophysics Data System (ADS)

Yue, Yingchao; Fan, Wenhui; Xiao, Tianyuan; Ma, Cheng

2013-07-01

High level architecture(HLA) is the open standard in the collaborative simulation field. Scholars have been paying close attention to theoretical research on and engineering applications of collaborative simulation based on HLA/RTI, which extends HLA in various aspects like functionality and efficiency. However, related study on the load balancing problem of HLA collaborative simulation is insufficient. Without load balancing, collaborative simulation under HLA/RTI may encounter performance reduction or even fatal errors. In this paper, load balancing is further divided into static problems and dynamic problems. A multi-objective model is established and the randomness of model parameters is taken into consideration for static load balancing, which makes the model more credible. The Monte Carlo based optimization algorithm(MCOA) is excogitated to gain static load balance. For dynamic load balancing, a new type of dynamic load balancing problem is put forward with regards to the variable-structured collaborative simulation under HLA/RTI. In order to minimize the influence against the running collaborative simulation, the ordinal optimization based algorithm(OOA) is devised to shorten the optimization time. Furthermore, the two algorithms are adopted in simulation experiments of different scenarios, which demonstrate their effectiveness and efficiency. An engineering experiment about collaborative simulation under HLA/RTI of high speed electricity multiple units(EMU) is also conducted to indentify credibility of the proposed models and supportive utility of MCOA and OOA to practical engineering systems. The proposed research ensures compatibility of traditional HLA, enhances the ability for assigning simulation loads onto computing units both statically and dynamically, improves the performance of collaborative simulation system and makes full use of the hardware resources.

Insights into low-latitude cloud feedbacks from high-resolution models.

PubMed

Bretherton, Christopher S

2015-11-13

Cloud feedbacks are a leading source of uncertainty in the climate sensitivity simulated by global climate models (GCMs). Low-latitude boundary-layer and cumulus cloud regimes are particularly problematic, because they are sustained by tight interactions between clouds and unresolved turbulent circulations. Turbulence-resolving models better simulate such cloud regimes and support the GCM consensus that they contribute to positive global cloud feedbacks. Large-eddy simulations using sub-100 m grid spacings over small computational domains elucidate marine boundary-layer cloud response to greenhouse warming. Four observationally supported mechanisms contribute: 'thermodynamic' cloudiness reduction from warming of the atmosphere-ocean column, 'radiative' cloudiness reduction from CO2- and H2O-induced increase in atmospheric emissivity aloft, 'stability-induced' cloud increase from increased lower tropospheric stratification, and 'dynamical' cloudiness increase from reduced subsidence. The cloudiness reduction mechanisms typically dominate, giving positive shortwave cloud feedback. Cloud-resolving models with horizontal grid spacings of a few kilometres illuminate how cumulonimbus cloud systems affect climate feedbacks. Limited-area simulations and superparameterized GCMs show upward shift and slight reduction of cloud cover in a warmer climate, implying positive cloud feedbacks. A global cloud-resolving model suggests tropical cirrus increases in a warmer climate, producing positive longwave cloud feedback, but results are sensitive to subgrid turbulence and ice microphysics schemes. © 2015 The Author(s).

An investigation of angular stiffness and damping coefficients of an axial spline coupling in high-speed rotating machinery

NASA Technical Reports Server (NTRS)

Ku, C.-P. Roger; Walton, James F., Jr.; Lund, Jorgen W.

1994-01-01

This paper provided an opportunity to quantify the angular stiffness and equivalent viscous damping coefficients of an axial spline coupling used in high-speed turbomachinery. A unique test methodology and data reduction procedures were developed. The bending moments and angular deflections transmitted across an axial spline coupling were measured while a nonrotating shaft was excited by an external shaker. A rotor dynamics computer program was used to simulate the test conditions and to correlate the angular stiffness and damping coefficients. In addition, sensitivity analyses were performed to show that the accuracy of the dynamic coefficients do not rely on the accuracy of the data reduction procedures.

Application of Pinniped Vibrissae to Aeropropulsion

NASA Technical Reports Server (NTRS)

Shyam, Vikram (Principal Investigator); Ameri, Ali; Poinsatte, Phil; Thurman, Doug; Wroblewski, Adam; Snyder, Chris

2015-01-01

Vibrissae of Phoca Vitulina (Harbor Seal) and Mirounga Angustirostris (Elephant Seal) possess undulations along their length. Harbor Seal Vibrissae were shown to reduce vortex induced vibrations and reduce drag compared to appropriately scaled cylinders and ellipses. Samples of Harbor Seal vibrissae, Elephant Seal vibrissae and California Sea Lion vibrissae were collected from the Marine Mammal Center in California. CT scanning, microscopy and 3D scanning techniques were utilized to characterize the whiskers. Computational fluid dynamics simulations of the whiskers were carried out to compare them to an ellipse and a cylinder. Leading edge parameters from the whiskers were used to create a 3D profile based on a modern power turbine blade. The NASA SW-2 facility was used to perform wind tunnel cascade testing on the 'Seal Blades'. Computational Fluid Dynamics simulations were used to study incidence angles from -37 to +10 degrees on the aerodynamic performance of the Seal Blade. The tests and simulations were conducted at a Reynolds number of 100,000. The Seal Blades showed consistent performance improvements over the baseline configuration. It was determined that a fuel burn reduction of approximately 5 could be achieved for a fixed wing aircraft. Noise reduction potential is also explored.

Persistent model order reduction for complex dynamical systems using smooth orthogonal decomposition

NASA Astrophysics Data System (ADS)

Ilbeigi, Shahab; Chelidze, David

2017-11-01

Full-scale complex dynamic models are not effective for parametric studies due to the inherent constraints on available computational power and storage resources. A persistent reduced order model (ROM) that is robust, stable, and provides high-fidelity simulations for a relatively wide range of parameters and operating conditions can provide a solution to this problem. The fidelity of a new framework for persistent model order reduction of large and complex dynamical systems is investigated. The framework is validated using several numerical examples including a large linear system and two complex nonlinear systems with material and geometrical nonlinearities. While the framework is used for identifying the robust subspaces obtained from both proper and smooth orthogonal decompositions (POD and SOD, respectively), the results show that SOD outperforms POD in terms of stability, accuracy, and robustness.

Influence of feedbacks from simulated crop growth on integrated regional hydrologic simulations under climate scenarios

NASA Astrophysics Data System (ADS)

van Walsum, P. E. V.

2011-11-01

Climate change impact modelling of hydrologic responses is hampered by climate-dependent model parameterizations. Reducing this dependency was one of the goals of extending the regional hydrologic modelling system SIMGRO with a two-way coupling to the crop growth simulation model WOFOST. The coupling includes feedbacks to the hydrologic model in terms of the root zone depth, soil cover, leaf area index, interception storage capacity, crop height and crop factor. For investigating whether such feedbacks lead to significantly different simulation results, two versions of the model coupling were set up for a test region: one with exogenous vegetation parameters, the "static" model, and one with endogenous simulation of the crop growth, the "dynamic" model WOFOST. The used parameterization methods of the static/dynamic vegetation models ensure that for the current climate the simulated long-term average of the actual evapotranspiration is the same for both models. Simulations were made for two climate scenarios. Owing to the higher temperatures in combination with a higher CO2-concentration of the atmosphere, a forward time shift of the crop development is simulated in the dynamic model; the used arable land crop, potatoes, also shows a shortening of the growing season. For this crop, a significant reduction of the potential transpiration is simulated compared to the static model, in the example by 15% in a warm, dry year. In consequence, the simulated crop water stress (the unit minus the relative transpiration) is lower when the dynamic model is used; also the simulated increase of crop water stress due to climate change is lower; in the example, the simulated increase is 15 percentage points less (of 55) than when a static model is used. The static/dynamic models also simulate different absolute values of the transpiration. The difference is most pronounced for potatoes at locations with ample moisture supply; this supply can either come from storage release of a good soil or from capillary rise. With good supply of moisture, the dynamic model simulates up to 10% less actual evapotranspiration than the static one in the example. This can lead to cases where the dynamic model predicts a slight increase of the recharge in a climate scenario, where the static model predicts a decrease. The use of a dynamic model also affects the simulated demand for surface water from external sources; especially the timing is affected. The proposed modelling approach uses postulated relationships that require validation with controlled field trials. In the Netherlands there is a lack of experimental facilities for performing such validations.

A family of dynamic models for large-eddy simulation

NASA Technical Reports Server (NTRS)

Carati, D.; Jansen, K.; Lund, T.

1995-01-01

Since its first application, the dynamic procedure has been recognized as an effective means to compute rather than prescribe the unknown coefficients that appear in a subgrid-scale model for Large-Eddy Simulation (LES). The dynamic procedure is usually used to determine the nondimensional coefficient in the Smagorinsky (1963) model. In reality the procedure is quite general and it is not limited to the Smagorinsky model by any theoretical or practical constraints. The purpose of this note is to consider a generalized family of dynamic eddy viscosity models that do not necessarily rely on the local equilibrium assumption built into the Smagorinsky model. By invoking an inertial range assumption, it will be shown that the coefficients in the new models need not be nondimensional. This additional degree of freedom allows the use of models that are scaled on traditionally unknown quantities such as the dissipation rate. In certain cases, the dynamic models with dimensional coefficients are simpler to implement, and allow for a 30% reduction in the number of required filtering operations.

Strain-dependent Damage Evolution and Velocity Reduction in Fault Zones Induced by Earthquake Rupture

NASA Astrophysics Data System (ADS)

Zhong, J.; Duan, B.

2009-12-01

Low-velocity fault zones (LVFZs) with reduced seismic velocities relative to the surrounding wall rocks are widely observed around active faults. The presence of such a zone will affect rupture propagation, near-field ground motion, and off-fault damage in subsequent earth-quakes. In this study, we quantify the reduction of seismic velocities caused by dynamic rup-ture on a 2D planar fault surrounded by a low-velocity fault zone. First, we implement the damage rheology (Lyakhovsky et al. 1997) in EQdyna (Duan and Oglesby 2006), an explicit dynamic finite element code. We further extend this damage rheology model to include the dependence of strains on crack density. Then, we quantify off-fault continuum damage distribution and velocity reduction induced by earthquake rupture with the presence of a preexisting LVFZ. We find that the presence of a LVFZ affects the tempo-spatial distribu-tions of off-fault damage. Because lack of constraint in some damage parameters, we further investigate the relationship between velocity reduction and these damage prameters by a large suite of numerical simulations. Slip velocity, slip, and near-field ground motions computed from damage rheology are also compared with those from off-fault elastic or elastoplastic responses. We find that the reduction in elastic moduli during dynamic rupture has profound impact on these quantities.

Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

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

Junghans, Christoph; Agarwal, Animesh; Delle Site, Luigi

Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.

Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

DOE PAGES

Junghans, Christoph; Agarwal, Animesh; Delle Site, Luigi

2017-06-01

Here, we discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multi scale fashion occurs.

Reduction of vibration forces transmitted from a radiator cooling fan to a vehicle body

NASA Astrophysics Data System (ADS)

Lim, Jonghyuk; Sim, Woojeong; Yun, Seen; Lee, Dongkon; Chung, Jintai

2018-04-01

This article presents methods for reducing transmitted vibration forces caused by mass unbalance of the radiator cooling fan during vehicle idling. To identify the effects of mass unbalance upon the vibration characteristics, vibration signals of the fan blades were experimentally measured both with and without an added mass. For analyzing the vibration forces transmitted to the vehicle body, a dynamic simulation model was established that reflected the vibration characteristics of the actual system. This process included a method described herein for calculating the equivalent stiffness and the equivalent damping of the shroud stators and rubber mountings. The dynamic simulation model was verified by comparing its results with experimental results of the radiator cooling fan. The dynamic simulation model was used to analyze the transmitted vibration forces at the rubber mountings. Also, a measure was established to evaluate the effects of varying the design parameters upon the transmitted vibration forces. We present design guidelines based on these analyses to reduce the transmitted vibration forces of the radiator cooling fan.

Phosphorus feedbacks constraining tropical ecosystem responses to changes in atmospheric CO2 and climate

NASA Astrophysics Data System (ADS)

Yang, Xiaojuan; Thornton, Peter E.; Ricciuto, Daniel M.; Hoffman, Forrest M.

2016-07-01

The effects of phosphorus (P) availability on carbon (C) cycling in the Amazon region are investigated using CLM-CNP. We demonstrate that the coupling of P dynamics reduces the simulated historical terrestrial C sink due to increasing atmospheric CO2 concentrations ([CO2]) by about 26%. Our exploratory simulations show that the response of tropical forest C cycling to increasing [CO2] depends on how elevated CO2 affects phosphatase enzyme production. The effects of warming are more complex, depending on the interactions between humidity, C, and nutrient dynamics. While a simulation with low humidity generally shows the reduction of net primary productivity (NPP), a second simulation with higher humidity suggests overall increases in NPP due to the dominant effects of reduced water stress and more nutrient availability. Our simulations point to the need for (1) new observations on how elevated [CO2] affects phosphatase enzyme production and (2) more tropical leaf-scale measurements under different temperature/humidity conditions with different soil P availability.

Dynamic ambulance reallocation for the reduction of ambulance response times using system status management.

PubMed

Lam, Sean Shao Wei; Zhang, Ji; Zhang, Zhong Cheng; Oh, Hong Choon; Overton, Jerry; Ng, Yih Yng; Ong, Marcus Eng Hock

2015-02-01

Dynamically reassigning ambulance deployment locations throughout a day to balance ambulance availability and demands can be effective in reducing response times. The objectives of this study were to model dynamic ambulance allocation plans in Singapore based on the system status management (SSM) strategy and to evaluate the dynamic deployment plans using a discrete event simulation (DES) model. The geographical information system-based analysis and mathematical programming were used to develop the dynamic ambulance deployment plans for SSM based on ambulance calls data from January 1, 2011, to June 30, 2011. A DES model that incorporated these plans was used to compare the performance of the dynamic SSM strategy against static reallocation policies under various demands and travel time uncertainties. When the deployment plans based on the SSM strategy were followed strictly, the DES model showed that the geographical information system-based plans resulted in approximately 13-second reduction in the median response times compared to the static reallocation policy, whereas the mathematical programming-based plans resulted in approximately a 44-second reduction. The response times and coverage performances were still better than the static policy when reallocations happened for only 60% of all the recommended moves. Dynamically reassigning ambulance deployment locations based on the SSM strategy can result in superior response times and coverage performance compared to static reallocation policies even when the dynamic plans were not followed strictly. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of Turbulence Modeling on an Excited Jet

NASA Technical Reports Server (NTRS)

Brown, Clifford A.; Hixon, Ray

2010-01-01

The flow dynamics in a high-speed jet are dominated by unsteady turbulent flow structures in the plume. Jet excitation seeks to control these flow structures through the natural instabilities present in the initial shear layer of the jet. Understanding and optimizing the excitation input, for jet noise reduction or plume mixing enhancement, requires many trials that may be done experimentally or computationally at a significant cost savings. Numerical simulations, which model various parts of the unsteady dynamics to reduce the computational expense of the simulation, must adequately capture the unsteady flow dynamics in the excited jet for the results are to be used. Four CFD methods are considered for use in an excited jet problem, including two turbulence models with an Unsteady Reynolds Averaged Navier-Stokes (URANS) solver, one Large Eddy Simulation (LES) solver, and one URANS/LES hybrid method. Each method is used to simulate a simplified excited jet and the results are evaluated based on the flow data, computation time, and numerical stability. The knowledge gained about the effect of turbulence modeling and CFD methods from these basic simulations will guide and assist future three-dimensional (3-D) simulations that will be used to understand and optimize a realistic excited jet for a particular application.

Bayesian model reduction and empirical Bayes for group (DCM) studies

PubMed Central

Friston, Karl J.; Litvak, Vladimir; Oswal, Ashwini; Razi, Adeel; Stephan, Klaas E.; van Wijk, Bernadette C.M.; Ziegler, Gabriel; Zeidman, Peter

2016-01-01

This technical note describes some Bayesian procedures for the analysis of group studies that use nonlinear models at the first (within-subject) level – e.g., dynamic causal models – and linear models at subsequent (between-subject) levels. Its focus is on using Bayesian model reduction to finesse the inversion of multiple models of a single dataset or a single (hierarchical or empirical Bayes) model of multiple datasets. These applications of Bayesian model reduction allow one to consider parametric random effects and make inferences about group effects very efficiently (in a few seconds). We provide the relatively straightforward theoretical background to these procedures and illustrate their application using a worked example. This example uses a simulated mismatch negativity study of schizophrenia. We illustrate the robustness of Bayesian model reduction to violations of the (commonly used) Laplace assumption in dynamic causal modelling and show how its recursive application can facilitate both classical and Bayesian inference about group differences. Finally, we consider the application of these empirical Bayesian procedures to classification and prediction. PMID:26569570

Modeling and Characterization of Dynamic Failure of Soda-lime Glass Under High Speed Impact

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

Liu, Wenning N.; Sun, Xin; Chen, Weinong W.

2012-05-27

In this paper, the impact-induced dynamic failure of a soda-lime glass block is studied using an integrated experimental/analytical approach. The Split Hopkinson Pressure Bar (SHPB) technique is used to conduct dynamic failure test of soda-lime glass first. The damage growth patterns and stress histories are reported for various glass specimen designs. Making use of a continuum damage mechanics (CDM)-based constitutive model, the initial failure and subsequent stiffness reduction of glass are simulated and investigated. Explicit finite element analyses are used to simulate the glass specimen impact event. A maximum shear stress-based damage evolution law is used in describing the glassmore » damage process under combined compression/shear loading. The impact test results are used to quantify the critical shear stress for the soda-lime glass under examination.« less

Gain in computational efficiency by vectorization in the dynamic simulation of multi-body systems

NASA Technical Reports Server (NTRS)

Amirouche, F. M. L.; Shareef, N. H.

1991-01-01

An improved technique for the identification and extraction of the exact quantities associated with the degrees of freedom at the element as well as the flexible body level is presented. It is implemented in the dynamic equations of motions based on the recursive formulation of Kane et al. (1987) and presented in a matrix form, integrating the concepts of strain energy, the finite-element approach, modal analysis, and reduction of equations. This technique eliminates the CPU intensive matrix multiplication operations in the code's hot spots for the dynamic simulation of the interconnected rigid and flexible bodies. A study of a simple robot with flexible links is presented by comparing the execution times on a scalar machine and a vector-processor with and without vector options. Performance figures demonstrating the substantial gains achieved by the technique are plotted.

Computational aspects of real-time simulation of rotary-wing aircraft. M.S. Thesis

NASA Technical Reports Server (NTRS)

Houck, J. A.

1976-01-01

A study was conducted to determine the effects of degrading a rotating blade element rotor mathematical model suitable for real-time simulation of rotorcraft. Three methods of degradation were studied, reduction of number of blades, reduction of number of blade segments, and increasing the integration interval, which has the corresponding effect of increasing blade azimuthal advance angle. The three degradation methods were studied through static trim comparisons, total rotor force and moment comparisons, single blade force and moment comparisons over one complete revolution, and total vehicle dynamic response comparisons. Recommendations are made concerning model degradation which should serve as a guide for future users of this mathematical model, and in general, they are in order of minimum impact on model validity: (1) reduction of number of blade segments; (2) reduction of number of blades; and (3) increase of integration interval and azimuthal advance angle. Extreme limits are specified beyond which a different rotor mathematical model should be used.

Effects of rotor model degradation on the accuracy of rotorcraft real time simulation

NASA Technical Reports Server (NTRS)

Houck, J. A.; Bowles, R. L.

1976-01-01

The effects are studied of degrading a rotating blade element rotor mathematical model to meet various real-time simulation requirements of rotorcraft. Three methods of degradation were studied: reduction of number of blades, reduction of number of blade segments, and increasing the integration interval, which has the corresponding effect of increasing blade azimuthal advance angle. The three degradation methods were studied through static trim comparisons, total rotor force and moment comparisons, single blade force and moment comparisons over one complete revolution, and total vehicle dynamic response comparisons. Recommendations are made concerning model degradation which should serve as a guide for future users of this mathematical model, and in general, they are in order of minimum impact on model validity: (1) reduction of number of blade segments, (2) reduction of number of blades, and (3) increase of integration interval and azimuthal advance angle. Extreme limits are specified beyond which the rotating blade element rotor mathematical model should not be used.

Numerical study of anomalous dynamic scaling behaviour of (1+1)-dimensional Das Sarma-Tamborenea model

NASA Astrophysics Data System (ADS)

Xun, Zhi-Peng; Tang, Gang; Han, Kui; Hao, Da-Peng; Xia, Hui; Zhou, Wei; Yang, Xi-Quan; Wen, Rong-Ji; Chen, Yu-Ling

2010-07-01

In order to discuss the finite-size effect and the anomalous dynamic scaling behaviour of Das Sarma-Tamborenea growth model, the (1+1)-dimensional Das Sarma-Tamborenea model is simulated on a large length scale by using the kinetic Monte-Carlo method. In the simulation, noise reduction technique is used in order to eliminate the crossover effect. Our results show that due to the existence of the finite-size effect, the effective global roughness exponent of the (1+1)-dimensional Das Sarma-Tamborenea model systematically decreases with system size L increasing when L > 256. This finding proves the conjecture by Aarao Reis[Aarao Reis F D A 2004 Phys. Rev. E 70 031607]. In addition, our simulation results also show that the Das Sarma-Tamborenea model in 1+1 dimensions indeed exhibits intrinsic anomalous scaling behaviour.

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

Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories inmore » a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.« less

Dynamic test/analysis correlation using reduced analytical models

NASA Technical Reports Server (NTRS)

Mcgowan, Paul E.; Angelucci, A. Filippo; Javeed, Mehzad

1992-01-01

Test/analysis correlation is an important aspect of the verification of analysis models which are used to predict on-orbit response characteristics of large space structures. This paper presents results of a study using reduced analysis models for performing dynamic test/analysis correlation. The reduced test-analysis model (TAM) has the same number and orientation of DOF as the test measurements. Two reduction methods, static (Guyan) reduction and the Improved Reduced System (IRS) reduction, are applied to the test/analysis correlation of a laboratory truss structure. Simulated test results and modal test data are used to examine the performance of each method. It is shown that selection of DOF to be retained in the TAM is critical when large structural masses are involved. In addition, the use of modal test results may provide difficulties in TAM accuracy even if a large number of DOF are retained in the TAM.

Dynamic evaluation of CMAQ part I: Separating the effects of ...

EPA Pesticide Factsheets

A dynamic evaluation of the Community Multiscale Air Quality (CMAQ) modeling system version 5.0.1 was conducted to evaluate the model's ability to predict changes in ozone levels between 2002 and 2005, a time period characterized by emission reductions associated with the EPA's Nitrogen Oxides State Implementation Plan as well as significant reductions in mobile source emissions. Model results for the summers of 2002 and 2005 were compared to simulations from a previous version of CMAQ to assess the impact of model updates on predicted pollutant response. Changes to the model treatment of emissions, meteorology and chemistry had substantial impacts on the simulated ozone concentrations. While the median bias for high summertime ozone decreased in both years compared to previous simulations, the observed decrease in ozone from 2002 to 2005 in the eastern US continued to be underestimated by the model. Additional “cross” simulations were used to decompose the model predicted change in ozone into the change due to emissions, the change due to meteorology and any remaining change not explained individually by these two components. The decomposition showed that the emission controls led to a decrease in modeled high summertime ozone close to twice as large as the decrease attributable to changes in meteorology alone. Quantifying the impact of retrospective emission controls by removing the impacts of meteorology during the control period can be a valuable approac

ExoMars Entry Demonstrator Module Dynamic Stability

NASA Astrophysics Data System (ADS)

Dormieux, Marc; Gulhan, Ali; Berner, Claude

2011-05-01

In the frame of ExoMars DM aerodynamics characterization, pitch damping derivatives determination is required as it drives the parachute deployment conditions. Series of free-flight and free- oscillation tests (captive model) have been conducted with particular attention for data reduction. 6 Degrees- of-Freedom (DoF) analysis tools require the knowledge of local damping derivatives. In general ground tests do not provide them directly but only effective damping derivatives. Free-flight (ballistic range) tests with full oscillations around trim angle have been performed at ISL for 0.5

Towards Real-Time Pilot-in-the-Loop Simulation of Rotorcraft With Fully-Coupled CFD Solutions of Rotor / Terrain Interactions

NASA Astrophysics Data System (ADS)

Oruc, Ilker

This thesis presents the development of computationally efficient coupling of Navier-Stokes CFD with a helicopter flight dynamics model, with the ultimate goal of real-time simulation of fully coupled aerodynamic interactions between rotor flow and the surrounding terrain. A particular focus of the research is on coupled airwake effects in the helicopter / ship dynamic interface. A computationally efficient coupling interface was developed between the helicopter flight dynamics model, GENHEL-PSU and the Navier-Stokes solvers, CRUNCH/CRAFT-CFD using both FORTRAN and C/C++ programming languages. In order to achieve real-time execution speeds, the main rotor was modeled with a simplified actuator disk using unsteady momentum sources, instead of resolving the full blade geometry in the CFD. All the airframe components, including the fuselage are represented by single aerodynamic control points in the CFD calculations. The rotor downwash influence on the fuselage and empennage are calculated by using the CFD predicted local flow velocities at these aerodynamic control points defined on the helicopter airframe. In the coupled simulations, the flight dynamics model is free to move within a computational domain, where the main rotor forces are translated into source terms in the momentum equations of the Navier-Stokes equations. Simultaneously, the CFD calculates induced velocities those are fed back to the simulation and affect the aerodynamic loads in the flight dynamics. The CFD solver models the inflow, ground effect, and interactional aerodynamics in the flight dynamics simulation, and these calculations can be coupled with solution of the external flow (e.g. ship airwake effects). The developed framework was utilized for various investigations of hovering, forward flight and helicopter/terrain interaction simulations including standard ground effect, partial ground effect, sloped terrain, and acceleration in ground effect; and results compared with different flight and experimental data. In near ground cases, the fully-coupled flight dynamics and CFD simulations predicted roll oscillations due to interactions of the rotor downwash, ground plane, and the feedback controller, which are not predicted by the conventional simulation models. Fully coupled simulations of a helicopter accelerating near ground predicted flow formations similar to the recirculation and ground vortex flow regimes observed in experiments. The predictions of hover power reductions due to ground effect compared well to a recent experimental data and the results showed 22% power reduction for a hover flight z/R=0.55 above ground level. Fully coupled simulations performed for a helicopter hovering over and approaching to a ship flight deck and results compared with the standalone GENHEL-PSU simulations without ship airwake and one-way coupled simulations. The fully-coupled simulations showed higher pilot workload compared to the other two cases. In order to increase the execution speeds of the CFD calculations, several improvements were made on the CFD solver. First, the initial coupling approach File I/O was replaced with a more efficient method called Multiple Program Multiple Data MPI framework, where the two executables communicate with each other by MPI calls. Next, the unstructured solver (CRUNCH CFD), which is 2nd-order accurate in space, was replaced with the faster running structured solver (CRAFT CFD) that is 5th-order accurate in space. Other improvements including a more efficient k-d tree search algorithm and the bounding of the source term search space within a small region of the grid surrounding the rotor were made on the CFD solver. The final improvement was to parallelize the search task with the CFD solver tasks within the solver. To quantify the speed-up of the improvements to the coupling interface described above, a study was performed to demonstrate the speedup achieved from each of the interface improvements. The improvements made on the CFD solver showed more than 40 times speedup from the baseline file I/O and unstructured solver CRUNCH CFD. Using a structured CFD solver with 5th-order spacial accuracy provided the largest reductions in execution times. Disregarding the solver numeric, the total speedup of all of the interface improvements including the MPMD rotor point exchange, k-d tree search algorithm, bounded search space, and paralleled search task, was approximately 231%, more than a factor of 2. All these improvements provided the necessary speedup for approach real-time CFD. (Abstract shortened by ProQuest.).

Towards a comprehensive framework for cosimulation of dynamic models with an emphasis on time stepping

NASA Astrophysics Data System (ADS)

Hoepfer, Matthias

Over the last two decades, computer modeling and simulation have evolved as the tools of choice for the design and engineering of dynamic systems. With increased system complexities, modeling and simulation become essential enablers for the design of new systems. Some of the advantages that modeling and simulation-based system design allows for are the replacement of physical tests to ensure product performance, reliability and quality, the shortening of design cycles due to the reduced need for physical prototyping, the design for mission scenarios, the invoking of currently nonexisting technologies, and the reduction of technological and financial risks. Traditionally, dynamic systems are modeled in a monolithic way. Such monolithic models include all the data, relations and equations necessary to represent the underlying system. With increased complexity of these models, the monolithic model approach reaches certain limits regarding for example, model handling and maintenance. Furthermore, while the available computer power has been steadily increasing according to Moore's Law (a doubling in computational power every 10 years), the ever-increasing complexities of new models have negated the increased resources available. Lastly, modern systems and design processes are interdisciplinary, enforcing the necessity to make models more flexible to be able to incorporate different modeling and design approaches. The solution to bypassing the shortcomings of monolithic models is cosimulation. In a very general sense, co-simulation addresses the issue of linking together different dynamic sub-models to a model which represents the overall, integrated dynamic system. It is therefore an important enabler for the design of interdisciplinary, interconnected, highly complex dynamic systems. While a basic co-simulation setup can be very easy, complications can arise when sub-models display behaviors such as algebraic loops, singularities, or constraints. This work frames the co-simulation approach to modeling and simulation. It lays out the general approach to dynamic system co-simulation, and gives a comprehensive overview of what co-simulation is and what it is not. It creates a taxonomy of the requirements and limits of co-simulation, and the issues arising with co-simulating sub-models. Possible solutions towards resolving the stated problems are investigated to a certain depth. A particular focus is given to the issue of time stepping. It will be shown that for dynamic models, the selection of the simulation time step is a crucial issue with respect to computational expense, simulation accuracy, and error control. The reasons for this are discussed in depth, and a time stepping algorithm for co-simulation with unknown dynamic sub-models is proposed. Motivations and suggestions for the further treatment of selected issues are presented.

Shock Waves Mitigation at Blunt Bodies Using Needles and Shells Against a Supersonic Flow

NASA Technical Reports Server (NTRS)

Gilinsky, M.; Blankson, I. M.; Sakharov, V. I.; Shvets, A. I.

2004-01-01

The paper contains some experimental and numerical simulation test results on cylindrical blunt body drag reduction using thin spikes or shell mounted in front of a body against a supersonic flow. Experimental tests were conducted using the Aeromechanics and Gas Dynamics Laboratory facilities at the Institute of Mechanics of Moscow State University (IMMSU). Numerical simulations utilizing NASA and IM/MSU codes were conducted at the Hampton University Fluid Mechanics and Acoustics Laboratory. The main purpose of this research is to examine the efficiency of application of multiple spikes for drag reduction and flow stability at the front of a blunt body in different flight conditions, i.e. Mach number, angle of attack, etc. The principal conclusions of these test results are: multiple spike/needle application leads to decrease of drag reduction benefits by comparison with the case of one central mounted needle at the front of a blunt body, but increase lift benefits.

Noise and Dissipation on Coadjoint Orbits

NASA Astrophysics Data System (ADS)

Arnaudon, Alexis; De Castro, Alex L.; Holm, Darryl D.

2018-02-01

We derive and study stochastic dissipative dynamics on coadjoint orbits by incorporating noise and dissipation into mechanical systems arising from the theory of reduction by symmetry, including a semidirect product extension. Random attractors are found for this general class of systems when the Lie algebra is semi-simple, provided the top Lyapunov exponent is positive. We study in details two canonical examples, the free rigid body and the heavy top, whose stochastic integrable reductions are found and numerical simulations of their random attractors are shown.

Load reduction of a monopile wind turbine tower using optimal tuned mass dampers

NASA Astrophysics Data System (ADS)

Tong, Xin; Zhao, Xiaowei; Zhao, Shi

2017-07-01

We investigate to apply tuned mass dampers (TMDs) (one in the fore-aft direction, one in the side-side direction) to suppress the vibration of a monopile wind turbine tower. Using the spectral element method, we derive a finite-dimensional state-space model Σd from an infinite-dimensional model Σ of a monopile wind turbine tower stabilised by a TMD located in the nacelle. Σ and Σd can be used to represent the dynamics of the tower and TMD in either the fore-aft direction or the side-side direction. The wind turbine tower subsystem of Σ is modelled as a non-uniform SCOLE (NASA Spacecraft Control Laboratory Experiment) system consisting of an Euler-Bernoulli beam equation describing the dynamics of the flexible tower and the Newton-Euler rigid body equations describing the dynamics of the heavy rotor-nacelle assembly (RNA) by neglecting any coupling with blade motions. Σd can be used for fast and accurate simulation for the dynamics of the wind turbine tower as well as for optimal TMD designs. We show that Σd agrees very well with the FAST (fatigue, aerodynamics, structures and turbulence) simulation of the NREL 5-MW wind turbine model. We optimise the parameters of the TMD by minimising the frequency-limited ?-norm of the transfer function matrix of Σd which has input of force and torque acting on the RNA, and output of tower-top displacement. The performances of the optimal TMDs in the fore-aft and side-side directions are tested through FAST simulations, which achieve substantial fatigue load reductions. This research also demonstrates how to optimally tune TMDs to reduce vibrations of flexible structures described by partial differential equations.

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

NASA Technical Reports Server (NTRS)

Campbell, Bryan A.; Bezos, Gaudy M.

1989-01-01

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

Construction of edge cracks pre-criterion model based on hot rolling experiment and simulation of AZ31 magnesium alloy

NASA Astrophysics Data System (ADS)

Ning, Fangkun; Jia, Weitao; Hou, Jian; Chen, Xingrui; Le, Qichi

2018-05-01

Various fracture criteria, especially Johnson and Cook (J-C) model and (normalized) Cockcroft and Latham (C-L) criterion were contrasted and discussed. Based on normalized C-L criterion, adopted in this paper, FE simulation was carried out and hot rolling experiments under temperature range of 200 °C–350 °C, rolling reduction rate of 25%–40% and rolling speed from 7–21 r/min was implemented. The microstructure was observed by optical microscope and damage values of simulation results were contrasted with the length of cracks on diverse parameters. The results show that the plate generated less edge cracks and the microstructure emerged slight shear bands and fine dynamic recrystallization grains rolled at 350 °C, 40% reduction and 14 r/min. The edge cracks pre-criterion model was obtained combined with Zener-Hollomon equation and deformation activation energy.

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

D'Azevedo, Eduardo; Abbott, Stephen; Koskela, Tuomas

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning.

High-temperature annealing of graphite: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Petersen, Andrew; Gillette, Victor

2018-05-01

A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

Dynamic ocean management increases the efficiency and efficacy of fisheries management.

PubMed

Dunn, Daniel C; Maxwell, Sara M; Boustany, Andre M; Halpin, Patrick N

2016-01-19

In response to the inherent dynamic nature of the oceans and continuing difficulty in managing ecosystem impacts of fisheries, interest in the concept of dynamic ocean management, or real-time management of ocean resources, has accelerated in the last several years. However, scientists have yet to quantitatively assess the efficiency of dynamic management over static management. Of particular interest is how scale influences effectiveness, both in terms of how it reflects underlying ecological processes and how this relates to potential efficiency gains. Here, we address the empirical evidence gap and further the ecological theory underpinning dynamic management. We illustrate, through the simulation of closures across a range of spatiotemporal scales, that dynamic ocean management can address previously intractable problems at scales associated with coactive and social patterns (e.g., competition, predation, niche partitioning, parasitism, and social aggregations). Furthermore, it can significantly improve the efficiency of management: as the resolution of the closures used increases (i.e., as the closures become more targeted), the percentage of target catch forgone or displaced decreases, the reduction ratio (bycatch/catch) increases, and the total time-area required to achieve the desired bycatch reduction decreases. In the scenario examined, coarser scale management measures (annual time-area closures and monthly full-fishery closures) would displace up to four to five times the target catch and require 100-200 times more square kilometer-days of closure than dynamic measures (grid-based closures and move-on rules). To achieve similar reductions in juvenile bycatch, the fishery would forgo or displace between USD 15-52 million in landings using a static approach over a dynamic management approach.

Dynamic Ocean Management Increases the Efficiency and Efficacy of Fisheries Management

NASA Astrophysics Data System (ADS)

Dunn, D. C.; Maxwell, S.; Boustany, A. M.; Halpin, P. N.

2016-12-01

In response to the inherent dynamic nature of the oceans and continuing difficulty in managing ecosystem impacts of fisheries, interest in the concept of dynamic ocean management, or real-time management of ocean resources, has accelerated in the last several years. However, scientists have yet to quantitatively assess the efficiency of dynamic management over static management. Of particular interest is how scale influences effectiveness, both in terms of how it reflects underlying ecological processes and how this relates to potential efficiency gains. In this presentation, we attempt to address both the empirical evidence gap and further the ecological theory underpinning dynamic management. We illustrate, through the simulation of closures across a range of spatiotemporal scales, that dynamic ocean management can address previously intractable problems at scales associated with coactive and social patterns (e.g., competition, predation, niche partitioning, parasitism and social aggregations). Further, it can significantly improve the efficiency of management: as the resolution of the individual closures used increases (i.e., as the closures become more targeted) the percent of target catch forgone or displaced decreases, the reduction ratio (bycatch/catch) increases, and the total time-area required to achieve the desired bycatch reduction decreases. The coarser management measures (annual time-area closures and monthly full fishery closures) affected up to 4-5x the target catch and required 100-200x the time-area of the dynamic measures (grid-based closures and move-on rules). To achieve similar reductions in juvenile bycatch, the fishery would forgo or displace between USD 15-52 million in landings using a static approach over a dynamic management approach.

Model reduction for agent-based social simulation: coarse-graining a civil violence model.

PubMed

Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

Model reduction for agent-based social simulation: Coarse-graining a civil violence model

NASA Astrophysics Data System (ADS)

Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

Consistent Large-Eddy Simulation of a Temporal Mixing Layer Laden with Evaporating Drops. Part 2; A Posteriori Modelling

NASA Technical Reports Server (NTRS)

Leboissertier, Anthony; Okong'O, Nora; Bellan, Josette

2005-01-01

Large-eddy simulation (LES) is conducted of a three-dimensional temporal mixing layer whose lower stream is initially laden with liquid drops which may evaporate during the simulation. The gas-phase equations are written in an Eulerian frame for two perfect gas species (carrier gas and vapour emanating from the drops), while the liquid-phase equations are written in a Lagrangian frame. The effect of drop evaporation on the gas phase is considered through mass, species, momentum and energy source terms. The drop evolution is modelled using physical drops, or using computational drops to represent the physical drops. Simulations are performed using various LES models previously assessed on a database obtained from direct numerical simulations (DNS). These LES models are for: (i) the subgrid-scale (SGS) fluxes and (ii) the filtered source terms (FSTs) based on computational drops. The LES, which are compared to filtered-and-coarsened (FC) DNS results at the coarser LES grid, are conducted with 64 times fewer grid points than the DNS, and up to 64 times fewer computational than physical drops. It is found that both constant-coefficient and dynamic Smagorinsky SGS-flux models, though numerically stable, are overly dissipative and damp generated small-resolved-scale (SRS) turbulent structures. Although the global growth and mixing predictions of LES using Smagorinsky models are in good agreement with the FC-DNS, the spatial distributions of the drops differ significantly. In contrast, the constant-coefficient scale-similarity model and the dynamic gradient model perform well in predicting most flow features, with the latter model having the advantage of not requiring a priori calibration of the model coefficient. The ability of the dynamic models to determine the model coefficient during LES is found to be essential since the constant-coefficient gradient model, although more accurate than the Smagorinsky model, is not consistently numerically stable despite using DNS-calibrated coefficients. With accurate SGS-flux models, namely scale-similarity and dynamic gradient, the FST model allows up to a 32-fold reduction in computational drops compared to the number of physical drops, without degradation of accuracy; a 64-fold reduction leads to a slight decrease in accuracy.

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Computing Optimal Stochastic Portfolio Execution Strategies: A Parametric Approach Using Simulations

NASA Astrophysics Data System (ADS)

Moazeni, Somayeh; Coleman, Thomas F.; Li, Yuying

2010-09-01

Computing optimal stochastic portfolio execution strategies under appropriate risk consideration presents great computational challenge. We investigate a parametric approach for computing optimal stochastic strategies using Monte Carlo simulations. This approach allows reduction in computational complexity by computing coefficients for a parametric representation of a stochastic dynamic strategy based on static optimization. Using this technique, constraints can be similarly handled using appropriate penalty functions. We illustrate the proposed approach to minimize the expected execution cost and Conditional Value-at-Risk (CVaR).

Critical current and linewidth reduction in spin-torque nano-oscillators by delayed self-injection

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

Khalsa, Guru, E-mail: guru.khalsa@nist.gov; Stiles, M. D.; Grollier, J.

2015-06-15

Based on theoretical models, the dynamics of spin-torque nano-oscillators can be substantially modified by re-injecting the emitted signal to the input of the oscillator after some delay. Numerical simulations for vortex magnetic tunnel junctions show that with reasonable parameters this approach can decrease critical currents as much as 25% and linewidths by a factor of 4. Analytical calculations, which agree well with simulations, demonstrate that these results can be generalized to any kind of spin-torque oscillator.

Simulation of floor heating in a combined solar-biomass system integrated in a public bathhouse located in Marrakech

NASA Astrophysics Data System (ADS)

Krarouch, M.; Hamdi, H.; Lamghari, S.; Outzourhit, A.

2018-05-01

This study was conducted in the framework of the HYBRID-BATH project aiming at improving the energy efficiency of traditional Hammams (Turkish baths) and the reduction of the use of wood energy and therefore of greenhouse gases emissions. The present work focuses on the energetic performance of a two-room Hammam located in Marrakech. The rooms were heated by the ground using a hybrid system Micro-CSP/biomass boiler. The dynamic simulation of the system (Hammam coupled with the hybrid system Micro-CSP/biomass boiler) was conducted using TRNSYS18 software. The parametric study was performed on a Typical Meteorological Year data (TMY). This study is devoted to presenting the results of the dynamic simulation of a part of the Hammam investigated, in order to optimize the underfloor heating system. The models and the results of the simulations will be validated by comparisons with experimental results. The main objective is to optimize the operation of such system and to improve its performance.

Phonon thermal properties of graphene on h-BN from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zou, Ji-Hang; Cao, Bing-Yang

2017-03-01

Phonon thermal properties of graphene on hexagonal boron nitride are investigated by the molecular dynamics simulations combined with lattice dynamics theory. It is found that the dispersion curves have minor changes for supported graphene because the interlayer coupling is too weak to shift the harmonic phonon properties. The ZA and ZO phonon lifetimes are significantly reduced in supported graphene due to the breakdown of the symmetry-based selection rule. The dominant mean free path (MFP) of graphene is reduced from 90-800 nm to 60-500 nm at 300 K. The mode thermal conductivities of free and supported graphene are 3517 W/ (m.K) and 2200 W/ (m.K) at 300 K, respectively. The thermal conductivity of supported graphene decreases by about 37.4% due to the large reduction of flexural phonon lifetimes, and the relative contribution of flexural modes decreases from 35.0% to 16.7%.

Two-dimensional dynamic stall as simulated in a varying freestream

NASA Technical Reports Server (NTRS)

Pierce, G. A.; Kunz, D. L.; Malone, J. B.

1978-01-01

A low speed wind tunnel equipped with a axial gust generator to simulate the aerodynamic environment of a helicopter rotor was used to study the dynamic stall of a pitching blade in an effort to ascertain to what extent harmonic velocity perturbations in the freestream affect dynamic stall. The aerodynamic moment on a two dimensional, pitching blade model in both constant and pulsating airstream was measured. An operational analog computer was used to perform on-line data reduction and plots of moment versus angle of attack and work done by the moment were obtained. The data taken in the varying freestream were then compared to constant freestream data and to the results of two analytical methods. These comparisons show that the velocity perturbations have a significant effect on the pitching moment which can not be consistently predicted by the analytical methods, but had no drastic effect on the blade stability.

Hierarchial parallel computer architecture defined by computational multidisciplinary mechanics

NASA Technical Reports Server (NTRS)

Padovan, Joe; Gute, Doug; Johnson, Keith

1989-01-01

The goal is to develop an architecture for parallel processors enabling optimal handling of multi-disciplinary computation of fluid-solid simulations employing finite element and difference schemes. The goals, philosphical and modeling directions, static and dynamic poly trees, example problems, interpolative reduction, the impact on solvers are shown in viewgraph form.

Application of Pinniped Vibrissae to Aeropropulsion

NASA Technical Reports Server (NTRS)

Shyam, Vikram; Ameri, Ali; Poinsatte, Philip; Thurman, Douglas; Wroblewski, Adam; Snyder, Christopher

2015-01-01

Vibrissae of Phoca Vitulina (Harbor Seal) and Mirounga Angustirostris (Elephant Seal) possessundulations along their length. Harbor Seal Vibrissae were shown to reduce vortex induced vibrations and reduce dragcompared to appropriately scaled cylinders and ellipses. Samples of Harbor Seal vibrissae, Elephant Seal vibrissae andCalifornia Sea Lion vibrissae were collected from the Marine Mammal Center in California. CT scanning, microscopy and3D scanning techniques were utilized to characterize the whiskers. Computational fluid dynamics simulations of thewhiskers were carried out to compare them to an ellipse and a cylinder. Leading edge parameters from the whiskerswere used to create a 3D profile based on a modern power turbine blade. The NASA SW-2 facility was used to performwind tunnel cascade testing on the 'Seal Blades'. Computational Fluid Dynamics simulations were used to studyincidence angles from -37 to +10 degrees on the aerodynamic performance of the Seal Blade. The tests and simulationswere conducted at a Reynolds number of 100,000. The Seal Blades showed consistent performance improvements overthe baseline configuration. It was determined that a fuel burn reduction of approximately 5 could be achieved for a fixedwing aircraft. Noise reduction potential is also explored

Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation.

PubMed

Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

2016-12-14

NH 3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH 3 from atmospheric N 2 and oceanic H 2 O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH 3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH 3 . Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N 2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.

A molecular dynamics study of thermal transport in nanoparticle doped Argon like solid

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

Shahadat, Muhammad Rubayat Bin, E-mail: rubayat37@gmail.com; Ahmed, Shafkat; Morshed, A. K. M. M.

2016-07-12

Interfacial phenomena such as mass and type of the interstitial atom, nano scale material defect influence heat transfer and the effect become very significant with the reduction of the material size. Non Equilibrium Molecular Dynamics (NEMD) simulation was carried out in this study to investigate the effect of the interfacial phenomena on solid. Argon like solid was considered in this study and LJ potential was used for atomic interaction. Nanoparticles of different masses and different molecular defects were inserted inside the solid. From the molecular simulation, it was observed that a large interfacial mismatch due to change in mass inmore » the homogenous solid causes distortion of the phonon frequency causing increase in thermal resistance. Position of the doped nanoparticles have more profound effect on the thermal conductivity of the solid whereas influence of the mass ratio is not very significant. Interstitial atom positioned perpendicular to the heat flow causes sharp reduction in thermal conductivity. Structural defect caused by the molecular defect (void) also observed to significantly affect the thermal conductivity of the solid.« less

Nonlinear Dust Acoustic Waves in a Magnetized Dusty Plasma with Trapped and Superthermal Electrons

NASA Astrophysics Data System (ADS)

Ahmadi, Abrishami S.; Nouri, Kadijani M.

2014-06-01

In this work, the effects of superthermal and trapped electrons on the oblique propagation of nonlinear dust-acoustic waves in a magnetized dusty (complex) plasma are investigated. The dynamic of electrons is simulated by the generalized Lorentzian (κ) distribution function (DF). The dust grains are cold and their dynamics are simulated by hydrodynamic equations. Using the standard reductive perturbation technique (RPT) a nonlinear modified Korteweg-de Vries (mKdV) equation is derived. Two types of solitary waves; fast and slow dust acoustic solitons, exist in this plasma. Calculations reveal that compressive solitary structures are likely to propagate in this plasma where dust grains are negatively (or positively) charged. The properties of dust acoustic solitons (DASs) are also investigated numerically.

Simulation of linear mechanical systems

NASA Technical Reports Server (NTRS)

Sirlin, S. W.

1993-01-01

A dynamics and controls analyst is typically presented with a structural dynamics model and must perform various input/output tests and design control laws. The required time/frequency simulations need to be done many times as models change and control designs evolve. This paper examines some simple ways that open and closed loop frequency and time domain simulations can be done using the special structure of the system equations usually available. Routines were developed to run under Pro-Matlab in a mixture of the Pro-Matlab interpreter and FORTRAN (using the .mex facility). These routines are often orders of magnitude faster than trying the typical 'brute force' approach of using built-in Pro-Matlab routines such as bode. This makes the analyst's job easier since not only does an individual run take less time, but much larger models can be attacked, often allowing the whole model reduction step to be eliminated.

Ultrafast semi-metallic layer formation in detonating nitromethane

NASA Astrophysics Data System (ADS)

Reed, Evan; Manaa, M. Riad; Fried, Laurence; Glaesemann, Kurt; Joannopoulos, John

2008-03-01

We present the first quantum molecular dynamics simulations behind a detonation front (up to 0.2 ns) of the explosive nitromethane (CH3NO2) represented by the density-functional-based tight-binding method (DFTB). This simulation is enabled by our recently developed multi-scale shock wave molecular dynamics technique (MSST) that opens the door to longer duration simulations by several orders of magnitude. The electronic density of states around the Fermi energy initially increases as metastable material states are produced but then later decreases, perhaps unexpectedly. These changes indicate that the shock front is characterized by an increase in optical thickness and conductivity followed by a reduction around 100 picoseconds behind the front. We find that a significant population of intermediate metastable molecules are charged and charged species play an important role in the density of states evolution. The transient transformation to a semi-metallic state can be understood within the Anderson picture of metallization.

A semi-metallic layer in detonating nitromethane

NASA Astrophysics Data System (ADS)

Reed, Evan; Manaa, Riad; Fried, Laurence; Glaesemann, Kurt; Joannopoulos, John

2007-06-01

We present the first ever glimpse behind a detonation front in a chemically reactive quantum molecular dynamics simulation (up to 0.2 ns) of the explosive nitromethane (CH3NO2) represented by the density-functional-based tight-binding method (DFTB). This simulation is enabled by our recently developed multi-scale shock wave molecular dynamics technique (MSST) that opens the door to longer duration simulations by several orders of magnitude. The electronic DOS around the Fermi energy initially increases as metastable material states are produced but then later decreases, perhaps unexpectedly. These changes indicate that the shock front is characterized by an increase in optical thickness followed by a reduction in optical thickness hundreds of picoseconds behind the front, explaining recent experimental observations. We find that a significant population of intermediate metastable molecules are charged and charged species play an important role in the density of states evolution and a possible Mott metal-insulator transition.

Flow-induced voltage generation by moving a nano-sized ionic liquids droplet over a graphene sheet: Molecular dynamics simulation.

PubMed

Shao, Qunfeng; Jia, Jingjing; Guan, Yongji; He, Xiaodong; Zhang, Xiaoping

2016-03-28

In this work, the phenomenon of the voltage generation is explored by using the molecular dynamics simulations, which is performed by driving a nano-sized droplet of room temperature ionic liquids moving along the monolayer graphene sheet for the first time. The studies show that the cations and anions of the droplet will move with velocity nonlinearly increasing to saturation arising by the force balance. The traditional equation for calculating the induced voltage is developed by taking the charge density into consideration, and larger induced voltages in μV-scale are obtained from the nano-size simulation systems based on the ionic liquids (ILs) for its enhanced ionic drifting velocities. It is also derived that the viscosity acts as a reduction for the induced voltage by comparing systems composed of two types of ILs with different viscosity and temperature.

Magnetic field effect on the structural properties of a peptide model: Molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Housaindokht, Mohammad Reza; Moosavi, Fatemeh

2018-06-01

The effect of magnetization on the properties of a system containing a peptide model is studied by molecular dynamics simulation at a range of 298-318 K. Two mole fractions of 0.001 and 0.002 of peptide were simulated and the variation of hydrogen bond number, orientational ordering parameter, gyration radius, mean square displacement, as well as radial distribution function, were under consideration. The results show that applying magnetic field will increase the number of hydrogen bonds between water molecules by clustering them and decreases the interaction of water and peptide. This reduction may cause more available free space and enhance the movement of the peptide. As a result, the diffusion coefficient of the peptide becomes greater and its conformation changes. Orientational ordering parameter besides radius of gyration demonstrates that peptide is expanded by static magnetic field and its orientational ordering parameter is affected.

Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

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

Xin, H.; LaRue, J.; Oberg, H.

2015-04-16

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distributionmore » and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.« less

Molecular-dynamics simulations of thin films with a free surface

NASA Astrophysics Data System (ADS)

Peter, Simone; Meyer, Hendrik; Baschnagel, Joerg

2007-03-01

We present results [1,2] from molecular-dynamics simulations for a model of non-entangled short polymer chains in a free standing and a supported film geometry. We investigate the influence of confinement on static and dynamic properties of the melt. We find that the relaxation at the surfaces is faster in comparison to the bulk. We perform a layer-resolved analysis of the dynamics and show that it is possible to associate a gradient in critical temperatures Tc(y) with the gradient in the relaxation dynamics. This finding is in qualitative agreement with experimental results on supported polystyrene (PS) films [Ellison et al, Nat. Mater. 2, 695 (2003)]. Furthermore we show that the y-dependence of Tc(y) can be expressed in terms of the depression of Tc(h), the global Tc for a film of thickness h, if we assume that Tc(h) is the arithmetic mean of Tc(y) and parameterize the depression of Tc(h) by Tc(h)=Tc/(1+h0/h), a formula suggested by Herminghaus et al [Eur. Phys. J E 5, 531 (2001)] for the reduction of the glass transition temperature in supported PS films. We demonstrate the validity of this formula by comparing our simulation results to results from other simulations and experiments. [1] S. Peter, H. Meyer and J. Baschnagel, J. Polym. Sci. B, 44, 2951 (2006) [2] S. Peter, H. Meyer, J. Baschnagel and R, Seemann, J. Phys: Condens. Matter (2007)

INCA Modelling of the Lee System: strategies for the reduction of nitrogen loads

NASA Astrophysics Data System (ADS)

Flynn, N. J.; Paddison, T.; Whitehead, P. G.

The Integrated Nitrogen Catchment model (INCA) was applied successfully to simulate nitrogen concentrations in the River Lee, a northern tributary of the River Thames for 1995-1999. Leaching from urban and agricultural areas was found to control nitrogen dynamics in reaches unaffected by effluent discharges and abstractions; the occurrence of minimal flows resulted in an upward trend in nitrate concentration. Sewage treatment works (STW) discharging into the River Lee raised nitrate concentrations substantially, a problem which was compounded by abstractions in the Lower Lee. The average concentration of nitrate (NO3) for the simulation period 1995-96 was 7.87 mg N l-1. Ammonium (NH4) concentrations were simulated less successfully. However, concentrations of ammonium rarely rose to levels which would be of environmental concern. Scenarios were run through INCA to assess strategies for the reduction of nitrate concentrations in the catchment. The conversion of arable land to ungrazed vegetation or to woodland would reduce nitrate concentrations substantially, whilst inclusion of riparian buffer strips would be unsuccessful in reducing nitrate loading. A 50% reduction in nitrate loading from Luton STW would result in a fall of up to 5 mg N l-1 in the reach directly affected (concentrations fell from maxima of 13 to 8 mg N l-1 , nearly a 40 % reduction), whilst a 20% reduction in abstractions would reduce maximum peaks in concentration in the lower Lee by up to 4 mg l-1 (from 17 to 13 mg N l-1, nearly a 25 % reduction),.

Computer animation challenges for computational fluid dynamics

NASA Astrophysics Data System (ADS)

Vines, Mauricio; Lee, Won-Sook; Mavriplis, Catherine

2012-07-01

Computer animation requirements differ from those of traditional computational fluid dynamics (CFD) investigations in that visual plausibility and rapid frame update rates trump physical accuracy. We present an overview of the main techniques for fluid simulation in computer animation, starting with Eulerian grid approaches, the Lattice Boltzmann method, Fourier transform techniques and Lagrangian particle introduction. Adaptive grid methods, precomputation of results for model reduction, parallelisation and computation on graphical processing units (GPUs) are reviewed in the context of accelerating simulation computations for animation. A survey of current specific approaches for the application of these techniques to the simulation of smoke, fire, water, bubbles, mixing, phase change and solid-fluid coupling is also included. Adding plausibility to results through particle introduction, turbulence detail and concentration on regions of interest by level set techniques has elevated the degree of accuracy and realism of recent animations. Basic approaches are described here. Techniques to control the simulation to produce a desired visual effect are also discussed. Finally, some references to rendering techniques and haptic applications are mentioned to provide the reader with a complete picture of the challenges of simulating fluids in computer animation.

Phosphorus feedbacks constraining tropical ecosystem responses to changes in atmospheric CO 2 and climate

DOE PAGES

Yang, Xiaojuan; Thornton, Peter E.; Ricciuto, Daniel M.; ...

2016-07-14

The effects of phosphorus (P) availability on carbon (C) cycling in the Amazon region are investigated using CLM-CNP. Within this paper, we demonstrate that the coupling of P dynamics reduces the simulated historical terrestrial C sink due to increasing atmospheric CO 2 concentrations ([CO 2]) by about 26%. Our exploratory simulations show that the response of tropical forest C cycling to increasing [CO 2] depends on how elevated CO 2 affects phosphatase enzyme production. The effects of warming are more complex, depending on the interactions between humidity, C, and nutrient dynamics. While a simulation with low humidity generally shows themore » reduction of net primary productivity (NPP), a second simulation with higher humidity suggests overall increases in NPP due to the dominant effects of reduced water stress and more nutrient availability. Lastly, our simulations point to the need for (1) new observations on how elevated [CO 2] affects phosphatase enzyme production and (2) more tropical leaf-scale measurements under different temperature/humidity conditions with different soil P availability.« less

Solvent decompositions and physical properties of decomposition compounds in Li-ion battery electrolytes studied by DFT calculations and molecular dynamics simulations.

PubMed

Tasaki, Ken

2005-02-24

The density functional theory (DFT) calculations have been performed for the reduction decompositions of solvents widely used in Li-ion secondary battery electrolytes, ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonates (DMC), ethyl methyl carbonate (EMC), and diethyl carbonate (DEC), including a typical electrolyte additive, vinylene carbonate (VC), at the level of B3LYP/6-311+G(2d,p), both in the gas phase and solution using the polarizable conductor calculation model. In the gas phase, the first electron reduction for the cyclic carbonates and for the linear carbonates is found to be exothermic and endothermic, respectively, while the second electron reduction is endothermic for all the compounds examined. On the contrary, in solution both first and second electron reductions are exothermic for all the compounds. Among the solvents and the additive examined, the likelihood of undergoing the first electron reduction in solution was found in the order of EC > PC > VC > DMC > EMC > DEC with EC being the most likely reduced. VC, on the other hand, is most likely to undergo the second electron reduction among the compounds, in the order of VC > EC > PC. Based on the results, the experimentally demonstrated effectiveness of VC as an excellent electrolyte additive was discussed. The bulk thermodynamic properties of two dilithium alkylene glycol dicarbonates, dilithium ethylene glycol dicarbonate (Li-EDC) and dilithium 1,2-propylene glycol dicarbonate (Li-PDC), as the major component of solid-electrolyte interface (SEI) films were also examined through molecular dynamics (MD) simulations in order to understand the stability of the SEI film. It was found that film produced from a decomposition of EC, modeled by Li-EDC, has a higher density, more cohesive energy, and less solubility to the solvent than the film produced from decomposition of PC, Li-PDC. Further, MD simulations of the interface between the decomposition compound and graphite suggested that Li-EDC has more favorable interactions with the graphite surface than Li-PDC. The difference in the SEI film stability and the behavior of Li-ion battery cycling among the solvents were discussed in terms of the molecular structures.

Dynamic climate emulators for solar geoengineering

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

MacMartin, Douglas G.; Kravitz, Ben

2016-12-22

Climate emulators trained on existing simulations can be used to project project the climate effects that result from different possible future pathways of anthropogenic forcing, without further relying on general circulation model (GCM) simulations. We extend this idea to include different amounts of solar geoengineering in addition to different pathways of greenhouse gas concentrations, by training emulators from a multi-model ensemble of simulations from the Geoengineering Model Intercomparison Project (GeoMIP). The emulator is trained on the abrupt 4 × CO 2 and a compensating solar reduction simulation (G1), and evaluated by comparing predictions against a simulated 1 % per yearmore » CO 2 increase and a similarly smaller solar reduction (G2). We find reasonable agreement in most models for predicting changes in temperature and precipitation (including regional effects), and annual-mean Northern Hemisphere sea ice extent, with the difference between simulation and prediction typically being smaller than natural variability. This verifies that the linearity assumption used in constructing the emulator is sufficient for these variables over the range of forcing considered. Annual-minimum Northern Hemisphere sea ice extent is less well predicted, indicating a limit to the linearity assumption.« less

Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

PubMed Central

Skolnick, Jeffrey

2016-01-01

An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes. PMID:27634243

A novel coupling of noise reduction algorithms for particle flow simulations

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

Zimoń, M.J., E-mail: malgorzata.zimon@stfc.ac.uk; James Weir Fluids Lab, Mechanical and Aerospace Engineering Department, The University of Strathclyde, Glasgow G1 1XJ; Reese, J.M.

2016-09-15

Proper orthogonal decomposition (POD) and its extension based on time-windows have been shown to greatly improve the effectiveness of recovering smooth ensemble solutions from noisy particle data. However, to successfully de-noise any molecular system, a large number of measurements still need to be provided. In order to achieve a better efficiency in processing time-dependent fields, we have combined POD with a well-established signal processing technique, wavelet-based thresholding. In this novel hybrid procedure, the wavelet filtering is applied within the POD domain and referred to as WAVinPOD. The algorithm exhibits promising results when applied to both synthetically generated signals and particlemore » data. In this work, the simulations compare the performance of our new approach with standard POD or wavelet analysis in extracting smooth profiles from noisy velocity and density fields. Numerical examples include molecular dynamics and dissipative particle dynamics simulations of unsteady force- and shear-driven liquid flows, as well as phase separation phenomenon. Simulation results confirm that WAVinPOD preserves the dimensionality reduction obtained using POD, while improving its filtering properties through the sparse representation of data in wavelet basis. This paper shows that WAVinPOD outperforms the other estimators for both synthetically generated signals and particle-based measurements, achieving a higher signal-to-noise ratio from a smaller number of samples. The new filtering methodology offers significant computational savings, particularly for multi-scale applications seeking to couple continuum informations with atomistic models. It is the first time that a rigorous analysis has compared de-noising techniques for particle-based fluid simulations.« less

Dynamical significance of tides over the Bay of Bengal

NASA Astrophysics Data System (ADS)

Bhagawati, Chirantan; Pandey, Suchita; Dandapat, Sumit; Chakraborty, Arun

2018-06-01

Tides play a significant role in the ocean surface circulations and vertical mixing thereby influencing the Sea Surface Temperatures (SST) as well. This, in turn, plays an important role in the global circulation when used as a lower boundary condition in a global atmospheric general circulation model. Therefore in the present study, the dynamics of tides over the Bay of Bengal (BoB) is investigated through numerical simulations using a high resolution (1/12°) Regional Ocean Modeling System (ROMS). Based on statistical analysis it is observed that incorporation of explicit tidal forcing improves the model performance in simulating the basin averaged monthly surface circulation features by 64% compared to the simulation without tides. The model simulates also Mixed Layer Depth (MLD) and SST realistically. The energy exchange between tidal oscillations and eddies leads to redistribution of surface kinetic energy density with a net decrease of 0.012 J m-3 in the western Bay and a net increase of 0.007 J m-3 in the eastern Bay. The tidal forcing also affects the potential energy anomaly and vertical mixing thereby leading to a fall in monthly MLD over the BoB. The mixing due to tides leads to a subsequent reduction in monthly SST and a corresponding reduction in surface heat exchange. These results from the numerical simulation using ROMS reveal that tides have a significant influence over the air-sea heat exchange which is the most important parameter for prediction of Tropical Cyclone frequency and its future variability over the BoB.

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

PubMed Central

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

2011-01-01

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

Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study.

PubMed

Catte, Andrea; Patterson, James C; Jones, Martin K; Jerome, W Gray; Bashtovyy, Denys; Su, Zhengchang; Gu, Feifei; Chen, Jianguo; Aliste, Marcela P; Harvey, Stephen C; Li, Ling; Weinstein, Gilbert; Segrest, Jere P

2006-06-15

ApoA-I is a uniquely flexible lipid-scavenging protein capable of incorporating phospholipids into stable particles. Here we report molecular dynamics simulations on a series of progressively smaller discoidal high density lipoprotein particles produced by incremental removal of palmitoyloleoylphosphatidylcholine via four different pathways. The starting model contained 160 palmitoyloleoylphosphatidylcholines and a belt of two antiparallel amphipathic helical lipid-associating domains of apolipoprotein (apo) A-I. The results are particularly compelling. After a few nanoseconds of molecular dynamics simulation, independent of the starting particle and method of size reduction, all simulated double belts of the four lipidated apoA-I particles have helical domains that impressively approximate the x-ray crystal structure of lipid-free apoA-I, particularly between residues 88 and 186. These results provide atomic resolution models for two of the particles produced by in vitro reconstitution of nascent high density lipoprotein particles. These particles, measuring 95 angstroms and 78 angstroms by nondenaturing gradient gel electrophoresis, correspond in composition and in size/shape (by negative stain electron microscopy) to the simulated particles with molar ratios of 100:2 and 50:2, respectively. The lipids of the 100:2 particle family form minimal surfaces at their monolayer-monolayer interface, whereas the 50:2 particle family displays a lipid pocket capable of binding a dynamic range of phospholipid molecules.

Novel Changes in Discoidal High Density Lipoprotein Morphology: A Molecular Dynamics Study

PubMed Central

Catte, Andrea; Patterson, James C.; Jones, Martin K.; Jerome, W. Gray; Bashtovyy, Denys; Su, Zhengchang; Gu, Feifei; Chen, Jianguo; Aliste, Marcela P.; Harvey, Stephen C.; Li, Ling; Weinstein, Gilbert; Segrest, Jere P.

2006-01-01

ApoA-I is a uniquely flexible lipid-scavenging protein capable of incorporating phospholipids into stable particles. Here we report molecular dynamics simulations on a series of progressively smaller discoidal high density lipoprotein particles produced by incremental removal of palmitoyloleoylphosphatidylcholine via four different pathways. The starting model contained 160 palmitoyloleoylphosphatidylcholines and a belt of two antiparallel amphipathic helical lipid-associating domains of apolipoprotein (apo) A-I. The results are particularly compelling. After a few nanoseconds of molecular dynamics simulation, independent of the starting particle and method of size reduction, all simulated double belts of the four lipidated apoA-I particles have helical domains that impressively approximate the x-ray crystal structure of lipid-free apoA-I, particularly between residues 88 and 186. These results provide atomic resolution models for two of the particles produced by in vitro reconstitution of nascent high density lipoprotein particles. These particles, measuring 95 Å and 78 Å by nondenaturing gradient gel electrophoresis, correspond in composition and in size/shape (by negative stain electron microscopy) to the simulated particles with molar ratios of 100:2 and 50:2, respectively. The lipids of the 100:2 particle family form minimal surfaces at their monolayer-monolayer interface, whereas the 50:2 particle family displays a lipid pocket capable of binding a dynamic range of phospholipid molecules. PMID:16581834

SMI Compatible Simulation Scheduler Design for Reuse of Model Complying with Smp Standard

NASA Astrophysics Data System (ADS)

Koo, Cheol-Hea; Lee, Hoon-Hee; Cheon, Yee-Jin

2010-12-01

Software reusability is one of key factors which impacts cost and schedule on a software development project. It is very crucial also in satellite simulator development since there are many commercial simulator models related to satellite and dynamics. If these models can be used in another simulator platform, great deal of confidence and cost/schedule reduction would be achieved. Simulation model portability (SMP) is maintained by European Space Agency and many models compatible with SMP/simulation model interface (SMI) are available. Korea Aerospace Research Institute (KARI) is developing hardware abstraction layer (HAL) supported satellite simulator to verify on-board software of satellite. From above reasons, KARI wants to port these SMI compatible models to the HAL supported satellite simulator. To port these SMI compatible models to the HAL supported satellite simulator, simulation scheduler is preliminary designed according to the SMI standard.

Three-dimensional plant architecture and sunlit-shaded patterns: a stochastic model of light dynamics in canopies.

PubMed

Retkute, Renata; Townsend, Alexandra J; Murchie, Erik H; Jensen, Oliver E; Preston, Simon P

2018-05-25

Diurnal changes in solar position and intensity combined with the structural complexity of plant architecture result in highly variable and dynamic light patterns within the plant canopy. This affects productivity through the complex ways that photosynthesis responds to changes in light intensity. Current methods to characterize light dynamics, such as ray-tracing, are able to produce data with excellent spatio-temporal resolution but are computationally intensive and the resulting data are complex and high-dimensional. This necessitates development of more economical models for summarizing the data and for simulating realistic light patterns over the course of a day. High-resolution reconstructions of field-grown plants are assembled in various configurations to form canopies, and a forward ray-tracing algorithm is applied to the canopies to compute light dynamics at high (1 min) temporal resolution. From the ray-tracer output, the sunlit or shaded state for each patch on the plants is determined, and these data are used to develop a novel stochastic model for the sunlit-shaded patterns. The model is designed to be straightforward to fit to data using maximum likelihood estimation, and fast to simulate from. For a wide range of contrasting 3-D canopies, the stochastic model is able to summarize, and replicate in simulations, key features of the light dynamics. When light patterns simulated from the stochastic model are used as input to a model of photoinhibition, the predicted reduction in carbon gain is similar to that from calculations based on the (extremely costly) ray-tracer data. The model provides a way to summarize highly complex data in a small number of parameters, and a cost-effective way to simulate realistic light patterns. Simulations from the model will be particularly useful for feeding into larger-scale photosynthesis models for calculating how light dynamics affects the photosynthetic productivity of canopies.

Evaluation of Clipping Based Iterative PAPR Reduction Techniques for FBMC Systems

PubMed Central

Kollár, Zsolt

2014-01-01

This paper investigates filter bankmulticarrier (FBMC), a multicarrier modulation technique exhibiting an extremely low adjacent channel leakage ratio (ACLR) compared to conventional orthogonal frequency division multiplexing (OFDM) technique. The low ACLR of the transmitted FBMC signal makes it especially favorable in cognitive radio applications, where strict requirements are posed on out-of-band radiation. Large dynamic range resulting in high peak-to-average power ratio (PAPR) is characteristic of all sorts of multicarrier signals. The advantageous spectral properties of the high-PAPR FBMC signal are significantly degraded if nonlinearities are present in the transceiver chain. Spectral regrowth may appear, causing harmful interference in the neighboring frequency bands. This paper presents novel clipping based PAPR reduction techniques, evaluated and compared by simulations and measurements, with an emphasis on spectral aspects. The paper gives an overall comparison of PAPR reduction techniques, focusing on the reduction of the dynamic range of FBMC signals without increasing out-of-band radiation. An overview is presented on transmitter oriented techniques employing baseband clipping, which can maintain the system performance with a desired bit error rate (BER). PMID:24558338

Bayesian model reduction and empirical Bayes for group (DCM) studies.

PubMed

Friston, Karl J; Litvak, Vladimir; Oswal, Ashwini; Razi, Adeel; Stephan, Klaas E; van Wijk, Bernadette C M; Ziegler, Gabriel; Zeidman, Peter

2016-03-01

This technical note describes some Bayesian procedures for the analysis of group studies that use nonlinear models at the first (within-subject) level - e.g., dynamic causal models - and linear models at subsequent (between-subject) levels. Its focus is on using Bayesian model reduction to finesse the inversion of multiple models of a single dataset or a single (hierarchical or empirical Bayes) model of multiple datasets. These applications of Bayesian model reduction allow one to consider parametric random effects and make inferences about group effects very efficiently (in a few seconds). We provide the relatively straightforward theoretical background to these procedures and illustrate their application using a worked example. This example uses a simulated mismatch negativity study of schizophrenia. We illustrate the robustness of Bayesian model reduction to violations of the (commonly used) Laplace assumption in dynamic causal modelling and show how its recursive application can facilitate both classical and Bayesian inference about group differences. Finally, we consider the application of these empirical Bayesian procedures to classification and prediction. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Modeling nitrous oxide production and reduction in soil through explicit representation of denitrification enzyme kinetics.

PubMed

Zheng, Jianqiu; Doskey, Paul V

2015-02-17

An enzyme-explicit denitrification model with representations for pre- and de novo synthesized enzymes was developed to improve predictions of nitrous oxide (N2O) accumulations in soil and emissions from the surface. The metabolic model of denitrification is based on dual-substrate utilization and Monod growth kinetics. Enzyme synthesis/activation was incorporated into each sequential reduction step of denitrification to regulate dynamics of the denitrifier population and the active enzyme pool, which controlled the rate function. Parameterizations were developed from observations of the dynamics of N2O production and reduction in soil incubation experiments. The model successfully reproduced the dynamics of N2O and N2 accumulation in the incubations and revealed an important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Pre-synthesized denitrification enzymes contributed 20, 13, 43, and 62% of N2O that accumulated in 48 h incubations of soil collected from depths of 0-5, 5-10, 10-15, and 15-25 cm, respectively. An enzyme activity function (E) was defined to estimate the relative concentration of active enzymes and variation in response to environmental conditions. The value of E allows for activities of pre-synthesized denitrification enzymes to be differentiated from de novo synthesized enzymes. Incorporating explicit representations of denitrification enzyme kinetics into biogeochemical models is a promising approach for accurately simulating dynamics of the production and reduction of N2O in soils.

The simulation of temperature distribution and relative humidity with liquid concentration of 50% using computational fluid dynamics

NASA Astrophysics Data System (ADS)

Yohana, Eflita; Yulianto, Mohamad Endy; Kwang-Hwang, Choi; Putro, Bondantio; Yohanes Aditya W., A.

2015-12-01

The study of humidity distribution simulation inside a room has been widely conducted by using computational fluid dynamics (CFD). Here, the simulation was done by employing inputs in the experiment of air humidity reduction in a sample house. Liquid dessicant CaCl2was used in this study to absorb humidity in the air, so that the enormity of humidity reduction occured during the experiment could be obtained.The experiment was conducted in the morning at 8 with liquid desiccant concentration of 50%, nozzle dimension of 0.2 mms attached in dehumidifier, and the debit of air which entered the sample house was 2.35 m3/min. Both in inlet and outlet sides of the room, a DHT 11 censor was installed and used to note changes in humidity and temperature during the experiment. In normal condition without turning on the dehumidifier, the censor noted that the average temperature inside the room was 28°C and RH of 65%.The experiment result showed that the relative humidity inside a sample house was decreasing up to 52% in inlet position. Further, through the results obtained from CFD simulation, the temperature distribution and relative humidity inside the sample house could be seen. It showed that the concentration of liquid desiccant of 50% experienced a decrease while the relative humidity distribution was considerably good since the average RH was 55% followed by the increase in air temperature of 29.2° C inside the sample house.

New Cogging Torque Reduction Methods for Permanent Magnet Machine

NASA Astrophysics Data System (ADS)

Bahrim, F. S.; Sulaiman, E.; Kumar, R.; Jusoh, L. I.

2017-08-01

Permanent magnet type motors (PMs) especially permanent magnet synchronous motor (PMSM) are expanding its limbs in industrial application system and widely used in various applications. The key features of this machine include high power and torque density, extending speed range, high efficiency, better dynamic performance and good flux-weakening capability. Nevertheless, high in cogging torque, which may cause noise and vibration, is one of the threat of the machine performance. Therefore, with the aid of 3-D finite element analysis (FEA) and simulation using JMAG Designer, this paper proposed new method for cogging torque reduction. Based on the simulation, methods of combining the skewing with radial pole pairing method and skewing with axial pole pairing method reduces the cogging torque effect up to 71.86% and 65.69% simultaneously.

Multiphase flows of N immiscible incompressible fluids: A reduction-consistent and thermodynamically-consistent formulation and associated algorithm

NASA Astrophysics Data System (ADS)

Dong, S.

2018-05-01

We present a reduction-consistent and thermodynamically consistent formulation and an associated numerical algorithm for simulating the dynamics of an isothermal mixture consisting of N (N ⩾ 2) immiscible incompressible fluids with different physical properties (densities, viscosities, and pair-wise surface tensions). By reduction consistency we refer to the property that if only a set of M (1 ⩽ M ⩽ N - 1) fluids are present in the system then the N-phase governing equations and boundary conditions will exactly reduce to those for the corresponding M-phase system. By thermodynamic consistency we refer to the property that the formulation honors the thermodynamic principles. Our N-phase formulation is developed based on a more general method that allows for the systematic construction of reduction-consistent formulations, and the method suggests the existence of many possible forms of reduction-consistent and thermodynamically consistent N-phase formulations. Extensive numerical experiments have been presented for flow problems involving multiple fluid components and large density ratios and large viscosity ratios, and the simulation results are compared with the physical theories or the available physical solutions. The comparisons demonstrate that our method produces physically accurate results for this class of problems.

Application of computational fluid mechanics to atmospheric pollution problems

NASA Technical Reports Server (NTRS)

Hung, R. J.; Liaw, G. S.; Smith, R. E.

1986-01-01

One of the most noticeable effects of air pollution on the properties of the atmosphere is the reduction in visibility. This paper reports the results of investigations of the fluid dynamical and microphysical processes involved in the formation of advection fog on aerosols from combustion-related pollutants, as condensation nuclei. The effects of a polydisperse aerosol distribution, on the condensation/nucleation processes which cause the reduction in visibility are studied. This study demonstrates how computational fluid mechanics and heat transfer modeling can be applied to simulate the life cycle of the atmosphereic pollution problems.

Computational study: Reduction of iron corrosion in lead coolant of fast nuclear reactor

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

Arkundato, Artoto; Su'ud, Zaki; Abdullah, Mikrajuddin

2012-06-20

In this paper we report molecular dynamics simulation results of iron (cladding) corrosion in interaction with lead coolant of fast nuclear reactor. The goal of this work is to study effect of oxygen injection to the coolant to reduce iron corrosion. By evaluating diffusion coefficients, radial distribution functions, mean-square displacement curves and observation of crystal structure of iron before and after oxygen injection, we concluded that a significant reduction of corrosion can be achieved by issuing about 2% of oxygen atoms into lead coolant.

Elasto-Inertial Turbulence: From Subcritical Turbulence to Maximum Drag Reduction

NASA Astrophysics Data System (ADS)

Dubief, Yves; Sid, Samir; Egan, Raphael; Terrapon, Vincent

2015-11-01

Elasto Inertial Turbulence (EIT) is a turbulence state found so far in polymer solutions. Upon the appropriate initial perturbation, an autonomous regeneration cycle emerges between polymer dynamics, pressure and velocity fluctuations. This cycle is best explained by the Poisson equation derived from viscoelastic flow models such as FENE-P (used in this study). This presentation provides an overview of the structure of EIT in 2D channel flows for Reynolds numbers ranging from Reτ = 10 to 100 and for 3D simulations up to Ret au = 300 . For flows below the Newtonian critical Reynolds number, EIT increases the drag. For higher Reynolds numbers, EIT is surmised to be the energetic bound of Maximum Drag Reduction (MDR), the asymptotic state of drag reduction in polymer solutions. The very existence of EIT at low Reynolds numbers (Reτ < 60) highlights a backward energy transfer from the small scale polymer dynamics to larger flow scales. Similar dynamics is identified at higher Reynolds numbers, which could explain why polymer flows never become fully laminar. The authors acknowledge computational resources from CÉCI (F.R.S.-FNRS grant No.2.5020.11), the PRACE infrastructure, and the Vermont Advanced Computing Core.

Evaluation of new alternatives in wastewater treatment plants based on dynamic modelling and life cycle assessment (DM-LCA).

PubMed

Bisinella de Faria, A B; Spérandio, M; Ahmadi, A; Tiruta-Barna, L

2015-11-01

With a view to quantifying the energy and environmental advantages of Urine Source-Separation (USS) combined with different treatment processes, five wastewater treatment plant (WWTP) scenarios were compared to a reference scenario using Dynamic Modelling (DM) and Life Cycle Assessment (LCA), and an integrated DM-LCA framework was thus developed. Dynamic simulations were carried out in BioWin(®) in order to obtain a realistic evaluation of the dynamic behaviour and performance of plants under perturbation. LCA calculations were performed within Umberto(®) using the Ecoinvent database. A Python™ interface was used to integrate and convert simulation data and to introduce them into Umberto(®) to achieve a complete LCA evaluation comprising foreground and background processes. Comparisons between steady-state and dynamic simulations revealed the importance of considering dynamic aspects such as nutrient and flow peaks. The results of the evaluation highlighted the potential of the USS scenario for nutrient recovery whereas the Enhanced Primary Clarification (EPC) scenario gave increased biogas production and also notably decreased aeration consumption, leading to a positive energy balance. Both USS and EPC scenarios also showed increased stability of plant operation, with smaller daily averages of total nitrogen and phosphorus. In this context, USS and EPC results demonstrated that the coupled USS + EPC scenario and its combinations with agricultural spreading of N-rich effluent and nitritation/anaerobic deammonification could present an energy-positive balance with respectively 27% and 33% lower energy requirements and an increase in biogas production of 23%, compared to the reference scenario. The coupled scenarios also presented lesser environmental impacts (reduction of 31% and 39% in total endpoint impacts) along with effluent quality well within the specified limits. The marked environmental performance (reduction of global warming) when nitrogen is used in agriculture shows the importance of future research on sustainable solutions for nitrogen recovery. The contribution analysis of midpoint impacts also showed hotspots that it will be important to optimize further, such as plant infrastructure and direct N2O emissions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Thermal conductivity of tungsten: Effects of plasma-related structural defects from molecular-dynamics simulations

NASA Astrophysics Data System (ADS)

Hu, Lin; Wirth, Brian D.; Maroudas, Dimitrios

2017-08-01

We report results on the lattice thermal conductivities of tungsten single crystals containing nanoscale-sized pores or voids and helium (He) nanobubbles as a function of void/bubble size and gas pressure in the He bubbles based on molecular-dynamics simulations. For reference, we calculated lattice thermal conductivities of perfect tungsten single crystals along different crystallographic directions at room temperature and found them to be about 10% of the overall thermal conductivity of tungsten with a weak dependence on the heat flux direction. The presence of nanoscale voids in the crystal causes a significant reduction in its lattice thermal conductivity, which decreases with increasing void size. Filling the voids with He to form He nanobubbles and increasing the bubble pressure leads to further significant reduction of the tungsten lattice thermal conductivity, down to ˜20% of that of the perfect crystal. The anisotropy in heat conduction remains weak for tungsten single crystals containing nanoscale-sized voids and He nanobubbles throughout the pressure range examined. Analysis of the pressure and atomic displacement fields in the crystalline region that surrounds the He nanobubbles reveals that the significant reduction of tungsten lattice thermal conductivity in this region is due to phonon scattering from the nanobubbles, as well as lattice deformation around the nanobubbles and formation of lattice imperfections at higher bubble pressure.

Dynamic adaptive chemistry for turbulent flame simulations

NASA Astrophysics Data System (ADS)

Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

2013-02-01

The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.

Mountain bicycle frame testing as an example of practical implementation of hybrid simulation using RTFEM

NASA Astrophysics Data System (ADS)

Mucha, Waldemar; Kuś, Wacław

2018-01-01

The paper presents a practical implementation of hybrid simulation using Real Time Finite Element Method (RTFEM). Hybrid simulation is a technique for investigating dynamic material and structural properties of mechanical systems by performing numerical analysis and experiment at the same time. It applies to mechanical systems with elements too difficult or impossible to model numerically. These elements are tested experimentally, while the rest of the system is simulated numerically. Data between the experiment and numerical simulation are exchanged in real time. Authors use Finite Element Method to perform the numerical simulation. The following paper presents the general algorithm for hybrid simulation using RTFEM and possible improvements of the algorithm for computation time reduction developed by the authors. The paper focuses on practical implementation of presented methods, which involves testing of a mountain bicycle frame, where the shock absorber is tested experimentally while the rest of the frame is simulated numerically.

Network community-based model reduction for vortical flows

NASA Astrophysics Data System (ADS)

Gopalakrishnan Meena, Muralikrishnan; Nair, Aditya G.; Taira, Kunihiko

2018-06-01

A network community-based reduced-order model is developed to capture key interactions among coherent structures in high-dimensional unsteady vortical flows. The present approach is data-inspired and founded on network-theoretic techniques to identify important vortical communities that are comprised of vortical elements that share similar dynamical behavior. The overall interaction-based physics of the high-dimensional flow field is distilled into the vortical community centroids, considerably reducing the system dimension. Taking advantage of these vortical interactions, the proposed methodology is applied to formulate reduced-order models for the inter-community dynamics of vortical flows, and predict lift and drag forces on bodies in wake flows. We demonstrate the capabilities of these models by accurately capturing the macroscopic dynamics of a collection of discrete point vortices, and the complex unsteady aerodynamic forces on a circular cylinder and an airfoil with a Gurney flap. The present formulation is found to be robust against simulated experimental noise and turbulence due to its integrating nature of the system reduction.

Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations.

PubMed

Chillemi, Giovanni; D'Annessa, Ilda; Fiorani, Paola; Losasso, Carmen; Benedetti, Piero; Desideri, Alessandro

2008-10-01

The role of Thr729 in modulating the enzymatic function of human topoisomerase I has been characterized by molecular dynamics (MD) simulation. In detail, the structural-dynamical behaviour of the Thr729Lys and the Thr729Pro mutants have been characterized because of their in vivo and in vitro functional properties evidenced in the accompanying paper. Both mutants can bind to the DNA substrate and are enzymatically active, but while Thr729Lys is resistant even at high concentration of the camptothecin (CPT) anti-cancer drug, Thr729Pro shows only a mild reduction in drug sensitivity and in DNA binding. MD simulations show that the Thr729Lys mutation provokes a structural perturbation of the CPT-binding pocket. On the other hand, the Thr729Pro mutant maintains the wild-type structural scaffold, only increasing its rigidity. The simulations also show the complete abolishment, in the Thr729Lys mutant, of the protein communications between the C-terminal domain (where the active Tyr723 is located) and the linker domain, that plays an essential role in the control of the DNA rotation, thus explaining the distributive mode of action displayed by this mutant.

Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations

PubMed Central

Chillemi, Giovanni; D’Annessa, Ilda; Fiorani, Paola; Losasso, Carmen; Benedetti, Piero; Desideri, Alessandro

2008-01-01

The role of Thr729 in modulating the enzymatic function of human topoisomerase I has been characterized by molecular dynamics (MD) simulation. In detail, the structural–dynamical behaviour of the Thr729Lys and the Thr729Pro mutants have been characterized because of their in vivo and in vitro functional properties evidenced in the accompanying paper. Both mutants can bind to the DNA substrate and are enzymatically active, but while Thr729Lys is resistant even at high concentration of the camptothecin (CPT) anti-cancer drug, Thr729Pro shows only a mild reduction in drug sensitivity and in DNA binding. MD simulations show that the Thr729Lys mutation provokes a structural perturbation of the CPT-binding pocket. On the other hand, the Thr729Pro mutant maintains the wild-type structural scaffold, only increasing its rigidity. The simulations also show the complete abolishment, in the Thr729Lys mutant, of the protein communications between the C-terminal domain (where the active Tyr723 is located) and the linker domain, that plays an essential role in the control of the DNA rotation, thus explaining the distributive mode of action displayed by this mutant. PMID:18765473

Modeling of radiation damage recovery in particle detectors based on GaN

NASA Astrophysics Data System (ADS)

Gaubas, E.; Ceponis, T.; Pavlov, J.

2015-12-01

The pulsed characteristics of the capacitor-type and PIN diode type detectors based on GaN have been simulated using the dynamic and drift-diffusion models. The drift-diffusion current simulations have been implemented by employing the commercial software package Synopsys TCAD Sentaurus. The bipolar drift regime has been analyzed. The possible internal gain in charge collection through carrier multiplication processes determined by impact ionization has been considered in order to compensate carrier lifetime reduction due to radiation defects introduced into GaN material of detector.

An indigenous method for closed reduction of pediatric mandibular parasymphysis fracture.

PubMed

Kumar, Naresh; Singh, Akhilesh Kumar; Pandey, Arun; Verma, Vishal

2015-01-01

Mandibular fractures in children are very rare as compared to adults due to protected anatomic features of child and less exposure to road traffic accidents. Management becomes complicated due to inherent dynamic nature, instability of mixed dentition and fear of surgery. Conservative management can be done with the help of acrylic cap splints along with circum-mandibular wiring, intermaxillary fixation with eyelet wires, arch wires or open reduction and internal fixation with bio-resorbable plates. Different methods have various pros and cons. The choice of anesthesia is also very crucial sometimes. This case report describes a new method of closed reduction with 18 gauge needle simulated as an arch bar performed under local anaesthesia.

An indigenous method for closed reduction of pediatric mandibular parasymphysis fracture

PubMed Central

Kumar, Naresh; Singh, Akhilesh Kumar; Pandey, Arun; Verma, Vishal

2015-01-01

Mandibular fractures in children are very rare as compared to adults due to protected anatomic features of child and less exposure to road traffic accidents. Management becomes complicated due to inherent dynamic nature, instability of mixed dentition and fear of surgery. Conservative management can be done with the help of acrylic cap splints along with circum-mandibular wiring, intermaxillary fixation with eyelet wires, arch wires or open reduction and internal fixation with bio-resorbable plates. Different methods have various pros and cons. The choice of anesthesia is also very crucial sometimes. This case report describes a new method of closed reduction with 18 gauge needle simulated as an arch bar performed under local anaesthesia. PMID:27390498

Reconfigurable Control with Neural Network Augmentation for a Modified F-15 Aircraft

NASA Technical Reports Server (NTRS)

Burken, John J.

2007-01-01

This paper describes the performance of a simplified dynamic inversion controller with neural network supplementation. This 6 DOF (Degree-of-Freedom) simulation study focuses on the results with and without adaptation of neural networks using a simulation of the NASA modified F-15 which has canards. One area of interest is the performance of a simulated surface failure while attempting to minimize the inertial cross coupling effect of a [B] matrix failure (a control derivative anomaly associated with a jammed or missing control surface). Another area of interest and presented is simulated aerodynamic failures ([A] matrix) such as a canard failure. The controller uses explicit models to produce desired angular rate commands. The dynamic inversion calculates the necessary surface commands to achieve the desired rates. The simplified dynamic inversion uses approximate short period and roll axis dynamics. Initial results indicated that the transient response for a [B] matrix failure using a Neural Network (NN) improved the control behavior when compared to not using a neural network for a given failure, However, further evaluation of the controller was comparable, with objections io the cross coupling effects (after changes were made to the controller). This paper describes the methods employed to reduce the cross coupling effect and maintain adequate tracking errors. The IA] matrix failure results show that control of the aircraft without adaptation is more difficult [leas damped) than with active neural networks, Simulation results show Neural Network augmentation of the controller improves performance in terms of backing error and cross coupling reduction and improved performance with aerodynamic-type failures.

Breaking Computational Barriers: Real-time Analysis and Optimization with Large-scale Nonlinear Models via Model Reduction

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

Carlberg, Kevin Thomas; Drohmann, Martin; Tuminaro, Raymond S.

2014-10-01

Model reduction for dynamical systems is a promising approach for reducing the computational cost of large-scale physics-based simulations to enable high-fidelity models to be used in many- query (e.g., Bayesian inference) and near-real-time (e.g., fast-turnaround simulation) contexts. While model reduction works well for specialized problems such as linear time-invariant systems, it is much more difficult to obtain accurate, stable, and efficient reduced-order models (ROMs) for systems with general nonlinearities. This report describes several advances that enable nonlinear reduced-order models (ROMs) to be deployed in a variety of time-critical settings. First, we present an error bound for the Gauss-Newton with Approximatedmore » Tensors (GNAT) nonlinear model reduction technique. This bound allows the state-space error for the GNAT method to be quantified when applied with the backward Euler time-integration scheme. Second, we present a methodology for preserving classical Lagrangian structure in nonlinear model reduction. This technique guarantees that important properties--such as energy conservation and symplectic time-evolution maps--are preserved when performing model reduction for models described by a Lagrangian formalism (e.g., molecular dynamics, structural dynamics). Third, we present a novel technique for decreasing the temporal complexity --defined as the number of Newton-like iterations performed over the course of the simulation--by exploiting time-domain data. Fourth, we describe a novel method for refining projection-based reduced-order models a posteriori using a goal-oriented framework similar to mesh-adaptive h -refinement in finite elements. The technique allows the ROM to generate arbitrarily accurate solutions, thereby providing the ROM with a 'failsafe' mechanism in the event of insufficient training data. Finally, we present the reduced-order model error surrogate (ROMES) method for statistically quantifying reduced- order-model errors. This enables ROMs to be rigorously incorporated in uncertainty-quantification settings, as the error model can be treated as a source of epistemic uncertainty. This work was completed as part of a Truman Fellowship appointment. We note that much additional work was performed as part of the Fellowship. One salient project is the development of the Trilinos-based model-reduction software module Razor , which is currently bundled with the Albany PDE code and currently allows nonlinear reduced-order models to be constructed for any application supported in Albany. Other important projects include the following: 1. ROMES-equipped ROMs for Bayesian inference: K. Carlberg, M. Drohmann, F. Lu (Lawrence Berkeley National Laboratory), M. Morzfeld (Lawrence Berkeley National Laboratory). 2. ROM-enabled Krylov-subspace recycling: K. Carlberg, V. Forstall (University of Maryland), P. Tsuji, R. Tuminaro. 3. A pseudo balanced POD method using only dual snapshots: K. Carlberg, M. Sarovar. 4. An analysis of discrete v. continuous optimality in nonlinear model reduction: K. Carlberg, M. Barone, H. Antil (George Mason University). Journal articles for these projects are in progress at the time of this writing.« less

Order reduction, identification and localization studies of dynamical systems

NASA Astrophysics Data System (ADS)

Ma, Xianghong

In this thesis methods are developed for performing order reduction, system identification and induction of nonlinear localization in complex mechanical dynamic systems. General techniques are proposed for constructing low-order models of linear and nonlinear mechanical systems; in addition, novel mechanical designs are considered for inducing nonlinear localization phenomena for the purpose of enhancing their dynamical performance. The thesis is in three major parts. In the first part, the transient dynamics of an impulsively loaded multi-bay truss is numerically computed by employing the Direct Global Matrix (DGM) approach. The approach is applicable to large-scale flexible structures with periodicity. Karhunen-Loeve (K-L) decomposition is used to discretize the dynamics of the truss and to create the low-order models of the truss. The leading order K-L modes are recovered by an experiment, which shows the feasibility of K-L based order reduction technique. In the second part of the thesis, nonlinear localization in dynamical systems is studied through two applications. In the seismic base isolation study, it is shown that the dynamics are sensitive to the presence of nonlinear elements and that passive motion confinement can be induced under proper design. In the coupled rod system, numerical simulation of the transient dynamics shows that a nonlinear backlash spring can induce either nonlinear localization or delocalization in the form of beat phenomena. K-L decomposition and poincare maps are utilized to study the nonlinear effects. The study shows that nonlinear localization can be induced in complex structures through backlash. In the third and final part of the thesis, a new technique based on Green!s function method is proposed to identify the dynamics of practical bolted joints. By modeling the difference between the dynamics of the bolted structure and the corresponding unbolted one, one constructs a nonparametric model for the joint dynamics. Two applications are given with a bolted beam and a truss joint in order to show the applicability of the technique.

Quantitative EEG analysis using error reduction ratio-causality test; validation on simulated and real EEG data.

PubMed

Sarrigiannis, Ptolemaios G; Zhao, Yifan; Wei, Hua-Liang; Billings, Stephen A; Fotheringham, Jayne; Hadjivassiliou, Marios

2014-01-01

To introduce a new method of quantitative EEG analysis in the time domain, the error reduction ratio (ERR)-causality test. To compare performance against cross-correlation and coherence with phase measures. A simulation example was used as a gold standard to assess the performance of ERR-causality, against cross-correlation and coherence. The methods were then applied to real EEG data. Analysis of both simulated and real EEG data demonstrates that ERR-causality successfully detects dynamically evolving changes between two signals, with very high time resolution, dependent on the sampling rate of the data. Our method can properly detect both linear and non-linear effects, encountered during analysis of focal and generalised seizures. We introduce a new quantitative EEG method of analysis. It detects real time levels of synchronisation in the linear and non-linear domains. It computes directionality of information flow with corresponding time lags. This novel dynamic real time EEG signal analysis unveils hidden neural network interactions with a very high time resolution. These interactions cannot be adequately resolved by the traditional methods of coherence and cross-correlation, which provide limited results in the presence of non-linear effects and lack fidelity for changes appearing over small periods of time. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Capabilities of stochastic rainfall models as data providers for urban hydrology

NASA Astrophysics Data System (ADS)

Haberlandt, Uwe

2017-04-01

For planning of urban drainage systems using hydrological models, long, continuous precipitation series with high temporal resolution are needed. Since observed time series are often too short or not available everywhere, the use of synthetic precipitation is a common alternative. This contribution compares three precipitation models regarding their suitability to provide 5 minute continuous rainfall time series for a) sizing of drainage networks for urban flood protection and b) dimensioning of combined sewage systems for pollution reduction. The rainfall models are a parametric stochastic model (Haberlandt et al., 2008), a non-parametric probabilistic approach (Bárdossy, 1998) and a stochastic downscaling of dynamically simulated rainfall (Berg et al., 2013); all models are operated both as single site and multi-site generators. The models are applied with regionalised parameters assuming that there is no station at the target location. Rainfall and discharge characteristics are utilised for evaluation of the model performance. The simulation results are compared against results obtained from reference rainfall stations not used for parameter estimation. The rainfall simulations are carried out for the federal states of Baden-Württemberg and Lower Saxony in Germany and the discharge simulations for the drainage networks of the cities of Hamburg, Brunswick and Freiburg. Altogether, the results show comparable simulation performance for the three models, good capabilities for single site simulations but low skills for multi-site simulations. Remarkably, there is no significant difference in simulation performance comparing the tasks flood protection with pollution reduction, so the models are finally able to simulate both the extremes and the long term characteristics of rainfall equally well. Bárdossy, A., 1998. Generating precipitation time series using simulated annealing. Wat. Resour. Res., 34(7): 1737-1744. Berg, P., Wagner, S., Kunstmann, H., Schädler, G., 2013. High resolution regional climate model simulations for Germany: part I — validation. Climate Dynamics, 40(1): 401-414. Haberlandt, U., Ebner von Eschenbach, A.-D., Buchwald, I., 2008. A space-time hybrid hourly rainfall model for derived flood frequency analysis. Hydrol. Earth Syst. Sci., 12: 1353-1367.

A mathematical and experimental simulation of the hematological response to weightlessness

NASA Technical Reports Server (NTRS)

Kimzey, S. L.; Leonard, J. I.; Johnson, P. C.

1979-01-01

A mathematical model of erythropoiesis control was used to simulate the effects of bedrest and zero-g on the circulating red cell mass. The model incorporates the best current understanding of the dynamics of red cell production and destruction and the associated feedback regulation. Specifically studied were the hemodynamic responses of a 28-day bedrest study devised to simulate Skylab experience. The results support the hypothesis that red cell loss during supine bedrest is a normal physiological feedback process in response to hemoconcentration enhanced tissue oxygenation and suppression of red cell production. Model simulation suggested the possibilities that this period was marked by some combination of increased oxygen-hemoglobin affinity, small reduction in mean red cell life span, ineffective erythropoiesis, or abnormal reticulocytosis.

Comparison of blood flow models and acquisitions for quantitative myocardial perfusion estimation from dynamic CT

NASA Astrophysics Data System (ADS)

Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R.; La Riviere, Patrick J.; Alessio, Adam M.

2014-04-01

Myocardial blood flow (MBF) can be estimated from dynamic contrast enhanced (DCE) cardiac CT acquisitions, leading to quantitative assessment of regional perfusion. The need for low radiation dose and the lack of consensus on MBF estimation methods motivates this study to refine the selection of acquisition protocols and models for CT-derived MBF. DCE cardiac CT acquisitions were simulated for a range of flow states (MBF = 0.5, 1, 2, 3 ml (min g)-1, cardiac output = 3, 5, 8 L min-1). Patient kinetics were generated by a mathematical model of iodine exchange incorporating numerous physiological features including heterogenenous microvascular flow, permeability and capillary contrast gradients. CT acquisitions were simulated for multiple realizations of realistic x-ray flux levels. CT acquisitions that reduce radiation exposure were implemented by varying both temporal sampling (1, 2, and 3 s sampling intervals) and tube currents (140, 70, and 25 mAs). For all acquisitions, we compared three quantitative MBF estimation methods (two-compartment model, an axially-distributed model, and the adiabatic approximation to the tissue homogeneous model) and a qualitative slope-based method. In total, over 11 000 time attenuation curves were used to evaluate MBF estimation in multiple patient and imaging scenarios. After iodine-based beam hardening correction, the slope method consistently underestimated flow by on average 47.5% and the quantitative models provided estimates with less than 6.5% average bias and increasing variance with increasing dose reductions. The three quantitative models performed equally well, offering estimates with essentially identical root mean squared error (RMSE) for matched acquisitions. MBF estimates using the qualitative slope method were inferior in terms of bias and RMSE compared to the quantitative methods. MBF estimate error was equal at matched dose reductions for all quantitative methods and range of techniques evaluated. This suggests that there is no particular advantage between quantitative estimation methods nor to performing dose reduction via tube current reduction compared to temporal sampling reduction. These data are important for optimizing implementation of cardiac dynamic CT in clinical practice and in prospective CT MBF trials.

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

PubMed

Riniker, Sereina

2018-03-26

In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

Development of Models for High Precision Simulation of the Space Mission Microscope

NASA Astrophysics Data System (ADS)

Bremer, Stefanie; List, Meike; Selig, Hanns; Lämmerzahl, Claus

MICROSCOPE is a French space mission for testing the Weak Equivalence Principle (WEP). The mission goal is the determination of the Eötvös parameter with an accuracy of 10-15. This will be achieved by means of two high-precision capacitive differential accelerometers, that are built by the French institute ONERA. At the German institute ZARM drop tower tests are carried out to verify the payload performance. Additionally, the mission data evaluation is prepared in close cooperation with the French partners CNES, ONERA and OCA. Therefore a comprehensive simulation of the real system including the science signal and all error sources is built for the development and testing of data reduction and data analysis algorithms to extract the WEP violation signal. Currently, the High Performance Satellite Dynamics Simulator (HPS), a cooperation project of ZARM and the DLR Institute of Space Systems, is adapted to the MICROSCOPE mission for the simulation of test mass and satellite dynamics. Models of environmental disturbances like solar radiation pressure are considered, too. Furthermore detailed modeling of the on-board capacitive sensors is done.

Carbon Corrosion in PEM Fuel Cells and the Development of Accelerated Stress Tests

DOE PAGES

Macauley, Natalia; Papadias, Dennis D.; Fairweather, Joseph; ...

2018-03-15

Here, carbon corrosion is an important degradation mechanism that can impair PEMFC performance through the destruction of catalyst connectivity, collapse of the electrode pore structure, loss of hydrophobic character, and an increase of the catalyst particle size. In this study, carbon corrosion was quantified in situ by measurement of carbon dioxide in the fuel cell exhaust gases through non-dispersive infrared spectroscopy during simulated drive cycle operations consisting of potential cycling with varying upper and lower potential limits. These studies were conducted for three different types of carbon supports. A reduction in the catalyst layer thickness was observed during a simulatedmore » drive cycle operation with a concomitant decrease in catalyst layer porosity, which led to performance losses due to increased mass transport limitations. The observed thickness reduction was primarily due to compaction of the catalyst layer, with the actual mass of carbon oxidation (loss) contributing only a small fraction (< 20%). The dynamics of carbon corrosion are presented along with a model that simulates the transient and dynamic corrosion rates observed in our experiments. Accelerated carbon corrosion stress tests are presented and their effects are compared to those observed for the drive cycle test.« less

Carbon Corrosion in PEM Fuel Cells and the Development of Accelerated Stress Tests

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

Macauley, Natalia; Papadias, Dennis D.; Fairweather, Joseph

Here, carbon corrosion is an important degradation mechanism that can impair PEMFC performance through the destruction of catalyst connectivity, collapse of the electrode pore structure, loss of hydrophobic character, and an increase of the catalyst particle size. In this study, carbon corrosion was quantified in situ by measurement of carbon dioxide in the fuel cell exhaust gases through non-dispersive infrared spectroscopy during simulated drive cycle operations consisting of potential cycling with varying upper and lower potential limits. These studies were conducted for three different types of carbon supports. A reduction in the catalyst layer thickness was observed during a simulatedmore » drive cycle operation with a concomitant decrease in catalyst layer porosity, which led to performance losses due to increased mass transport limitations. The observed thickness reduction was primarily due to compaction of the catalyst layer, with the actual mass of carbon oxidation (loss) contributing only a small fraction (< 20%). The dynamics of carbon corrosion are presented along with a model that simulates the transient and dynamic corrosion rates observed in our experiments. Accelerated carbon corrosion stress tests are presented and their effects are compared to those observed for the drive cycle test.« less

Dynamic model for preventing mental retardation in the population: the importance of poverty and deprivation.

PubMed

McDermott, S W; Altekruse, J M

1994-01-01

A dynamic simulation model is used to answer the question, "What is the most effective child health policy initiative for the prevention of mental retardation (MR)?" The impact of medical strategies is contrasted with social interventions to see how they affect the prevalence of MR in the general population. The model is based on data from four U.S. Census and California Vital Statistics reports (1960, 1970, 1980, 1990). An interstate comparison (California and South Carolina) uses 1990 data. The results of the simulations reveal that medical interventions to improve the developmental outcome of low birth weight (LBW) infants did not cause a reduction in the rate of MR in the population after a 24-year trial period. In contrast, reducing the proportion of children living in poverty who are exposed to environmental deprivation significantly decreased (10%) MR at the end of the model's time period. This analysis supports the view that long-term reduction in MR prevalence is attainable by modifying public policies that influence children's development. Effective MR prevention calls for public policy committed to multifaceted health and educational services for both affected parents and their young children.

Defect-Engineered Heat Transport in Graphene: A Route to High Efficient Thermal Rectification

PubMed Central

Zhao, Weiwei; Wang, Yanlei; Wu, Zhangting; Wang, Wenhui; Bi, Kedong; Liang, Zheng; Yang, Juekuan; Chen, Yunfei; Xu, Zhiping; Ni, Zhenhua

2015-01-01

Low-dimensional materials such as graphene provide an ideal platform to probe the correlation between thermal transport and lattice defects, which could be engineered at the molecular level. In this work, we perform molecular dynamics simulations and non-contact optothermal Raman measurements to study this correlation. We find that oxygen plasma treatment could reduce the thermal conductivity of graphene significantly even at extremely low defect concentration (∼83% reduction for ∼0.1% defects), which could be attributed mainly to the creation of carbonyl pair defects. Other types of defects such as hydroxyl, epoxy groups and nano-holes demonstrate much weaker effects on the reduction where the sp2 nature of graphene is better preserved. With the capability of selectively functionalizing graphene, we propose an asymmetric junction between graphene and defective graphene with a high thermal rectification ratio of ∼46%, as demonstrated by our molecular dynamics simulation results. Our findings provide fundamental insights into the physics of thermal transport in defective graphene, and two-dimensional materials in general, which could help on the future design of functional applications such as optothermal and electrothermal devices. PMID:26132747

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

NASA Astrophysics Data System (ADS)

Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Róg, Tomasz

2016-09-01

The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone - a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

Impacts of licensed premises trading hour policies on alcohol-related harms.

PubMed

Atkinson, Jo-An; Prodan, Ante; Livingston, Michael; Knowles, Dylan; O'Donnell, Eloise; Room, Robin; Indig, Devon; Page, Andrew; McDonnell, Geoff; Wiggers, John

2018-07-01

Evaluations of alcohol policy changes demonstrate that restriction of trading hours of both 'on'- and 'off'-licence venues can be an effective means of reducing rates of alcohol-related harm. Despite this, the effects of different trading hour policy options over time, accounting for different contexts and demographic characteristics, and the common co-occurrence of other harm reduction strategies in trading hour policy initiatives, are difficult to estimate. The aim of this study was to use dynamic simulation modelling to compare estimated impacts over time of a range of trading hour policy options on various indicators of acute alcohol-related harm. An agent-based model of alcohol consumption in New South Wales, Australia was developed using existing research evidence, analysis of available data and a structured approach to incorporating expert opinion. Five policy scenarios were simulated, including restrictions to trading hours of on-licence venues and extensions to trading hours of bottle shops. The impact of the scenarios on four measures of alcohol-related harm were considered: total acute harms, alcohol-related violence, emergency department (ED) presentations and hospitalizations. Simulation of a 3 a.m. (rather than 5 a.m.) closing time resulted in an estimated 12.3 ± 2.4% reduction in total acute alcohol-related harms, a 7.9 ± 0.8% reduction in violence, an 11.9 ± 2.1% reduction in ED presentations and a 9.5 ± 1.8% reduction in hospitalizations. Further reductions were achieved simulating a 1 a.m. closing time, including a 17.5 ± 1.1% reduction in alcohol-related violence. Simulated extensions to bottle shop trading hours resulted in increases in rates of all four measures of harm, although most of the effects came from increasing operating hours from 10 p.m. to 11 p.m. An agent-based simulation model suggests that restricting trading hours of licensed venues reduces rates of alcohol-related harm and extending trading hours of bottle shops increases rates of alcohol-related harm. The model can estimate the effects of a range of policy options. © 2018 The Authors. Addiction published by John Wiley & Sons Ltd on behalf of Society for the Study of Addiction.

Dispersal and fallout simulations for urban consequences management (u)

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

Grinstein, Fernando F; Wachtor, Adam J; Nelson, Matt

2010-01-01

Hazardous chemical, biological, or radioactive releases from leaks, spills, fires, or blasts, may occur (intentionally or accidentally) in urban environments during warfare or as part of terrorist attacks on military bases or other facilities. The associated contaminant dispersion is complex and semi-chaotic. Urban predictive simulation capabilities can have direct impact in many threat-reduction areas of interest, including, urban sensor placement and threat analysis, contaminant transport (CT) effects on surrounding civilian population (dosages, evacuation, shelter-in-place), education and training of rescue teams and services. Detailed simulations for the various processes involved are in principle possible, but generally not fast. Predicting urban airflowmore » accompanied by CT presents extremely challenging requirements. Crucial technical issues include, simulating turbulent fluid and particulate transport, initial and boundary condition modeling incorporating a consistent stratified urban boundary layer with realistic wind fluctuations, and post-processing of the simulation results for practical consequences management. Relevant fluid dynamic processes to be simulated include, detailed energetic and contaminant sources, complex building vortex shedding and flows in recirculation zones, and modeling of particle distributions, including particulate fallout, as well as deposition, re-suspension and evaporation. Other issues include, modeling building damage effects due to eventual blasts, addressing appropriate regional and atmospheric data reduction.« less

Shock simulations of a single-site coarse-grain RDX model using the dissipative particle dynamics method with reactivity

NASA Astrophysics Data System (ADS)

Sellers, Michael S.; Lísal, Martin; Schweigert, Igor; Larentzos, James P.; Brennan, John K.

2017-01-01

In discrete particle simulations, when an atomistic model is coarse-grained, a tradeoff is made: a boost in computational speed for a reduction in accuracy. The Dissipative Particle Dynamics (DPD) methods help to recover lost accuracy of the viscous and thermal properties, while giving back a relatively small amount of computational speed. Since its initial development for polymers, one of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. In 2007, Maillet, Soulard, and Stoltz introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We present an extended and generalized version of the DPD-RX method, and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Demonstration simulations of reacting RDX are performed under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its transition to hot product gases within DPD-RX is presented. Additionally, we discuss several examples of the effect of shock speed and microstructure on the corresponding material chemistry.

An NMR database for simulations of membrane dynamics.

PubMed

Leftin, Avigdor; Brown, Michael F

2011-03-01

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Aging analysis of high performance FinFET flip-flop under Dynamic NBTI simulation configuration

NASA Astrophysics Data System (ADS)

Zainudin, M. F.; Hussin, H.; Halim, A. K.; Karim, J.

2018-03-01

A mechanism known as Negative-bias Temperature Instability (NBTI) degrades a main electrical parameters of a circuit especially in terms of performance. So far, the circuit design available at present are only focussed on high performance circuit without considering the circuit reliability and robustness. In this paper, the main circuit performances of high performance FinFET flip-flop such as delay time, and power were studied with the presence of the NBTI degradation. The aging analysis was verified using a 16nm High Performance Predictive Technology Model (PTM) based on different commands available at Synopsys HSPICE. The results shown that the circuit under the longer dynamic NBTI simulation produces the highest impact in the increasing of gate delay and decrease in the average power reduction from a fresh simulation until the aged stress time under a nominal condition. In addition, the circuit performance under a varied stress condition such as temperature and negative stress gate bias were also studied.

Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation.

PubMed

Fu, Yankai; Yan, Tingxuan; Xu, Xia

2017-09-28

Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.

Inconsistencies in Numerical Simulations of Dynamical Systems Using Interval Arithmetic

NASA Astrophysics Data System (ADS)

Nepomuceno, Erivelton G.; Peixoto, Márcia L. C.; Martins, Samir A. M.; Rodrigues, Heitor M.; Perc, Matjaž

Over the past few decades, interval arithmetic has been attracting widespread interest from the scientific community. With the expansion of computing power, scientific computing is encountering a noteworthy shift from floating-point arithmetic toward increased use of interval arithmetic. Notwithstanding the significant reliability of interval arithmetic, this paper presents a theoretical inconsistency in a simulation of dynamical systems using a well-known implementation of arithmetic interval. We have observed that two natural interval extensions present an empty intersection during a finite time range, which is contrary to the fundamental theorem of interval analysis. We have proposed a procedure to at least partially overcome this problem, based on the union of the two generated pseudo-orbits. This paper also shows a successful case of interval arithmetic application in the reduction of interval width size on the simulation of discrete map. The implications of our findings on the reliability of scientific computing using interval arithmetic have been properly addressed using two numerical examples.

Generalized Predictive Control of Dynamic Systems with Rigid-Body Modes

NASA Technical Reports Server (NTRS)

Kvaternik, Raymond G.

2013-01-01

Numerical simulations to assess the effectiveness of Generalized Predictive Control (GPC) for active control of dynamic systems having rigid-body modes are presented. GPC is a linear, time-invariant, multi-input/multi-output predictive control method that uses an ARX model to characterize the system and to design the controller. Although the method can accommodate both embedded (implicit) and explicit feedforward paths for incorporation of disturbance effects, only the case of embedded feedforward in which the disturbances are assumed to be unknown is considered here. Results from numerical simulations using mathematical models of both a free-free three-degree-of-freedom mass-spring-dashpot system and the XV-15 tiltrotor research aircraft are presented. In regulation mode operation, which calls for zero system response in the presence of disturbances, the simulations showed reductions of nearly 100%. In tracking mode operations, where the system is commanded to follow a specified path, the GPC controllers produced the desired responses, even in the presence of disturbances.

Active Control of Solar Array Dynamics During Spacecraft Maneuvers

NASA Technical Reports Server (NTRS)

Ross, Brant A.; Woo, Nelson; Kraft, Thomas G.; Blandino, Joseph R.

2016-01-01

Recent NASA mission plans require spacecraft to undergo potentially significant maneuvers (or dynamic loading events) with large solar arrays deployed. Therefore there is an increased need to understand and possibly control the nonlinear dynamics in the spacecraft system during such maneuvers. The development of a nonlinear controller is described. The utility of using a nonlinear controller to reduce forces and motion in a solar array wing during a loading event is demonstrated. The result is dramatic reductions in system forces and motion during a 10 second loading event. A motion curve derived from the simulation with the closed loop controller is used to obtain similar benefits with a simpler motion control approach.

About the structural role of disulfide bridges in serum albumins: evidence from protein simulated unfolding.

PubMed

Paris, Guillaume; Kraszewski, Sebastian; Ramseyer, Christophe; Enescu, Mironel

2012-11-01

The role of the 17 disulfide (S-S) bridges in preserving the native conformation of human serum albumin (HSA) is investigated by performing classical molecular dynamics (MD) simulations on protein structures with intact and, respectively, reduced S-S bridges. The thermal unfolding simulations predict a clear destabilization of the protein secondary structure upon reduction of the S-S bridges as well as a significant distortion of the tertiary structure that is revealed by the changes in the protein native contacts fraction. The effect of the S-S bridges reduction on the protein compactness was tested by calculating Gibbs free energy profiles with respect to the protein gyration radius. The theoretical results obtained using the OPLS-AA and the AMBER ff03 force fields are in agreement with the available experimental data. Beyond the validation of the simulation method, the results here reported provide new insights into the mechanism of the protein reductive/oxidative unfolding/folding processes. It is predicted that in the native conformation of the protein, the thiol (-SH) groups belonging to the same reduced S-S bridge are located in potential wells that maintain them in contact. The -SH pairs can be dispatched by specific conformational transitions of the peptide chain located in the neighborhood of the cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding unfolding equilibria

NASA Astrophysics Data System (ADS)

Denschlag, Robert; Lingenheil, Martin; Tavan, Paul

2008-06-01

Replica exchange (RE) molecular dynamics (MD) simulations are frequently applied to sample the folding-unfolding equilibria of β-hairpin peptides in solution, because efficiency gains are expected from this technique. Using a three-state Markov model featuring key aspects of β-hairpin folding we show that RE simulations can be less efficient than conventional techniques. Furthermore we demonstrate that one is easily seduced to erroneously assign convergence to the RE sampling, because RE ensembles can rapidly reach long-lived stationary states. We conclude that typical REMD simulations covering a few tens of nanoseconds are by far too short for sufficient sampling of β-hairpin folding-unfolding equilibria.

Dynamic PET image reconstruction integrating temporal regularization associated with respiratory motion correction for applications in oncology

NASA Astrophysics Data System (ADS)

Merlin, Thibaut; Visvikis, Dimitris; Fernandez, Philippe; Lamare, Frédéric

2018-02-01

Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks, by combining a respiratory motion correction approach with temporal regularization in a unique reconstruction algorithm for dynamic PET imaging. Elastic transformation parameters for the motion correction are estimated from the non-attenuation-corrected PET images. The derived displacement matrices are subsequently used in a list-mode based OSEM reconstruction algorithm integrating a temporal regularization between the 3D dynamic PET frames, based on temporal basis functions. These functions are simultaneously estimated at each iteration, along with their relative coefficients for each image voxel. Quantitative evaluation has been performed using dynamic FDG PET/CT acquisitions of lung cancer patients acquired on a GE DRX system. The performance of the proposed method is compared with that of a standard multi-frame OSEM reconstruction algorithm. The proposed method achieved substantial improvements in terms of noise reduction while accounting for loss of contrast due to respiratory motion. Results on simulated data showed that the proposed 4D algorithms led to bias reduction values up to 40% in both tumor and blood regions for similar standard deviation levels, in comparison with a standard 3D reconstruction. Patlak parameter estimations on reconstructed images with the proposed reconstruction methods resulted in 30% and 40% bias reduction in the tumor and lung region respectively for the Patlak slope, and a 30% bias reduction for the intercept in the tumor region (a similar Patlak intercept was achieved in the lung area). Incorporation of the respiratory motion correction using an elastic model along with a temporal regularization in the reconstruction process of the PET dynamic series led to substantial quantitative improvements and motion artifact reduction. Future work will include the integration of a linear FDG kinetic model, in order to directly reconstruct parametric images.

Dynamic PET image reconstruction integrating temporal regularization associated with respiratory motion correction for applications in oncology.

PubMed

Merlin, Thibaut; Visvikis, Dimitris; Fernandez, Philippe; Lamare, Frédéric

2018-02-13

Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks, by combining a respiratory motion correction approach with temporal regularization in a unique reconstruction algorithm for dynamic PET imaging. Elastic transformation parameters for the motion correction are estimated from the non-attenuation-corrected PET images. The derived displacement matrices are subsequently used in a list-mode based OSEM reconstruction algorithm integrating a temporal regularization between the 3D dynamic PET frames, based on temporal basis functions. These functions are simultaneously estimated at each iteration, along with their relative coefficients for each image voxel. Quantitative evaluation has been performed using dynamic FDG PET/CT acquisitions of lung cancer patients acquired on a GE DRX system. The performance of the proposed method is compared with that of a standard multi-frame OSEM reconstruction algorithm. The proposed method achieved substantial improvements in terms of noise reduction while accounting for loss of contrast due to respiratory motion. Results on simulated data showed that the proposed 4D algorithms led to bias reduction values up to 40% in both tumor and blood regions for similar standard deviation levels, in comparison with a standard 3D reconstruction. Patlak parameter estimations on reconstructed images with the proposed reconstruction methods resulted in 30% and 40% bias reduction in the tumor and lung region respectively for the Patlak slope, and a 30% bias reduction for the intercept in the tumor region (a similar Patlak intercept was achieved in the lung area). Incorporation of the respiratory motion correction using an elastic model along with a temporal regularization in the reconstruction process of the PET dynamic series led to substantial quantitative improvements and motion artifact reduction. Future work will include the integration of a linear FDG kinetic model, in order to directly reconstruct parametric images.

The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions

PubMed Central

2012-01-01

Background It is well known that the deterministic dynamics of biochemical reaction networks can be more easily studied if timescale separation conditions are invoked (the quasi-steady-state assumption). In this case the deterministic dynamics of a large network of elementary reactions are well described by the dynamics of a smaller network of effective reactions. Each of the latter represents a group of elementary reactions in the large network and has associated with it an effective macroscopic rate law. A popular method to achieve model reduction in the presence of intrinsic noise consists of using the effective macroscopic rate laws to heuristically deduce effective probabilities for the effective reactions which then enables simulation via the stochastic simulation algorithm (SSA). The validity of this heuristic SSA method is a priori doubtful because the reaction probabilities for the SSA have only been rigorously derived from microscopic physics arguments for elementary reactions. Results We here obtain, by rigorous means and in closed-form, a reduced linear Langevin equation description of the stochastic dynamics of monostable biochemical networks in conditions characterized by small intrinsic noise and timescale separation. The slow-scale linear noise approximation (ssLNA), as the new method is called, is used to calculate the intrinsic noise statistics of enzyme and gene networks. The results agree very well with SSA simulations of the non-reduced network of elementary reactions. In contrast the conventional heuristic SSA is shown to overestimate the size of noise for Michaelis-Menten kinetics, considerably under-estimate the size of noise for Hill-type kinetics and in some cases even miss the prediction of noise-induced oscillations. Conclusions A new general method, the ssLNA, is derived and shown to correctly describe the statistics of intrinsic noise about the macroscopic concentrations under timescale separation conditions. The ssLNA provides a simple and accurate means of performing stochastic model reduction and hence it is expected to be of widespread utility in studying the dynamics of large noisy reaction networks, as is common in computational and systems biology. PMID:22583770

WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard; Lorenz, Ulf

2017-04-01

WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. The graphical capabilities allow visualization of quantum dynamics 'on the fly', including Wigner phase space representations. Being easy to use and highly versatile, WavePacket is well suited for the teaching of quantum mechanics as well as for research projects in atomic, molecular and optical physics or in physical or theoretical chemistry. The present Part I deals with the description of closed quantum systems in terms of Schrödinger equations. The emphasis is on discrete variable representations for spatial discretization as well as various techniques for temporal discretization. The upcoming Part II will focus on open quantum systems and dimension reduction; it also describes the codes for optimal control of quantum dynamics. The present work introduces the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge platform, where extensive Wiki-documentation as well as worked-out demonstration examples can be found.

Evolution of Flexible Multibody Dynamics for Simulation Applications Supporting Human Spaceflight

NASA Technical Reports Server (NTRS)

Huynh, An; Brain, Thomas A.; MacLean, John R.; Quiocho, Leslie J.

2016-01-01

During the course of transition from the Space Shuttle and International Space Station programs to the Orion and Journey to Mars exploration programs, a generic flexible multibody dynamics formulation and associated software implementation has evolved to meet an ever changing set of requirements at the NASA Johnson Space Center (JSC). Challenging problems related to large transitional topologies and robotic free-flyer vehicle capture/ release, contact dynamics, and exploration missions concept evaluation through simulation (e.g., asteroid surface operations) have driven this continued development. Coupled with this need is the requirement to oftentimes support human spaceflight operations in real-time. Moreover, it has been desirable to allow even more rapid prototyping of on-orbit manipulator and spacecraft systems, to support less complex infrastructure software for massively integrated simulations, to yield further computational efficiencies, and to take advantage of recent advances and availability of multi-core computing platforms. Since engineering analysis, procedures development, and crew familiarity/training for human spaceflight is fundamental to JSC's charter, there is also a strong desire to share and reuse models in both the non-realtime and real-time domains, with the goal of retaining as much multibody dynamics fidelity as possible. Three specific enhancements are reviewed here: (1) linked list organization to address large transitional topologies, (2) body level model order reduction, and (3) parallel formulation/implementation. This paper provides a detailed overview of these primary updates to JSC's flexible multibody dynamics algorithms as well as a comparison of numerical results to previous formulations and associated software.

The plastoquinol-plastoquinone exchange mechanism in photosystem II: insight from molecular dynamics simulations.

PubMed

Zobnina, Veranika; Lambreva, Maya D; Rea, Giuseppina; Campi, Gaetano; Antonacci, Amina; Scognamiglio, Viviana; Giardi, Maria Teresa; Polticelli, Fabio

2017-01-01

In the photosystem II (PSII) of oxygenic photosynthetic organisms, the reaction center (RC) core mediates the light-induced electron transfer leading to water splitting and production of reduced plastoquinone molecules. The reduction of plastoquinone to plastoquinol lowers PSII affinity for the latter and leads to its release. However, little is known about the role of protein dynamics in this process. Here, molecular dynamics simulations of the complete PSII complex embedded in a lipid bilayer have been used to investigate the plastoquinol release mechanism. A distinct dynamic behavior of PSII in the presence of plastoquinol is observed which, coupled to changes in charge distribution and electrostatic interactions, causes disruption of the interactions seen in the PSII-plastoquinone complex and leads to the "squeezing out" of plastoquinol from the binding pocket. Displacement of plastoquinol closes the second water channel, recently described in a 2.9 Å resolution PSII structure (Guskov et al. in Nat Struct Mol Biol 16:334-342, 2009), allowing to rule out the proposed "alternating" mechanism of plastoquinol-plastoquinone exchange, while giving support to the "single-channel" one. The performed simulations indicated a pivotal role of D 1 -Ser264 in modulating the dynamics of the plastoquinone binding pocket and plastoquinol-plastoquinone exchange via its interaction with D 1 -His252 residue. The effects of the disruption of this hydrogen bond network on the PSII redox reactions were experimentally assessed in the D 1 site-directed mutant Ser264Lys.

Assessment of regional downscaling simulations for long term mean, excess and deficit Indian Summer Monsoons

NASA Astrophysics Data System (ADS)

Varikoden, Hamza; Mujumdar, M.; Revadekar, J. V.; Sooraj, K. P.; Ramarao, M. V. S.; Sanjay, J.; Krishnan, R.

2018-03-01

This study undertakes a comprehensive assessment of dynamical downscaling of summer monsoon (June-September; JJAS) rainfall over heterogeneous regions namely the Western Ghats (WG), Central India (CI) and North-Eastern Region (NER) for long term mean, excess and deficit episodes for the historical period from 1951 to 2005. This downscaling assessment is based on six Coordinated Regional Climate Downscaling Experiments (CORDEX) for South Asia (SAS) region, their five driving Global Climate Models (GCM) simulations along with observations from India Meteorological Department (IMD) and Asian Precipitation Highly Resolved Observational Integrated Towards Evaluation for Water Resources (APHRODITE). The analysis reveals an overall reduction of dry bias in rainfall across the regions of Indian sub-continent in most of the downscaled CORDEX-SAS models and in their ensemble mean as compared to that of driving GCMs. The interannual variabilities during historical period are reasonably captured by the ensemble means of CORDEX-SAS simulations with an underestimation of 0.43%, 38% and 52% for the WG, CI and NER, respectively. Upon careful examination of the CORDEX-SAS models and their driving GCMs revealed considerable improvement in the regionally downscaled rainfall. The value addition of dynamical downscaling is apparent over the WG in Regional Climate Model (RCM) simulations with an improvement of more than 30% for the long term mean, excess and deficit episodes from their driving GCMs. In the case of NER, the improvement in the downscaled rainfall product is more than 10% for all the episodes. However, the value addition in the CORDEX-SAS simulations for CI region, dominantly influenced by synoptic scale processes, is not clear. Nevertheless, the reduction of dry bias in the complex topographical regions is remarkable. The relative performance of dynamical downscaling of rainfall over complex topography in response to local forcing and orographic lifting depict the value addition (30% over WG and 10% over NER, with a statistical significance of more than 5% level), when compared with the synoptic scale system induced rainfall over the plains of central-India.

CHROTRAN, 1.0

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

Hansen, Scott K.; Pandey, Sachin; Karra, Satish

2017-04-13

CHROTRAN is a fork of the widely-used PFLOTRAN flow and reactive transport numerical simulation code. It implements custom physics and chemistry appropriate to the design of in-situ reduction of heavy metals such as Cr(VI) in groundwater. CHROTRAN includes full dynamics for five species: the metal to be remediated, an electron donor, biofilm, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, and biofilm inactivation. The software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injectionmore » points, and features full coupling between flow and reactive transport, allowing for assessment of the effect of bio-fouling.« less

Perspectives in biological physics: the nDDB project for a neutron Dynamics Data Bank for biological macromolecules.

PubMed

Rusevich, Leonid; García Sakai, Victoria; Franzetti, Bruno; Johnson, Mark; Natali, Francesca; Pellegrini, Eric; Peters, Judith; Pieper, Jörg; Weik, Martin; Zaccai, Giuseppe

2013-07-01

Neutron spectroscopy provides experimental data on time-dependent trajectories, which can be directly compared to molecular dynamics simulations. Its importance in helping us to understand biological macromolecules at a molecular level is demonstrated by the results of a literature survey over the last two to three decades. Around 300 articles in refereed journals relate to neutron scattering studies of biological macromolecular dynamics, and the results of the survey are presented here. The scope of the publications ranges from the general physics of protein and solvent dynamics, to the biologically relevant dynamics-function relationships in live cells. As a result of the survey we are currently setting up a neutron Dynamics Data Bank (nDDB) with the aim to make the neutron data on biological systems widely available. This will benefit, in particular, the MD simulation community to validate and improve their force fields. The aim of the database is to expose and give easy access to a body of experimental data to the scientific community. The database will be populated with as much of the existing data as possible. In the future it will give value, as part of a bigger whole, to high throughput data, as well as more detailed studies. A range and volume of experimental data will be of interest in determining how quantitatively MD simulations can reproduce trends across a range of systems and to what extent such trends may depend on sample preparation and data reduction and analysis methods. In this context, we strongly encourage researchers in the field to deposit their data in the nDDB.

Departure of microscopic friction from macroscopic drag in molecular fluid dynamics

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

Hanasaki, Itsuo; Fujiwara, Daiki; Kawano, Satoyuki, E-mail: kawano@me.es.osaka-u.ac.jp

2016-03-07

Friction coefficient of the Langevin equation and drag of spherical macroscopic objects in steady flow at low Reynolds numbers are usually regarded as equivalent. We show that the microscopic friction can be different from the macroscopic drag when the mass is taken into account for particles with comparable scale to the surrounding fluid molecules. We illustrate it numerically by molecular dynamics simulation of chloride ion in water. Friction variation by the atomistic mass effect beyond the Langevin regime can be of use in the drag reduction technology as well as the electro or thermophoresis.

Brine rejection from freezing salt solutions: a molecular dynamics study.

PubMed

Vrbka, Lubos; Jungwirth, Pavel

2005-09-30

The atmospherically and technologically very important process of brine rejection from freezing salt solutions is investigated with atomic resolution using molecular dynamics simulations. The present calculations allow us to follow the motion of each water molecule and salt ion and to propose a microscopic mechanism of brine rejection, in which a fluctuation (reduction) of the ion density in the vicinity of the ice front is followed by the growth of a new ice layer. The presence of salt slows down the freezing process, which leads to the formation of an almost neat ice next to a disordered brine layer.

Marginal turbulent state of viscoelastic fluids: A polymer drag reduction perspective.

PubMed

Xi, Li; Bai, Xue

2016-04-01

The laminar-turbulent (LT) transition of dilute polymer solutions is of great interest not only for the complex transition dynamics itself, but also for its potential link to the maximum drag reduction (MDR) phenomenon. We present an in-depth investigation of the edge state (ES), an asymptotic solution on the LT boundary, in viscoelastic channel flow. For given Re and simulation domain size, mean flow statistics of the ES do not vary with the introduction of polymers, proving that there is a region of turbulent states not susceptible to polymer drag reduction effects. The dynamics of the ES features low-frequency fluctuations and in the longer domains we studied it is nearly periodic with regular bursts of turbulent activities separated by extended quiescent periods. Its flow field is dominated by elongated vortices and streaks, with very weak extensional and rotational flow motions. Polymer stretching is almost exclusively contributed by the mean shear and polymer-turbulence interaction is minimal. Flow structures and the kinematics of the ES match hibernating turbulence, an MDR-like phase intermittently occurring in turbulent dynamics. Its observation now seems to result from recurrent visits to certain parts of the ES. The ES offers explanations for the existence and universality of MDR, the quantitative magnitude of which, however, still remains unsolved.

Marginal turbulent state of viscoelastic fluids: A polymer drag reduction perspective

NASA Astrophysics Data System (ADS)

Xi, Li; Bai, Xue

2016-04-01

The laminar-turbulent (LT) transition of dilute polymer solutions is of great interest not only for the complex transition dynamics itself, but also for its potential link to the maximum drag reduction (MDR) phenomenon. We present an in-depth investigation of the edge state (ES), an asymptotic solution on the LT boundary, in viscoelastic channel flow. For given Re and simulation domain size, mean flow statistics of the ES do not vary with the introduction of polymers, proving that there is a region of turbulent states not susceptible to polymer drag reduction effects. The dynamics of the ES features low-frequency fluctuations and in the longer domains we studied it is nearly periodic with regular bursts of turbulent activities separated by extended quiescent periods. Its flow field is dominated by elongated vortices and streaks, with very weak extensional and rotational flow motions. Polymer stretching is almost exclusively contributed by the mean shear and polymer-turbulence interaction is minimal. Flow structures and the kinematics of the ES match hibernating turbulence, an MDR-like phase intermittently occurring in turbulent dynamics. Its observation now seems to result from recurrent visits to certain parts of the ES. The ES offers explanations for the existence and universality of MDR, the quantitative magnitude of which, however, still remains unsolved.

Concurrent musculoskeletal dynamics and finite element analysis predicts altered gait patterns to reduce foot tissue loading.

PubMed

Halloran, Jason P; Ackermann, Marko; Erdemir, Ahmet; van den Bogert, Antonie J

2010-10-19

Current computational methods for simulating locomotion have primarily used muscle-driven multibody dynamics, in which neuromuscular control is optimized. Such simulations generally represent joints and soft tissue as simple kinematic or elastic elements for computational efficiency. These assumptions limit application in studies such as ligament injury or osteoarthritis, where local tissue loading must be predicted. Conversely, tissue can be simulated using the finite element method with assumed or measured boundary conditions, but this does not represent the effects of whole body dynamics and neuromuscular control. Coupling the two domains would overcome these limitations and allow prediction of movement strategies guided by tissue stresses. Here we demonstrate this concept in a gait simulation where a musculoskeletal model is coupled to a finite element representation of the foot. Predictive simulations incorporated peak plantar tissue deformation into the objective of the movement optimization, as well as terms to track normative gait data and minimize fatigue. Two optimizations were performed, first without the strain minimization term and second with the term. Convergence to realistic gait patterns was achieved with the second optimization realizing a 44% reduction in peak tissue strain energy density. The study demonstrated that it is possible to alter computationally predicted neuromuscular control to minimize tissue strain while including desired kinematic and muscular behavior. Future work should include experimental validation before application of the methodology to patient care. Copyright © 2010 Elsevier Ltd. All rights reserved.

A fractional calculus perspective of distributed propeller design

NASA Astrophysics Data System (ADS)

Tenreiro Machado, J.; Galhano, Alexandra M.

2018-02-01

A new generation of aircraft with distributed propellers leads to operational performances superior to those exhibited by standard designs. Computational simulations and experimental tests show a reduction of fuel consumption and noise. This paper proposes an analogy between aerodynamics and electrical circuits. The model reveals properties similar to those of fractional-order systems and gives a deeper insight into the dynamics of multi-propeller coupling.

Evaluation of stormwater micropollutant source control and end-of-pipe control strategies using an uncertainty-calibrated integrated dynamic simulation model.

PubMed

Vezzaro, L; Sharma, A K; Ledin, A; Mikkelsen, P S

2015-03-15

The estimation of micropollutant (MP) fluxes in stormwater systems is a fundamental prerequisite when preparing strategies to reduce stormwater MP discharges to natural waters. Dynamic integrated models can be important tools in this step, as they can be used to integrate the limited data provided by monitoring campaigns and to evaluate the performance of different strategies based on model simulation results. This study presents an example where six different control strategies, including both source-control and end-of-pipe treatment, were compared. The comparison focused on fluxes of heavy metals (copper, zinc) and organic compounds (fluoranthene). MP fluxes were estimated by using an integrated dynamic model, in combination with stormwater quality measurements. MP sources were identified by using GIS land usage data, runoff quality was simulated by using a conceptual accumulation/washoff model, and a stormwater retention pond was simulated by using a dynamic treatment model based on MP inherent properties. Uncertainty in the results was estimated with a pseudo-Bayesian method. Despite the great uncertainty in the MP fluxes estimated by the runoff quality model, it was possible to compare the six scenarios in terms of discharged MP fluxes, compliance with water quality criteria, and sediment accumulation. Source-control strategies obtained better results in terms of reduction of MP emissions, but all the simulated strategies failed in fulfilling the criteria based on emission limit values. The results presented in this study shows how the efficiency of MP pollution control strategies can be quantified by combining advanced modeling tools (integrated stormwater quality model, uncertainty calibration). Copyright © 2014 Elsevier Ltd. All rights reserved.

Mathematical analysis of a lymphatic filariasis model with quarantine and treatment.

PubMed

Mwamtobe, Peter M; Simelane, Simphiwe M; Abelman, Shirley; Tchuenche, Jean M

2017-03-16

Lymphatic filariasis is a globally neglected tropical parasitic disease which affects individuals of all ages and leads to an altered lymphatic system and abnormal enlargement of body parts. A mathematical model of lymphatic filariaris with intervention strategies is developed and analyzed. Control of infections is analyzed within the model through medical treatment of infected-acute individuals and quarantine of infected-chronic individuals. We derive the effective reproduction number, [Formula: see text] and its interpretation/investigation suggests that treatment contributes to a reduction in lymphatic filariasis cases faster than quarantine. However, this reduction is greater when the two intervention approaches are applied concurrently. Numerical simulations are carried out to monitor the dynamics of the filariasis model sub-populations for various parameter values of the associated reproduction threshold. Lastly, sensitivity analysis on key parameters that drive the disease dynamics is performed in order to identify their relative importance on the disease transmission.

A Computational Fluid Dynamic Model for a Novel Flash Ironmaking Process

NASA Astrophysics Data System (ADS)

Perez-Fontes, Silvia E.; Sohn, Hong Yong; Olivas-Martinez, Miguel

A computational fluid dynamic model for a novel flash ironmaking process based on the direct gaseous reduction of iron oxide concentrates is presented. The model solves the three-dimensional governing equations including both gas-phase and gas-solid reaction kinetics. The turbulence-chemistry interaction in the gas-phase is modeled by the eddy dissipation concept incorporating chemical kinetics. The particle cloud model is used to track the particle phase in a Lagrangian framework. A nucleation and growth kinetics rate expression is adopted to calculate the reduction rate of magnetite concentrate particles. Benchmark experiments reported in the literature for a nonreacting swirling gas jet and a nonpremixed hydrogen jet flame were simulated for validation. The model predictions showed good agreement with measurements in terms of gas velocity, gas temperature and species concentrations. The relevance of the computational model for the analysis of a bench reactor operation and the design of an industrial-pilot plant is discussed.

Generation of linear dynamic models from a digital nonlinear simulation

NASA Technical Reports Server (NTRS)

Daniele, C. J.; Krosel, S. M.

1979-01-01

The results and methodology used to derive linear models from a nonlinear simulation are presented. It is shown that averaged positive and negative perturbations in the state variables can reduce numerical errors in finite difference, partial derivative approximations and, in the control inputs, can better approximate the system response in both directions about the operating point. Both explicit and implicit formulations are addressed. Linear models are derived for the F 100 engine, and comparisons of transients are made with the nonlinear simulation. The problem of startup transients in the nonlinear simulation in making these comparisons is addressed. Also, reduction of the linear models is investigated using the modal and normal techniques. Reduced-order models of the F 100 are derived and compared with the full-state models.

A Lagrangian analysis of a sudden stratospheric warming - Comparison of a model simulation and LIMS observations

NASA Technical Reports Server (NTRS)

Pierce, R. B.; Remsberg, Ellis E.; Fairlie, T. D.; Blackshear, W. T.; Grose, William L.; Turner, Richard E.

1992-01-01

Lagrangian area diagnostics and trajectory techniques are used to investigate the radiative and dynamical characteristics of a spontaneous sudden warming which occurred during a 2-yr Langley Research Center model simulation. The ability of the Langley Research Center GCM to simulate the major features of the stratospheric circulation during such highly disturbed periods is illustrated by comparison of the simulated warming to the observed circulation during the LIMS observation period. The apparent sink of vortex area associated with Rossby wave-breaking accounts for the majority of the reduction of the size of the vortex and also acts to offset the radiatively driven increase in the area occupied by the 'surf zone'. Trajectory analysis of selected material lines substantiates the conclusions from the area diagnostics.

Thermodynamic properties of triangle-well fluids in two dimensions: MC and MD simulations.

PubMed

Reyes, Yuri; Bárcenas, Mariana; Odriozola, Gerardo; Orea, Pedro

2016-11-07

With the aim of providing complementary data of the thermodynamics properties of the triangular well potential, the vapor/liquid phase diagrams for such potential with different interaction ranges were calculated in two dimensions by Monte Carlo and molecular dynamics simulations; also, the vapor/liquid interfacial tension was calculated. As reported for other interaction potentials, it was observed that the reduction of the dimensionality makes the phase diagram to shrink. Finally, with the aid of reported data for the same potential in three dimensions, it was observed that this potential does not follow the principle of corresponding states.

A review of the structure and dynamics of nanoconfined water and ionic liquids via molecular dynamics simulation.

PubMed

Foroutan, Masumeh; Fatemi, S Mahmood; Esmaeilian, Farshad

2017-02-01

During the past decade, the research on fluids in nanoconfined geometries has received considerable attention as a consequence of their wide applications in different fields. Several nanoconfined systems such as water and ionic liquids, together with an equally impressive array of nanoconfining media such as carbon nanotube, graphene and graphene oxide have received increasingly growing interest in the past years. Water is the first system that has been reviewed in this article, due to its important role in transport phenomena in environmental sciences. Water is often considered as a highly nanoconfined system, due to its reduction to a few layers of water molecules between the extended surface of large macromolecules. The second system discussed here is ionic liquids, which have been widely studied in the modern green chemistry movement. Considering the great importance of ionic liquids in industry, and also their oil/water counterpart, nanoconfined ionic liquid system has become an important area of research with many fascinating applications. Furthermore, the method of molecular dynamics simulation is one of the major tools in the theoretical study of water and ionic liquids in nanoconfinement, which increasingly has been joined with experimental procedures. In this way, the choice of water and ionic liquids in nanoconfinement is justified by applying molecular dynamics simulation approaches in this review article.

Mechanistic insights into electrochemical reduction of CO2 over Ag using density functional theory and transport models

PubMed Central

Goodpaster, Jason D.; Weber, Adam Z.

2017-01-01

Electrochemical reduction of CO2 using renewable sources of electrical energy holds promise for converting CO2 to fuels and chemicals. Since this process is complex and involves a large number of species and physical phenomena, a comprehensive understanding of the factors controlling product distribution is required. While the most plausible reaction pathway is usually identified from quantum-chemical calculation of the lowest free-energy pathway, this approach can be misleading when coverages of adsorbed species determined for alternative mechanism differ significantly, since elementary reaction rates depend on the product of the rate coefficient and the coverage of species involved in the reaction. Moreover, cathode polarization can influence the kinetics of CO2 reduction. Here, we present a multiscale framework for ab initio simulation of the electrochemical reduction of CO2 over an Ag(110) surface. A continuum model for species transport is combined with a microkinetic model for the cathode reaction dynamics. Free energies of activation for all elementary reactions are determined from density functional theory calculations. Using this approach, three alternative mechanisms for CO2 reduction were examined. The rate-limiting step in each mechanism is **COOH formation at higher negative potentials. However, only via the multiscale simulation was it possible to identify the mechanism that leads to a dependence of the rate of CO formation on the partial pressure of CO2 that is consistent with experiments. Simulations based on this mechanism also describe the dependence of the H2 and CO current densities on cathode voltage that are in strikingly good agreement with experimental observation. PMID:28973926

A Study of Longitudinal Control Problems at Low and Negative Damping and Stability with Emphasis on Effects of Motion Cues

NASA Technical Reports Server (NTRS)

Sadoff, Melvin; McFadden, Norman M.; Heinle, Donovan R.

1961-01-01

As part of a general investigation to determine the effects of simulator motions on pilot opinion and task performance over a wide range of vehicle longitudinal dynamics, a cooperative NASA-AMAL program was conducted on the centrifuge at Johnsville, Pennsylvania. The test parameters and measurements for this program duplicated those of earlier studies made at Ames Research Center with a variable-stability airplane and with a pitch-roll chair flight simulator. Particular emphasis was placed on the minimum basic damping and stability the pilots would accept and on the minimum dynamics they considered controllable in the event of stability-augmentation system failure. Results of the centrifuge-simulator program indicated that small positive damping was required by the pilots over most of the frequency range covered for configurations rated acceptable for emergency conditions only (e.g., failure of a pitch damper). It was shown that the pilot's tolerance for unstable dynamics was dependent primarily on the value of damping. For configurations rated acceptable for emergency operation only, the allowable instability and damping corresponded to a divergence time to double amplitude of about 1 second. Comparisons were made of centrifuge, pitch-chair and fixed-cockpit simulator tests with flight tests. Pilot ratings indicated that the effects of incomplete or spurious motion cues provided by these three modes of simulation were important only for high-frequency, lightly damped dynamics or unstable, moderately damped dynamics. The pitch- chair simulation, which provided accurate angular-acceleration cues to the pilot, compared most favorably with flight. For the centrifuge simulation, which furnished accurate normal accelerations but spurious pitching and longitudinal accelerations, there was a deterioration of pilots' opinion relative to flight results. Results of simulator studies with an analog pilot replacing the human pilot illustrated the adaptive capability of human pilots in coping with the wide range of vehicle dynamics and the control problems covered in this study. It was shown that pilot-response characteristics, deduced by the analog-pilot method, could be related to pilot opinion. Possible application of these results for predicting flight-control problems was illustrated by means of an example control-problem analysis. The results of a brief evaluation of a pencil-type side-arm controller in the centrifuge showed a considerable improvement in the pilots' ability to cope with high-frequency, low-damping dynamics, compared to results obtained with the center stick. This improvement with the pencil controller was attributed primarily to a marked reduction in the adverse effects of large and exaggerated pitching and longitudinal accelerations on pilot control precision.

Local dynamic subgrid-scale models in channel flow

NASA Technical Reports Server (NTRS)

Cabot, William H.

1994-01-01

The dynamic subgrid-scale (SGS) model has given good results in the large-eddy simulation (LES) of homogeneous isotropic or shear flow, and in the LES of channel flow, using averaging in two or three homogeneous directions (the DA model). In order to simulate flows in general, complex geometries (with few or no homogeneous directions), the dynamic SGS model needs to be applied at a local level in a numerically stable way. Channel flow, which is inhomogeneous and wall-bounded flow in only one direction, provides a good initial test for local SGS models. Tests of the dynamic localization model were performed previously in channel flow using a pseudospectral code and good results were obtained. Numerical instability due to persistently negative eddy viscosity was avoided by either constraining the eddy viscosity to be positive or by limiting the time that eddy viscosities could remain negative by co-evolving the SGS kinetic energy (the DLk model). The DLk model, however, was too expensive to run in the pseudospectral code due to a large near-wall term in the auxiliary SGS kinetic energy (k) equation. One objective was then to implement the DLk model in a second-order central finite difference channel code, in which the auxiliary k equation could be integrated implicitly in time at great reduction in cost, and to assess its performance in comparison with the plane-averaged dynamic model or with no model at all, and with direct numerical simulation (DNS) and/or experimental data. Other local dynamic SGS models have been proposed recently, e.g., constrained dynamic models with random backscatter, and with eddy viscosity terms that are averaged in time over material path lines rather than in space. Another objective was to incorporate and test these models in channel flow.

Understanding the hydrogen transfer mechanism for the biodegradation of 2,4,6-trinitrotoluene catalyzed by pentaerythritol tetranitrate reductase: molecular dynamics simulations.

PubMed

Yang, Zhilin; Chen, Junxian; Zhou, Yang; Huang, Hui; Xu, Dingguo; Zhang, Chaoyang

2018-05-03

The explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic pollutant. Biodegradation is inevitably one of the most cost-effective and enviromentally friendly means of removing TNT pollution. However, the aromatic derivatives from the reduction of nitro groups by several classic enzymes are still toxic. Besides the reduction of nitro groups, pentaerythritol tetranitrate reductase (PETNR) offers a potential route to ring fission and complete degradation of TNT through the pathway of the Meisenheimer complex. This work is devoted to deeply understand the essence of the Meisenheimer pathway and mainly focus on the crucial hydrogen-transfer reaction by means of molecular dynamics (MD) simulations. We obtain three valuable findings. Firstly, the parallel π-π stacking between TNT and the flavin mononucleotide (FMN) cofactor is a precondition. The key residue controlling this conformation is His181. Although His184 does not interact with TNT, the mutation from His184 to Asn184 would abolish the π-π structure. Secondly, the data of the empirical valence bond (EVB) show that the Meisenheimer pathway is predominant because its activation barrier is 6.7 kcal mol-1 far less than that of nitro reduction (26.6 kcal mol-1). Finally, based on the results of thermodynamic integration (TI), the type of transferred hydrogen is also ensured, that is, the H anion (H-) for the Meisenheimer complex and the H radical (H˙) for nitro reduction. Our findings provide an exhaustive understanding for the first hydrogen transfer reaction that has a decisive effect on two competing pathways, and help in searching for and designing new enzymes that can effectively degrade TNT.

Determining residual reduction algorithm kinematic tracking weights for a sidestep cut via numerical optimization.

PubMed

Samaan, Michael A; Weinhandl, Joshua T; Bawab, Sebastian Y; Ringleb, Stacie I

2016-12-01

Musculoskeletal modeling allows for the determination of various parameters during dynamic maneuvers by using in vivo kinematic and ground reaction force (GRF) data as inputs. Differences between experimental and model marker data and inconsistencies in the GRFs applied to these musculoskeletal models may not produce accurate simulations. Therefore, residual forces and moments are applied to these models in order to reduce these differences. Numerical optimization techniques can be used to determine optimal tracking weights of each degree of freedom of a musculoskeletal model in order to reduce differences between the experimental and model marker data as well as residual forces and moments. In this study, the particle swarm optimization (PSO) and simplex simulated annealing (SIMPSA) algorithms were used to determine optimal tracking weights for the simulation of a sidestep cut. The PSO and SIMPSA algorithms were able to produce model kinematics that were within 1.4° of experimental kinematics with residual forces and moments of less than 10 N and 18 Nm, respectively. The PSO algorithm was able to replicate the experimental kinematic data more closely and produce more dynamically consistent kinematic data for a sidestep cut compared to the SIMPSA algorithm. Future studies should use external optimization routines to determine dynamically consistent kinematic data and report the differences between experimental and model data for these musculoskeletal simulations.

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

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

Hoang, Tuan L.; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, CA 94550; Marian, Jaime, E-mail: jmarian@ucla.edu

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a proceduremore » for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe{sup 3+}, He{sup +} and H{sup +}) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.« less

Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials

NASA Astrophysics Data System (ADS)

Hoang, Tuan L.; Marian, Jaime; Bulatov, Vasily V.; Hosemann, Peter

2015-11-01

An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a procedure for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe3+, He+ and H+) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.

High Temperature Modification of SNCR Technology and its Impact on NOx Removal Process

NASA Astrophysics Data System (ADS)

Blejchař, Tomáš; Konvička, Jaroslav; von der Heide, Bernd; Malý, Rostislav; Maier, Miloš

2018-06-01

SNCR (Selective non-catalytic reduction) Technology is currently being used to reach the emission limit for nitrogen oxides at fossil fuel fired power plant and/or heating plant and optimum temperature for SNCR process is in range 850 - 1050°C. Modified SNCR technology is able to reach reduction 60% of nitrogen oxides at temperature up to 1250°C. So the technology can also be installed where the flue gas temperature is too high in combustion chamber. Modified SNCR was tested using generally known SNCR chemistry implemented in CFD (Computation fluid dynamics) code. CFD model was focused on detail simulation of reagent injection and influence of flue gas temperature. Than CFD simulation was compared with operating data of boiler where the modified SNCR technology is installed. By comparing the experiment results with the model, the effect on nitrous oxides removal process and temperature of flue gas at the injection region.

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

NASA Astrophysics Data System (ADS)

Ferguson, Andrew L.; Panagiotopoulos, Athanassios Z.; Debenedetti, Pablo G.; Kevrekidis, Ioannis G.

2011-04-01

Nonlinear dimensionality reduction techniques can be applied to molecular simulation trajectories to systematically extract a small number of variables with which to parametrize the important dynamical motions of the system. For molecular systems exhibiting free energy barriers exceeding a few kBT, inadequate sampling of the barrier regions between stable or metastable basins can lead to a poor global characterization of the free energy landscape. We present an adaptation of a nonlinear dimensionality reduction technique known as the diffusion map that extends its applicability to biased umbrella sampling simulation trajectories in which restraining potentials are employed to drive the system into high free energy regions and improve sampling of phase space. We then propose a bootstrapped approach to iteratively discover good low-dimensional parametrizations by interleaving successive rounds of umbrella sampling and diffusion mapping, and we illustrate the technique through a study of alanine dipeptide in explicit solvent.

A model for the catalytic reduction of NO with CO and N desorption

NASA Astrophysics Data System (ADS)

Díaz, J. J.; Buendía, G. M.

2018-02-01

In this work we have investigated by Monte Carlo simulations the dynamical behavior of a modified Yaldram-Khan (YK) model for the catalytic reduction of NO on a surface. Our model is simulated on a square lattice and includes the individual desorption of CO molecules and N atoms, processes associated with temperature effects. When CO desorption is added, strong fluctuations appear, which are associated with the spreading of N checkerboard structures on the surface. These structures take a long time to coalesce, allowing the existence of a unsteady but long lasting reactive state. N desorption also favors the reactivity of the system, this time by diminishing the size of the N structures and impeding their coalescence. The combined desorption of CO and N produces a reactive state as well, where reactive zones among N structures can take place on the surface.

A robust computational technique for model order reduction of two-time-scale discrete systems via genetic algorithms.

PubMed

Alsmadi, Othman M K; Abo-Hammour, Zaer S

2015-01-01

A robust computational technique for model order reduction (MOR) of multi-time-scale discrete systems (single input single output (SISO) and multi-input multioutput (MIMO)) is presented in this paper. This work is motivated by the singular perturbation of multi-time-scale systems where some specific dynamics may not have significant influence on the overall system behavior. The new approach is proposed using genetic algorithms (GA) with the advantage of obtaining a reduced order model, maintaining the exact dominant dynamics in the reduced order, and minimizing the steady state error. The reduction process is performed by obtaining an upper triangular transformed matrix of the system state matrix defined in state space representation along with the elements of B, C, and D matrices. The GA computational procedure is based on maximizing the fitness function corresponding to the response deviation between the full and reduced order models. The proposed computational intelligence MOR method is compared to recently published work on MOR techniques where simulation results show the potential and advantages of the new approach.

Stream-wise distribution of skin-friction drag reduction on a flat plate with bubble injection

NASA Astrophysics Data System (ADS)

Qin, Shijie; Chu, Ning; Yao, Yan; Liu, Jingting; Huang, Bin; Wu, Dazhuan

2017-03-01

To investigate the stream-wise distribution of skin-friction drag reduction on a flat plate with bubble injection, both experiments and simulations of bubble drag reduction (BDR) have been conducted in this paper. Drag reductions at various flow speeds and air injection rates have been tested in cavitation tunnel experiments. Visualization of bubble flow pattern is implemented synchronously. The computational fluid dynamics (CFD) method, in the framework of Eulerian-Eulerian two fluid modeling, coupled with population balance model (PBM) is used to simulate the bubbly flow along the flat plate. A wide range of bubble sizes considering bubble breakup and coalescence is modeled based on experimental bubble distribution images. Drag and lift forces are fully modeled based on applicable closure models. Both predicted drag reductions and bubble distributions are in reasonable concordance with experimental results. Stream-wise distribution of BDR is revealed based on CFD-PBM numerical results. In particular, four distinct regions with different BDR characteristics are first identified and discussed in this study. Thresholds between regions are extracted and discussed. And it is highly necessary to fully understand the stream-wise distribution of BDR in order to establish a universal scaling law. Moreover, mechanism of stream-wise distribution of BDR is analysed based on the near-wall flow parameters. The local drag reduction is a direct result of near-wall max void fraction. And the near-wall velocity gradient modified by the presence of bubbles is considered as another important factor for bubble drag reduction.

Mass reduction patterning of silicon-on-oxide-based micromirrors

NASA Astrophysics Data System (ADS)

Hall, Harris J.; Green, Andrew; Dooley, Sarah; Schmidt, Jason D.; Starman, LaVern A.; Langley, Derrick; Coutu, Ronald A.

2016-10-01

It has long been recognized in the design of micromirror-based optical systems that balancing static flatness of the mirror surface through structural design with the system's mechanical dynamic response is challenging. Although a variety of mass reduction approaches have been presented in the literature to address this performance trade, there has been little quantifiable comparison reported. In this work, different mass reduction approaches, some unique to the work, are quantifiably compared with solid plate thinning in both curvature and mass using commercial finite element simulation of a specific square silicon-on-insulator-based micromirror geometry. Other important considerations for micromirror surfaces, including surface profile and smoothness, are also discussed. Fabrication of one of these geometries, a two-dimensional tessellated square pattern, was performed in the presence of a 400-μm-tall central post structure using a simple single mask process. Limited experimental curvature measurements of fabricated samples are shown to correspond well with properly characterized simulation results and indicate ˜67% improvement in radius of curvature in comparison to a solid plate design of equivalent mass.

Selected-node stochastic simulation algorithm

NASA Astrophysics Data System (ADS)

Duso, Lorenzo; Zechner, Christoph

2018-04-01

Stochastic simulations of biochemical networks are of vital importance for understanding complex dynamics in cells and tissues. However, existing methods to perform such simulations are associated with computational difficulties and addressing those remains a daunting challenge to the present. Here we introduce the selected-node stochastic simulation algorithm (snSSA), which allows us to exclusively simulate an arbitrary, selected subset of molecular species of a possibly large and complex reaction network. The algorithm is based on an analytical elimination of chemical species, thereby avoiding explicit simulation of the associated chemical events. These species are instead described continuously in terms of statistical moments derived from a stochastic filtering equation, resulting in a substantial speedup when compared to Gillespie's stochastic simulation algorithm (SSA). Moreover, we show that statistics obtained via snSSA profit from a variance reduction, which can significantly lower the number of Monte Carlo samples needed to achieve a certain performance. We demonstrate the algorithm using several biological case studies for which the simulation time could be reduced by orders of magnitude.

Stochastic dynamic analysis of marine risers considering Gaussian system uncertainties

NASA Astrophysics Data System (ADS)

Ni, Pinghe; Li, Jun; Hao, Hong; Xia, Yong

2018-03-01

This paper performs the stochastic dynamic response analysis of marine risers with material uncertainties, i.e. in the mass density and elastic modulus, by using Stochastic Finite Element Method (SFEM) and model reduction technique. These uncertainties are assumed having Gaussian distributions. The random mass density and elastic modulus are represented by using the Karhunen-Loève (KL) expansion. The Polynomial Chaos (PC) expansion is adopted to represent the vibration response because the covariance of the output is unknown. Model reduction based on the Iterated Improved Reduced System (IIRS) technique is applied to eliminate the PC coefficients of the slave degrees of freedom to reduce the dimension of the stochastic system. Monte Carlo Simulation (MCS) is conducted to obtain the reference response statistics. Two numerical examples are studied in this paper. The response statistics from the proposed approach are compared with those from MCS. It is noted that the computational time is significantly reduced while the accuracy is kept. The results demonstrate the efficiency of the proposed approach for stochastic dynamic response analysis of marine risers.

Analysis and Design of International Emission Trading Markets Applying System Dynamics Techniques

NASA Astrophysics Data System (ADS)

Hu, Bo; Pickl, Stefan

2010-11-01

The design and analysis of international emission trading markets is an important actual challenge. Time-discrete models are needed to understand and optimize these procedures. We give an introduction into this scientific area and present actual modeling approaches. Furthermore, we develop a model which is embedded in a holistic problem solution. Measures for energy efficiency are characterized. The economic time-discrete "cap-and-trade" mechanism is influenced by various underlying anticipatory effects. With a systematic dynamic approach the effects can be examined. First numerical results show that fair international emissions trading can only be conducted with the use of protective export duties. Furthermore a comparatively high price which evokes emission reduction inevitably has an inhibiting effect on economic growth according to our model. As it always has been expected it is not without difficulty to find a balance between economic growth and emission reduction. It can be anticipated using our System Dynamics model simulation that substantial changes must be taken place before international emissions trading markets can contribute to global GHG emissions mitigation.

E9-Im9 Colicin DNase−Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study

PubMed Central

2008-01-01

Protein−protein transient and dynamic interactions underlie all biological processes. The molecular dynamics (MD) of the E9 colicin DNase protein, its Im9 inhibitor protein, and their E9-Im9 recognition complex are investigated by combining multiple-copy (MC) MD and accelerated MD (aMD) explicit-solvent simulation approaches, after validation with crystalline-phase and solution experiments. Im9 shows higher flexibility than its E9 counterpart. Im9 displays a significant reduction of backbone flexibility and a remarkable increase in motional correlation upon E9 association. Im9 loops 23−31 and 54−64 open with respect to the E9-Im9 X-ray structure and show high conformational diversity. Upon association a large fraction (∼20 nm2) of E9 and Im9 protein surfaces become inaccessible to water. Numerous salt bridges transiently occurring throughout our six 50 ns long MC-MD simulations are not present in the X-ray model. Among these Im9 Glu31−E9 Arg96 and Im9 Glu41−Lys89 involve interface interactions. Through the use of 10 ns of Im9 aMD simulation, we reconcile the largest thermodynamic impact measured for Asp51Ala mutation with Im9 structure and dynamics. Lys57 acts as an essential molecular switch to shift Im9 surface loop towards an ideal configuration for E9 inhibition. This is achieved by switching Asp60−Lys57 and Asp62−Lys57 hydrogen bonds to Asp51−Lys57 salt bridge. E9-Im9 recognition involves shifts of conformational distributions, reorganization of intramolecular hydrogen bond patterns, and formation of new inter- and intramolecular interactions. The description of key transient biological interactions can be significantly enriched by the dynamic and atomic-level information provided by computer simulations. PMID:19053689

Confusing placebo effect with natural history in epilepsy: A big data approach.

PubMed

Goldenholz, Daniel M; Moss, Robert; Scott, Jonathan; Auh, Sungyoung; Theodore, William H

2015-09-01

For unknown reasons, placebos reduce seizures in clinical trials in many patients. It is also unclear why some drugs showing statistical superiority to placebo in one trial may fail to do so in another. Using Seizuretracker.com, a patient-centered database of 684,825 seizures, we simulated "placebo" and "drug" trials. These simulations were employed to clarify the sources of placebo effects in epilepsy, and to identify methods of diminishing placebo effects. Simulation 1 included 9 trials with a 6-week baseline and 6-week test period, starting at time 0, 3, 6…24 months. Here, "placebo" reduced seizures regardless of study start time. Regression-to-the-mean persisted only for 3 to 6 months. Simulation 2 comprised a 6-week baseline and then 2 years of follow-up. Seizure frequencies continued to improve throughout follow-up. Although the group improved, individuals switched from improvement to worsening and back. Simulation 3 involved a placebo-controlled "drug" trial, to explore methods of placebo response reduction. An efficacious "drug" failed to demonstrate a significant effect compared with "placebo" (p = 0.12), although modifications either in study start time (p = 0.025) or baseline population reduction (p = 0.0028) allowed the drug to achieve a statistically significant effect compared with placebo. In epilepsy clinical trials, some seizure reduction traditionally attributed to placebo effect may reflect the natural course of the disease itself. Understanding these dynamics will allow future investigations into optimal clinical trial design and may lead to identification of more effective therapies. Ann Neurol 2015;78:329-336. © 2015 American Neurological Association.

Glass Transition and Molecular Mobility in Styrene-Butadiene Rubber Modified Asphalt.

PubMed

Khabaz, Fardin; Khare, Rajesh

2015-11-05

Asphalt, a soft matter consisting of more than a thousand chemical species, is of vital importance for the transportation infrastructure, yet it poses significant challenges for microscopic theory and modeling approaches due to its multicomponent nature. Polymeric additives can potentially enhance the thermo-mechanical properties of asphalt, thus helping reduce the road repair costs; rational design of such systems requires knowledge of the molecular structure and dynamics of these systems. We have used molecular dynamics (MD) simulations to investigate the volumetric, structural, and dynamic properties of the neat asphalt as well as styrene-butadiene rubber (SBR) modified asphalt systems. The volume-temperature behavior of the asphalt systems exhibited a glass transition phenomenon, akin to that observed in experiments. The glass transition temperature, room temperature density, and coefficient of volume thermal expansion of the neat asphalt systems so evaluated were in agreement with experimental data when the effect of the high cooling rate used in simulations was accounted for. While the volumetric properties of SBR modified asphalt were found to be insensitive to the presence of the SBR additive, the addition of SBR led to an increase in the aggregation of asphaltene molecules. Furthermore, addition of SBR caused a reduction in the mobility of the constituent molecules of asphalt, with the reduction being more significant for the larger constituent molecules. Similar to other glass forming liquids, the reciprocal of the diffusion coefficient of the selected molecules was observed to follow the Vogel-Fulcher-Tammann (VFT) behavior as a function of temperature. These results suggest the potential for using polymeric additives for enhancing the dynamic mechanical properties of asphalt without affecting its volumetric properties.

Influence of the feedback loops in the trp operon of B. subtilis on the system dynamic response and noise amplitude.

PubMed

Zamora-Chimal, Criseida; Santillán, Moisés; Rodríguez-González, Jesús

2012-10-07

In this paper we introduce a mathematical model for the tryptophan operon regulatory pathway in Bacillus subtilis. This model considers the transcription-attenuation, and the enzyme-inhibition regulatory mechanisms. Special attention is paid to the estimation of all the model parameters from reported experimental data. With the aid of this model we investigate, from a mathematical-modeling point of view, whether the existing multiplicity of regulatory feedback loops is advantageous in some sense, regarding the dynamic response and the biochemical noise in the system. The tryptophan operon dynamic behavior is studied by means of deterministic numeric simulations, while the biochemical noise is analyzed with the aid of stochastic simulations. The model feasibility is tested comparing its stochastic and deterministic results with experimental reports. Our results for the wildtype and for a couple of mutant bacterial strains suggest that the enzyme-inhibition feedback loop, dynamically accelerates the operon response, and plays a major role in the reduction of biochemical noise. Also, the transcription-attenuation feedback loop makes the trp operon sensitive to changes in the endogenous tryptophan level, and increases the amplitude of the biochemical noise. Copyright © 2012 Elsevier Ltd. All rights reserved.

Development and Verification of the Soil-Pile Interaction Extension for SubDyn

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

Damiani, Rick R; Wendt, Fabian F

SubDyn is the substructure structural-dynamics module for the aero-hydro-servo-elastic tool FAST v8. SubDyn uses a finite-element model (FEM) to simulate complex multimember lattice structures connected to conventional turbines and towers, and it can make use of the Craig-Bampton model reduction. Here we describe the newly added capability to handle soil-pile stiffness and compare results for monopile and jacket-based offshore wind turbines as obtained with FAST v8, SACS, and EDP (the latter two are modeling software packages commonly used in the offshore oil and gas industry). The level of agreement in terms of modal properties and loads for the entire offshoremore » wind turbine components is excellent, thus allowing SubDyn and FAST v8 to accurately simulate offshore wind turbines on fixed-bottom structures and accounting for the effect of soil dynamics, thus reducing risk to the project.« less

Exploring the reversal of enantioselectivity on a zinc-dependent alcohol dehydrogenase† †Electronic supplementary information (ESI) available. See DOI: 10.1039/C7OB00482F Click here for additional data file.

PubMed Central

Maria-Solano, Miguel A.; Romero-Rivera, Adrian

2017-01-01

Alcohol Dehydrogenase (ADH) enzymes catalyse the reversible reduction of prochiral ketones to the corresponding alcohols. These enzymes present two differently shaped active site pockets, which dictate their substrate scope and selectivity. In this study, we computationally evaluate the effect of two commonly reported active site mutations (I86A, and W110T) on a secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) through Molecular Dynamics simulations. Our results indicate that the introduced mutations induce dramatic changes in the shape of the active site, but most importantly they impact the substrate–enzyme interactions. We demonstrate that the combination of Molecular Dynamics simulations with the tools POVME and NCIplot corresponds to a powerful strategy for rationalising and engineering the stereoselectivity of ADH variants. PMID:28436515

Expert systems for automated maintenance of a Mars oxygen production system

NASA Astrophysics Data System (ADS)

Huang, Jen-Kuang; Ho, Ming-Tsang; Ash, Robert L.

1992-08-01

Application of expert system concepts to a breadboard Mars oxygen processor unit have been studied and tested. The research was directed toward developing the methodology required to enable autonomous operation and control of these simple chemical processors at Mars. Failure detection and isolation was the key area of concern, and schemes using forward chaining, backward chaining, knowledge-based expert systems, and rule-based expert systems were examined. Tests and simulations were conducted that investigated self-health checkout, emergency shutdown, and fault detection, in addition to normal control activities. A dynamic system model was developed using the Bond-Graph technique. The dynamic model agreed well with tests involving sudden reductions in throughput. However, nonlinear effects were observed during tests that incorporated step function increases in flow variables. Computer simulations and experiments have demonstrated the feasibility of expert systems utilizing rule-based diagnosis and decision-making algorithms.

A study of waste and delivery valve design modification to the pump performance

NASA Astrophysics Data System (ADS)

Harith, M. N.; Bakar, R. A.; Ramasamy, D.; Kardigama, K.; Quanjin, Ma

2018-04-01

This paper objective is to share design revolution of waste and delivery valve that contribute to the overall pump performance. In this paper, 3 new designs of waste and delivery valve pump are presented with comprehensive internal flow analysis using computational fluid dynamics (CFD) simulation over 4 cases that have been deeply study for one of the design chosen. 4 cases involving opening and closing both valve or either one. 0.265m height size of customized waste valve with an opening limiter and spring was used to demonstrate cyclic closing and opening valve operation extended up to 0.164m gap. Based on result, this characteristics contribute to 10-20% waste water reduction and enhancement of flow rate height up to 80m. Apart from that this paper also share some of pressure (dynamic, total, static), velocity (x, y, z axis) simulation including the vector flow were under different flow cases.

Spreading of correlations in the Falicov-Kimball model

NASA Astrophysics Data System (ADS)

Herrmann, Andreas J.; Antipov, Andrey E.; Werner, Philipp

2018-04-01

We study dynamical properties of the one- and two-dimensional Falicov-Kimball model using lattice Monte Carlo simulations. In particular, we calculate the spreading of charge correlations in the equilibrium model and after an interaction quench. The results show a reduction of the light-cone velocity with interaction strength at low temperature, while the phase velocity increases. At higher temperature, the initial spreading is determined by the Fermi velocity of the noninteracting system and the maximum range of the correlations decreases with increasing interaction strength. Charge order correlations in the disorder potential enhance the range of the correlations. We also use the numerically exact lattice Monte Carlo results to benchmark the accuracy of equilibrium and nonequilibrium dynamical cluster approximation calculations. It is shown that the bias introduced by the mapping to a periodized cluster is substantial, and that from a numerical point of view, it is more efficient to simulate the lattice model directly.

The Slow Dynamics of Intracellular Sodium Concentration Increase the Time Window of Neuronal Integration: A Simulation Study

PubMed Central

Zylbertal, Asaph; Yarom, Yosef; Wagner, Shlomo

2017-01-01

Changes in intracellular Na+ concentration ([Na+]i) are rarely taken into account when neuronal activity is examined. As opposed to Ca2+, [Na+]i dynamics are strongly affected by longitudinal diffusion, and therefore they are governed by the morphological structure of the neurons, in addition to the localization of influx and efflux mechanisms. Here, we examined [Na+]i dynamics and their effects on neuronal computation in three multi-compartmental neuronal models, representing three distinct cell types: accessory olfactory bulb (AOB) mitral cells, cortical layer V pyramidal cells, and cerebellar Purkinje cells. We added [Na+]i as a state variable to these models, and allowed it to modulate the Na+ Nernst potential, the Na+-K+ pump current, and the Na+-Ca2+ exchanger rate. Our results indicate that in most cases [Na+]i dynamics are significantly slower than [Ca2+]i dynamics, and thus may exert a prolonged influence on neuronal computation in a neuronal type specific manner. We show that [Na+]i dynamics affect neuronal activity via three main processes: reduction of EPSP amplitude in repeatedly active synapses due to reduction of the Na+ Nernst potential; activity-dependent hyperpolarization due to increased activity of the Na+-K+ pump; specific tagging of active synapses by extended Ca2+ elevation, intensified by concurrent back-propagating action potentials or complex spikes. Thus, we conclude that [Na+]i dynamics should be considered whenever synaptic plasticity, extensive synaptic input, or bursting activity are examined. PMID:28970791

Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer†

PubMed Central

Song, Yuhua; Guallar, Victor; Baker, Nathan A.

2008-01-01

Salicylate, an amphiphilic molecule and a popular member of non-steroidal antiinflammatory drug family, is known to affect hearing through reduction of the electromechanical coupling in the outer hair cells of the ear. This reduction of electromotility by salicylate has been widely studied but the molecular mechanism of the phenomenon is still unknown. In this study, we investigated one aspect of salicylate’s action; namely, the perturbation of electrical and mechanical membrane properties by salicylate in the absence of cytoskeletal or membrane-bound motor proteins such as prestin. In particular, we simulated the interaction of salicylate with a dipalmitoylphosphatidylcholine (DPPC) bilayer via atomically-detailed molecular dynamics simulations to observe the effect of salicylate on the microscopic and mesoscopic properties of the bilayer. The results demonstrate that salicylate interacts with the bilayer by associating at the water-DPPC interface in a nearly perpendicular orientation and penetrating more deeply into the bilayer than either sodium or chloride. This association has several affects on the membrane properties. First, binding of salicylate to the membrane displaces chloride from the bilayer-water interface. Second, salicylate influences the electrostatic potential and dielectric properties of the bilayer, with significant changes at the water-lipid bilayer interface. Third, salicylate association results in structural changes including decreased head group area per lipid and increased lipid tail order. However, salicylate does not significantly alter the mechanical properties of the DPPC bilayer; bulk compressibility, area compressibility, and bending modulus were only perturbed by small, statistically-insignificant amounts, by the presence of salicylate. The observations from these simulations are in qualitative agreement with experimental data and support the conclusion that salicylate influences the electrical but not the mechanical properties of DPPC membranes. PMID:16216066

An Eigensystem Realization Algorithm (ERA) for modal parameter identification and model reduction

NASA Technical Reports Server (NTRS)

Juang, J. N.; Pappa, R. S.

1985-01-01

A method, called the Eigensystem Realization Algorithm (ERA), is developed for modal parameter identification and model reduction of dynamic systems from test data. A new approach is introduced in conjunction with the singular value decomposition technique to derive the basic formulation of minimum order realization which is an extended version of the Ho-Kalman algorithm. The basic formulation is then transformed into modal space for modal parameter identification. Two accuracy indicators are developed to quantitatively identify the system modes and noise modes. For illustration of the algorithm, examples are shown using simulation data and experimental data for a rectangular grid structure.

Nonlinear Reduced-Order Simulation Using An Experimentally Guided Modal Basis

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Przekop, Adam

2012-01-01

A procedure is developed for using nonlinear experimental response data to guide the modal basis selection in a nonlinear reduced-order simulation. The procedure entails using nonlinear acceleration response data to first identify proper orthogonal modes. Special consideration is given to cases in which some of the desired response data is unavailable. Bases consisting of linear normal modes are then selected to best represent the experimentally determined transverse proper orthogonal modes and either experimentally determined inplane proper orthogonal modes or the special case of numerically computed in-plane companions. The bases are subsequently used in nonlinear modal reduction and dynamic response simulations. The experimental data used in this work is simulated to allow some practical considerations, such as the availability of in-plane response data and non-idealized test conditions, to be explored. Comparisons of the nonlinear reduced-order simulations are made with the surrogate experimental data to demonstrate the effectiveness of the approach.

Helioseismology of a Realistic Magnetoconvective Sunspot Simulation

NASA Technical Reports Server (NTRS)

Braun, D. C.; Birch, A. C.; Rempel, M.; Duvall, T. L., Jr.

2012-01-01

We compare helioseismic travel-time shifts measured from a realistic magnetoconvective sunspot simulation using both helioseismic holography and time-distance helioseismology, and measured from real sunspots observed with the Helioseismic and Magnetic Imager instrument on board the Solar Dynamics Observatory and the Michelson Doppler Imager instrument on board the Solar and Heliospheric Observatory. We find remarkable similarities in the travel-time shifts measured between the methodologies applied and between the simulated and real sunspots. Forward modeling of the travel-time shifts using either Born or ray approximation kernels and the sound-speed perturbations present in the simulation indicates major disagreements with the measured travel-time shifts. These findings do not substantially change with the application of a correction for the reduction of wave amplitudes in the simulated and real sunspots. Overall, our findings demonstrate the need for new methods for inferring the subsurface structure of sunspots through helioseismic inversions.

Shock Simulations of Single-Site Coarse-Grain RDX using the Dissipative Particle Dynamics Method with Reactivity

NASA Astrophysics Data System (ADS)

Sellers, Michael; Lisal, Martin; Schweigert, Igor; Larentzos, James; Brennan, John

2015-06-01

In discrete particle simulations, when an atomistic model is coarse-grained, a trade-off is made: a boost in computational speed for a reduction in accuracy. Dissipative Particle Dynamics (DPD) methods help to recover accuracy in viscous and thermal properties, while giving back a small amount of computational speed. One of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. Today, pairing the current evolution of DPD-RX with a coarse-grained potential and its chemical decomposition reactions allows for the simulation of the shock behavior of energetic materials at a timescale faster than an atomistic counterpart. In 2007, Maillet et al. introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We have recently extended the DPD-RX method and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its tranition to hot product gases within DPD-RX will be presented. Additionally, examples of the effect of microstructure on shock behavior will be shown. Approved for public release. Distribution is unlimited.

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

PubMed Central

Stadlbauer, Petr; Krepl, Miroslav; Cheatham, Thomas E.; Koča, Jaroslav; Šponer, Jiří

2013-01-01

Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales. PMID:23700306

Flame Dynamics and Chemistry in LRE Combustion Instability

DTIC Science & Technology

2016-12-22

simulation conditions are as follows: the upper boundary consists of a mixture of DME, oxygen and nitrogen at a fixed temperature of 300 K, while the lower...Fig. 11 a. However, the reduction effect of increased oxygen con- centration on the cool flame extinction temperature is again over- predicted by... temperature chemistry and extends the hysteresis between ignition and Fig. 11. Ignition and extinction temperatures at various strain rates and oxygen

Probing aerosol indirect effect on deep convection using idealized cloud-resolving simulations with parameterized large-scale dynamics.

NASA Astrophysics Data System (ADS)

Anber, U.; Wang, S.; Gentine, P.; Jensen, M. P.

2017-12-01

A framework is introduced to investigate the indirect impact of aerosol loading on tropical deep convection using 3-dimentional idealized cloud-system resolving simulations with coupled large-scale circulation. The large scale dynamics is parameterized using a spectral weak temperature gradient approximation that utilizes the dominant balance in the tropics between adiabatic cooling and diabatic heating. Aerosol loading effect is examined by varying the number concentration of nuclei (CCN) to form cloud droplets in the bulk microphysics scheme over a wide range from 30 to 5000 without including any radiative effect as the radiative cooling is prescribed at a constant rate, to isolate the microphysical effect. Increasing aerosol number concentration causes mean precipitation to decrease monotonically, despite the increase in cloud condensates. Such reduction in precipitation efficiency is attributed to reduction in the surface enthalpy fluxes, and not to the divergent circulation, as the gross moist stability remains unchanged. We drive a simple scaling argument based on the moist static energy budget, that enables a direct estimation of changes in precipitation given known changes in surfaces enthalpy fluxes and the constant gross moist stability. The impact on cloud hydrometers and microphysical properties is also examined and is consistent with the macro-physical picture.

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.

Reduced Osteogenesis of Human Osteogenic Precursors' Cells Cultured in the Random Positioning Machine

NASA Astrophysics Data System (ADS)

Gershovich, J. G.; Buravkova, L. B.

2008-06-01

Recent studies have shown that simulated microgravity (SMG) results in altered proliferation and differentiation not only osteoblasts but also affects on osteogenic capacity of mesenchymal stem cells (MSCs) from various sources. For present study we used system that simulates effects of microgravity produced by the Random Positioning Machine (RPM). Cultured MCSs from human bone marrow and human osteoblasts (OBs) were exposed to SMG at RPM for 10-40 days. Induced osteogenesis of these progenitor cells was compared with the appropriate static (1g) and dynamic (horizontal shaker) controls. Clinorotated OBs and MSCs showed proliferation rate lower than static and dynamic control groups of cells in the early terms of SMG. Significant reduction of ALP activity was detected after 10 days of clinorotation of MSCs. There was no such dramatic difference in ALP activity of MSCs derived cells between SMG and control groups after 20 days of clinorotation but the expression of ALP was still reduced. However, virtually no matrix mineralization was found in OBs cultured under SMG conditions in the presence of differentiation stimuli. The similar effect was observed when we assayed matrix calcification of MSCs derived cultures. Thus, our results confirm low gravity mediated reduction of osteogenesis of different osteogenic precursors' cells and can clarify the mechanisms of bone loss during spaceflight.

High-Performance Integrated Control of water quality and quantity in urban water reservoirs

NASA Astrophysics Data System (ADS)

Galelli, S.; Castelletti, A.; Goedbloed, A.

2015-11-01

This paper contributes a novel High-Performance Integrated Control framework to support the real-time operation of urban water supply storages affected by water quality problems. We use a 3-D, high-fidelity simulation model to predict the main water quality dynamics and inform a real-time controller based on Model Predictive Control. The integration of the simulation model into the control scheme is performed by a model reduction process that identifies a low-order, dynamic emulator running 4 orders of magnitude faster. The model reduction, which relies on a semiautomatic procedural approach integrating time series clustering and variable selection algorithms, generates a compact and physically meaningful emulator that can be coupled with the controller. The framework is used to design the hourly operation of Marina Reservoir, a 3.2 Mm3 storm-water-fed reservoir located in the center of Singapore, operated for drinking water supply and flood control. Because of its recent formation from a former estuary, the reservoir suffers from high salinity levels, whose behavior is modeled with Delft3D-FLOW. Results show that our control framework reduces the minimum salinity levels by nearly 40% and cuts the average annual deficit of drinking water supply by about 2 times the active storage of the reservoir (about 4% of the total annual demand).

Multiple mechanisms of Amazonian forest biomass losses in three dynamic global vegetation models under climate change.

PubMed

Galbraith, David; Levy, Peter E; Sitch, Stephen; Huntingford, Chris; Cox, Peter; Williams, Mathew; Meir, Patrick

2010-08-01

*The large-scale loss of Amazonian rainforest under some future climate scenarios has generally been considered to be driven by increased drying over Amazonia predicted by some general circulation models (GCMs). However, the importance of rainfall relative to other drivers has never been formally examined. *Here, we conducted factorial simulations to ascertain the contributions of four environmental drivers (precipitation, temperature, humidity and CO(2)) to simulated changes in Amazonian vegetation carbon (C(veg)), in three dynamic global vegetation models (DGVMs) forced with climate data based on HadCM3 for four SRES scenarios. *Increased temperature was found to be more important than precipitation reduction in causing losses of Amazonian C(veg) in two DGVMs (Hyland and TRIFFID), and as important as precipitation reduction in a third DGVM (LPJ). Increases in plant respiration, direct declines in photosynthesis and increases in vapour pressure deficit (VPD) all contributed to reduce C(veg) under high temperature, but the contribution of each mechanism varied greatly across models. Rising CO(2) mitigated much of the climate-driven biomass losses in the models. *Additional work is required to constrain model behaviour with experimental data under conditions of high temperature and drought. Current models may be overly sensitive to long-term elevated temperatures as they do not account for physiological acclimation.

Low-dimensional modelling of a transient cylinder wake using double proper orthogonal decomposition

NASA Astrophysics Data System (ADS)

Siegel, Stefan G.; Seidel, J.?Rgen; Fagley, Casey; Luchtenburg, D. M.; Cohen, Kelly; McLaughlin, Thomas

For the systematic development of feedback flow controllers, a numerical model that captures the dynamic behaviour of the flow field to be controlled is required. This poses a particular challenge for flow fields where the dynamic behaviour is nonlinear, and the governing equations cannot easily be solved in closed form. This has led to many versions of low-dimensional modelling techniques, which we extend in this work to represent better the impact of actuation on the flow. For the benchmark problem of a circular cylinder wake in the laminar regime, we introduce a novel extension to the proper orthogonal decomposition (POD) procedure that facilitates mode construction from transient data sets. We demonstrate the performance of this new decomposition by applying it to a data set from the development of the limit cycle oscillation of a circular cylinder wake simulation as well as an ensemble of transient forced simulation results. The modes obtained from this decomposition, which we refer to as the double POD (DPOD) method, correctly track the changes of the spatial modes both during the evolution of the limit cycle and when forcing is applied by transverse translation of the cylinder. The mode amplitudes, which are obtained by projecting the original data sets onto the truncated DPOD modes, can be used to construct a dynamic mathematical model of the wake that accurately predicts the wake flow dynamics within the lock-in region at low forcing amplitudes. This low-dimensional model, derived using nonlinear artificial neural network based system identification methods, is robust and accurate and can be used to simulate the dynamic behaviour of the wake flow. We demonstrate this ability not just for unforced and open-loop forced data, but also for a feedback-controlled simulation that leads to a 90% reduction in lift fluctuations. This indicates the possibility of constructing accurate dynamic low-dimensional models for feedback control by using unforced and transient forced data only.

Energy consumption and CO{sub 2} emissions in Iran, 2025

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

Mirzaei, Maryam

Climate change and global warming as the key human societies' threats are essentially associated with energy consumption and CO{sub 2} emissions. A system dynamic model was developed in this study to model the energy consumption and CO{sub 2} emission trends for Iran over 2000–2025. Energy policy factors are considered in analyzing the impact of different energy consumption factors on environmental quality. The simulation results show that the total energy consumption is predicted to reach 2150 by 2025, while that value in 2010 is 1910, which increased by 4.3% yearly. Accordingly, the total CO{sub 2} emissions in 2025 will reach 985more » million tonnes, which shows about 5% increase yearly. Furthermore, we constructed policy scenarios based on energy intensity reduction. The analysis show that CO{sub 2} emissions will decrease by 12.14% in 2025 compared to 2010 in the scenario of 5% energy intensity reduction, and 17.8% in the 10% energy intensity reduction scenario. The results obtained in this study provide substantial awareness regarding Irans future energy and CO{sub 2} emission outlines. - Highlights: • Creation of an energy consumption model using system dynamics. • The effect of different policies on energy consumption and emission reductions. • An ascending trend for the environmental costs caused by CO{sub 2} emissions is observed. • An urgent need for energy saving and emission reductions in Iran.« less

Quantitative evaluation of thickness reduction in corroded steel plates using surface SH waves

NASA Astrophysics Data System (ADS)

Suzuki, Keigo; Ha, Nguyen Phuong; Otobe, Yuichi; Tamura, Hiroshi; Sasaki, Eiichi

2018-04-01

This study evaluates the effect of reduction in plate thickness for a steel plate existing in concrete on guided ultrasonic SH (g-SH) waves. It has been found that the time of flight (TOF) increases if the plate thickness is reduced. The parameter investigated in this study is a delay time obtained from a TOF comparison between a healthy and a damaged plate. The wave propagation is simulated by dynamic Finite Element Analysis (FEA). The resulting data are then used to propose a theoretical equation for predicting TOF. The prediction of delay time obtained from the proposed equation is found to be in general agreement, with an error of 10% (or less), when compared with the experiment results, if the thickness reduction is over 3.65mm.

Modulation of thermal conductivity in kinked silicon nanowires: phonon interchanging and pinching effects.

PubMed

Jiang, Jin-Wu; Yang, Nuo; Wang, Bing-Shen; Rabczuk, Timon

2013-04-10

We perform molecular dynamics simulations to investigate the reduction of the thermal conductivity by kinks in silicon nanowires. The reduction percentage can be as high as 70% at room temperature. The temperature dependence of the reduction is also calculated. By calculating phonon polarization vectors, two mechanisms are found to be responsible for the reduced thermal conductivity: (1) the interchanging effect between the longitudinal and transverse phonon modes and (2) the pinching effect, that is, a new type of localization, for the twisting and transverse phonon modes in the kinked silicon nanowires. Our work demonstrates that the phonon interchanging and pinching effects, induced by kinking, are brand-new and effective ways in modulating heat transfer in nanowires, which enables the kinked silicon nanowires to be a promising candidate for thermoelectric materials.

Simulating Forest Carbon Dynamics in Response to Large-scale Fuel Reduction Treatments Under Projected Climate-fire Interactions in the Sierra Nevada Mountains, USA

NASA Astrophysics Data System (ADS)

Liang, S.; Hurteau, M. D.

2016-12-01

The interaction of warmer, drier climate and increasing large wildfires, coupled with increasing fire severity resulting from fire-exclusion are anticipated to undermine forest carbon (C) stock stability and C sink strength in the Sierra Nevada forests. Treatments, including thinning and prescribed burning, to reduce biomass and restore forest structure have proven effective at reducing fire severity and lessening C loss when treated stands are burned by wildfire. However, the current pace and scale of treatment implementation is limited, especially given recent increases in area burned by wildfire. In this study, we used a forest landscape model (LANDIS-II) to evaluate the role of implementation timing of large-scale fuel reduction treatments in influencing forest C stock and fluxes of Sierra Nevada forests with projected climate and larger wildfires. We ran 90-year simulations using climate and wildfire projections from three general circulation models driven by the A2 emission scenario. We simulated two different treatment implementation scenarios: a `distributed' (treatments implemented throughout the simulation) and an `accelerated' (treatments implemented during the first half century) scenario. We found that across the study area, accelerated implementation had 0.6-10.4 Mg ha-1 higher late-century aboveground biomass (AGB) and 1.0-2.2 g C m-2 yr-1 higher mean C sink strength than the distributed scenario, depending on specific climate-wildfire projections. Cumulative wildfire emissions over the simulation period were 0.7-3.9 Mg C ha-1 higher for distributed implementation relative to accelerated implementation. However, simulations with both implementation practices have considerably higher AGB and C sink strength as well as lower wildfire emission than simulations in the absence of fuel reduction treatments. The results demonstrate the potential for implementing large-scale fuel reduction treatments to enhance forest C stock stability and C sink strength under projected climate-wildfire interactions. Given climate and wildfire would become more stressful since the mid-century, a forward management action would grant us more C benefits.

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER [Book Chapter

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

D'Azevedo, Eduardo; Abbott, Stephen; Koskela, Tuomas

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning for balancing computational work in pushing particlesmore » and in grid related work, scalable and accurate discretization algorithms for non-linear Coulomb collisions, and communication-avoiding subcycling technology for pushing particles on both CPUs and GPUs are also utilized to dramatically improve the scalability and time-to-solution, hence enabling the difficult kinetic ITER edge simulation on a present-day leadership class computer.« less

Theory of activated glassy dynamics in randomly pinned fluids.

PubMed

Phan, Anh D; Schweizer, Kenneth S

2018-02-07

We generalize the force-level, microscopic, Nonlinear Langevin Equation (NLE) theory and its elastically collective generalization [elastically collective nonlinear Langevin equation (ECNLE) theory] of activated dynamics in bulk spherical particle liquids to address the influence of random particle pinning on structural relaxation. The simplest neutral confinement model is analyzed for hard spheres where there is no change of the equilibrium pair structure upon particle pinning. As the pinned fraction grows, cage scale dynamical constraints are intensified in a manner that increases with density. This results in the mobile particles becoming more transiently localized, with increases of the jump distance, cage scale barrier, and NLE theory mean hopping time; subtle changes of the dynamic shear modulus are predicted. The results are contrasted with recent simulations. Similarities in relaxation behavior are identified in the dynamic precursor regime, including a roughly exponential, or weakly supra-exponential, growth of the alpha time with pinning fraction and a reduction of dynamic fragility. However, the increase of the alpha time with pinning predicted by the local NLE theory is too small and severely so at very high volume fractions. The strong deviations are argued to be due to the longer range collective elasticity aspect of the problem which is expected to be modified by random pinning in a complex manner. A qualitative physical scenario is offered for how the three distinct aspects that quantify the elastic barrier may change with pinning. ECNLE theory calculations of the alpha time are then presented based on the simplest effective-medium-like treatment for how random pinning modifies the elastic barrier. The results appear to be consistent with most, but not all, trends seen in recent simulations. Key open problems are discussed with regard to both theory and simulation.

Theory of activated glassy dynamics in randomly pinned fluids

NASA Astrophysics Data System (ADS)

Phan, Anh D.; Schweizer, Kenneth S.

2018-02-01

We generalize the force-level, microscopic, Nonlinear Langevin Equation (NLE) theory and its elastically collective generalization [elastically collective nonlinear Langevin equation (ECNLE) theory] of activated dynamics in bulk spherical particle liquids to address the influence of random particle pinning on structural relaxation. The simplest neutral confinement model is analyzed for hard spheres where there is no change of the equilibrium pair structure upon particle pinning. As the pinned fraction grows, cage scale dynamical constraints are intensified in a manner that increases with density. This results in the mobile particles becoming more transiently localized, with increases of the jump distance, cage scale barrier, and NLE theory mean hopping time; subtle changes of the dynamic shear modulus are predicted. The results are contrasted with recent simulations. Similarities in relaxation behavior are identified in the dynamic precursor regime, including a roughly exponential, or weakly supra-exponential, growth of the alpha time with pinning fraction and a reduction of dynamic fragility. However, the increase of the alpha time with pinning predicted by the local NLE theory is too small and severely so at very high volume fractions. The strong deviations are argued to be due to the longer range collective elasticity aspect of the problem which is expected to be modified by random pinning in a complex manner. A qualitative physical scenario is offered for how the three distinct aspects that quantify the elastic barrier may change with pinning. ECNLE theory calculations of the alpha time are then presented based on the simplest effective-medium-like treatment for how random pinning modifies the elastic barrier. The results appear to be consistent with most, but not all, trends seen in recent simulations. Key open problems are discussed with regard to both theory and simulation.

Distributed and dynamic modelling of hydrology, phosphorus and ecology in the Hampshire Avon and Blashford Lakes: evaluating alternative strategies to meet WFD standards.

PubMed

Whitehead, P G; Jin, L; Crossman, J; Comber, S; Johnes, P J; Daldorph, P; Flynn, N; Collins, A L; Butterfield, D; Mistry, R; Bardon, R; Pope, L; Willows, R

2014-05-15

The issues of diffuse and point source phosphorus (P) pollution in the Hampshire Avon and Blashford Lakes are explored using a catchment model of the river system. A multibranch, process based, dynamic water quality model (INCA-P) has been applied to the whole river system to simulate water fluxes, total phosphorus (TP) and soluble reactive phosphorus (SRP) concentrations and ecology. The model has been used to assess impacts of both agricultural runoff and point sources from waste water treatment plants (WWTPs) on water quality. The results show that agriculture contributes approximately 40% of the phosphorus load and point sources the other 60% of the load in this catchment. A set of scenarios have been investigated to assess the impacts of alternative phosphorus reduction strategies and it is shown that a combined strategy of agricultural phosphorus reduction through either fertiliser reductions or better phosphorus management together with improved treatment at WWTPs would reduce the SRP concentrations in the river to acceptable levels to meet the EU Water Framework Directive (WFD) requirements. A seasonal strategy for WWTP phosphorus reductions would achieve significant benefits at reduced cost. Copyright © 2014 Elsevier B.V. All rights reserved.

An analytical bond-order potential for carbon

DOE PAGES

Zhou, Xiaowang; Ward, Donald K.; Foster, Michael E.

2015-05-27

Carbon is the most widely studied material today because it exhibits special properties not seen in any other materials when in nano dimensions such as nanotube and graphene. Reduction of material defects created during synthesis has become critical to realize the full potential of carbon structures. Molecular dynamics (MD) simulations, in principle, allow defect formation mechanisms to be studied with high fidelity, and can, therefore, help guide experiments for defect reduction. Such MD simulations must satisfy a set of stringent requirements. First, they must employ an interatomic potential formalism that is transferable to a variety of carbon structures. Second, themore » potential needs to be appropriately parameterized to capture the property trends of important carbon structures, in particular, diamond, graphite, graphene, and nanotubes. The potential must predict the crystalline growth of the correct phases during direct MD simulations of synthesis to achieve a predictive simulation of defect formation. An unlimited number of structures not included in the potential parameterization are encountered, thus the literature carbon potentials are often not sufficient for growth simulations. We have developed an analytical bond order potential for carbon, and have made it available through the public MD simulation package LAMMPS. We also demonstrate that our potential reasonably captures the property trends of important carbon phases. As a result, stringent MD simulations convincingly show that our potential accounts not only for the crystalline growth of graphene, graphite, and carbon nanotubes but also for the transformation of graphite to diamond at high pressure.« less

An analytical bond-order potential for carbon.

PubMed

Zhou, X W; Ward, D K; Foster, M E

2015-09-05

Carbon is the most widely studied material today because it exhibits special properties not seen in any other materials when in nano dimensions such as nanotube and graphene. Reduction of material defects created during synthesis has become critical to realize the full potential of carbon structures. Molecular dynamics (MD) simulations, in principle, allow defect formation mechanisms to be studied with high fidelity, and can, therefore, help guide experiments for defect reduction. Such MD simulations must satisfy a set of stringent requirements. First, they must employ an interatomic potential formalism that is transferable to a variety of carbon structures. Second, the potential needs to be appropriately parameterized to capture the property trends of important carbon structures, in particular, diamond, graphite, graphene, and nanotubes. Most importantly, the potential must predict the crystalline growth of the correct phases during direct MD simulations of synthesis to achieve a predictive simulation of defect formation. Because an unlimited number of structures not included in the potential parameterization are encountered, the literature carbon potentials are often not sufficient for growth simulations. We have developed an analytical bond order potential for carbon, and have made it available through the public MD simulation package LAMMPS. We demonstrate that our potential reasonably captures the property trends of important carbon phases. Stringent MD simulations convincingly show that our potential accounts not only for the crystalline growth of graphene, graphite, and carbon nanotubes but also for the transformation of graphite to diamond at high pressure. © 2015 Wiley Periodicals, Inc.

Post-processing interstitialcy diffusion from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bhardwaj, U.; Bukkuru, S.; Warrier, M.

2016-01-01

An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms.

Multistage reaction pathways in detonating high explosives

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; CACS Collaboration; ALCF Team

2015-06-01

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N2 and H2O within 10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct uni-molecular and intermolecular reaction pathways, respectively, for the rapid N2 and H2O productions. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555 and the Basic Research Program of Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-08-1-0036. All the simulations were performed at USC and Argonne LCF.

Post-processing interstitialcy diffusion from molecular dynamics simulations

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

Bhardwaj, U., E-mail: haptork@gmail.com; Bukkuru, S.; Warrier, M.

2016-01-15

An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures ismore » studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.« less

Numerical study of the magnetized friction force

NASA Astrophysics Data System (ADS)

Fedotov, A. V.; Bruhwiler, D. L.; Sidorin, A. O.; Abell, D. T.; Ben-Zvi, I.; Busby, R.; Cary, J. R.; Litvinenko, V. N.

2006-07-01

Fundamental advances in experimental nuclear physics will require ion beams with orders of magnitude luminosity increase and temperature reduction. One of the most promising particle accelerator techniques for achieving these goals is electron cooling, where the ion beam repeatedly transfers thermal energy to a copropagating electron beam. The dynamical friction force on a fully ionized gold ion moving through magnetized and unmagnetized electron distributions has been simulated, using molecular dynamics techniques that resolve close binary collisions. We present a comprehensive examination of theoretical models in use by the electron cooling community. Differences in these models are clarified, enabling the accurate design of future electron cooling systems for relativistic ion accelerators.

Dynamical behavior of susceptible-infected-recovered-susceptible epidemic model on weighted networks

NASA Astrophysics Data System (ADS)

Wu, Qingchu; Zhang, Fei

2018-02-01

We study susceptible-infected-recovered-susceptible epidemic model in weighted, regular, and random complex networks. We institute a pairwise-type mathematical model with a general transmission rate to evaluate the influence of the link-weight distribution on the spreading process. Furthermore, we develop a dimensionality reduction approach to derive the condition for the contagion outbreak. Finally, we analyze the influence of the heterogeneity of weight distribution on the outbreak condition for the scenario with a linear transmission rate. Our theoretical analysis is in agreement with stochastic simulations, showing that the heterogeneity of link-weight distribution can have a significant effect on the epidemic dynamics.

Damage-mitigating control of space propulsion systems for high performance and extended life

NASA Technical Reports Server (NTRS)

Ray, Asok; Wu, Min-Kuang; Dai, Xiaowen; Carpino, Marc; Lorenzo, Carl F.

1993-01-01

Calculations are presented showing that a substantial improvement in service life of a reusable rocket engine can be achieved by an insignificant reduction in the system dynamic performance. The paper introduces the concept of damage mitigation and formulates a continuous-time model of fatigue damage dynamics. For control of complex mechanical systems, damage prediction and damage mitigation are carried out based on the available sensory and operational information such that the plant can be inexpensively maintained and safely and efficiently steered under diverse operating conditions. The results of simulation experiments are presented for transient operations of a reusable rocket engine.

Mechanistic insights into electrochemical reduction of CO 2 over Ag using density functional theory and transport models

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

Singh, Meenesh R.; Goodpaster, Jason D.; Weber, Adam Z.

Electrochemical reduction of CO 2 using renewable sources of electrical energy holds promise for converting CO 2 to fuels and chemicals. Since this process is complex and involves a large number of species and physical phenomena, a comprehensive understanding of the factors controlling product distribution is required. While the most plausible reaction pathway is usually identified from quantum-chemical calculation of the lowest free-energy pathway, this approach can be misleading when coverages of adsorbed species determined for alternative mechanism differ significantly, since elementary reaction rates depend on the product of the rate coefficient and the coverage of species involved in themore » reaction. Moreover, cathode polarization can influence the kinetics of CO 2 reduction. Here in this work, we present a multiscale framework for ab initio simulation of the electrochemical reduction of CO 2 over an Ag(110) surface. A continuum model for species transport is combined with a microkinetic model for the cathode reaction dynamics. Free energies of activation for all elementary reactions are determined from density functional theory calculations. Using this approach, three alternative mechanisms for CO 2 reduction were examined. The rate-limiting step in each mechanism is **COOH formation at higher negative potentials. However, only via the multiscale simulation was it possible to identify the mechanism that leads to a dependence of the rate of CO formation on the partial pressure of CO 2 that is consistent with experiments. Additionally, simulations based on this mechanism also describe the dependence of the H 2 and CO current densities on cathode voltage that are in strikingly good agreement with experimental observation.« less

Mechanistic insights into electrochemical reduction of CO 2 over Ag using density functional theory and transport models

DOE PAGES

Singh, Meenesh R.; Goodpaster, Jason D.; Weber, Adam Z.; ...

2017-10-02

Electrochemical reduction of CO 2 using renewable sources of electrical energy holds promise for converting CO 2 to fuels and chemicals. Since this process is complex and involves a large number of species and physical phenomena, a comprehensive understanding of the factors controlling product distribution is required. While the most plausible reaction pathway is usually identified from quantum-chemical calculation of the lowest free-energy pathway, this approach can be misleading when coverages of adsorbed species determined for alternative mechanism differ significantly, since elementary reaction rates depend on the product of the rate coefficient and the coverage of species involved in themore » reaction. Moreover, cathode polarization can influence the kinetics of CO 2 reduction. Here in this work, we present a multiscale framework for ab initio simulation of the electrochemical reduction of CO 2 over an Ag(110) surface. A continuum model for species transport is combined with a microkinetic model for the cathode reaction dynamics. Free energies of activation for all elementary reactions are determined from density functional theory calculations. Using this approach, three alternative mechanisms for CO 2 reduction were examined. The rate-limiting step in each mechanism is **COOH formation at higher negative potentials. However, only via the multiscale simulation was it possible to identify the mechanism that leads to a dependence of the rate of CO formation on the partial pressure of CO 2 that is consistent with experiments. Additionally, simulations based on this mechanism also describe the dependence of the H 2 and CO current densities on cathode voltage that are in strikingly good agreement with experimental observation.« less

A generic multi-flex-body dynamics, controls simulation tool for space station

NASA Technical Reports Server (NTRS)

London, Ken W.; Lee, John F.; Singh, Ramen P.; Schubele, Buddy

1991-01-01

An order (n) multiflex body Space Station simulation tool is introduced. The flex multibody modeling is generic enough to model all phases of Space Station from build up through to Assembly Complete configuration and beyond. Multibody subsystems such as the Mobile Servicing System (MSS) undergoing a prescribed translation and rotation are also allowed. The software includes aerodynamic, gravity gradient, and magnetic field models. User defined controllers can be discrete or continuous. Extensive preprocessing of 'body by body' NASTRAN flex data is built in. A significant aspect, too, is the integrated controls design capability which includes model reduction and analytic linearization.

Design, construction and measurements of an alpha magnet as a solution for compact bunch compressor for the electron beam from Thermionic RF Gun

NASA Astrophysics Data System (ADS)

Rajabi, A.; Jazini, J.; Fathi, M.; Sharifian, M.; Shokri, B.

2018-03-01

The beam produced by a thermionic RF gun has wide energy spread that makes it unsuitable for direct usage in photon sources. Here in the present work, we optimize the extracted beam from a thermionic RF gun by a compact economical bunch compressor. A compact magnetic bunch compressor (Alpha magnet) is designed and constructed. A comparison between simulation results and experimental measurements shows acceptable conformity. The beam dynamics simulation results show a reduction of the energy spread as well as a compression of length less than 1 ps with 2.3 mm-mrad emittance.

Efficient direct yaw moment control: tyre slip power loss minimisation for four-independent wheel drive vehicle

NASA Astrophysics Data System (ADS)

Kobayashi, Takao; Katsuyama, Etsuo; Sugiura, Hideki; Ono, Eiichi; Yamamoto, Masaki

2018-05-01

This paper proposes an efficient direct yaw moment control (DYC) capable of minimising tyre slip power loss on contact patches for a four-independent wheel drive vehicle. Simulations identified a significant power loss reduction with a direct yaw moment due to a change in steer characteristics during acceleration or deceleration while turning. Simultaneously, the vehicle motion can be stabilised. As a result, the proposed control method can ensure compatibility between vehicle dynamics performance and energy efficiency. This paper also describes the results of a full-vehicle simulation that was conducted to examine the effectiveness of the proposed DYC.

Localization of vibrational modes leads to reduced thermal conductivity of amorphous heterostructures

NASA Astrophysics Data System (ADS)

Giri, Ashutosh; Donovan, Brian F.; Hopkins, Patrick E.

2018-05-01

We investigate the vibrational heat transfer mechanisms in amorphous Stillinger-Weber silicon and germanium-based alloys and heterostructures via equilibrium and nonequilibrium molecular dynamics simulations along with lattice dynamics calculations. We find that similar to crystalline alloys, amorphous alloys demonstrate large size effects in thermal conductivity, while layering the constituent materials into superlattice structures leads to length-independent thermal conductivities. The thermal conductivity of an amorphous SixGe1 -x alloy reduces by as much as ˜53 % compared to the thermal conductivity of amorphous silicon; compared to the larger reduction in crystalline phases due to alloying, we show that compositional disorder rather than structural disorder has a larger impact on the thermal conductivity reduction. Our thermal conductivity predictions for a-Si/a-Ge superlattices suggest that the alloy limit in amorphous SiGe-based structures can be surpassed with interface densities above ˜0.35 nm-1 . We attribute the larger reduction in thermal conductivity of layered Si/Ge heterostructures to greater localization of modes at and around the cutoff frequency of the softer layer as demonstrated via lattice dynamics calculations and diffusivities of individual eigenmodes calculated according to the Allen-Feldman theory [P. B. Allen and J. L. Feldman, Phys. Rev. B 48, 12581 (1993), 10.1103/PhysRevB.48.12581] for our amorphous SiGe-based alloys and superlattice structures.

Relevance of aerodynamic modelling for load reduction control strategies of two-bladed wind turbines

NASA Astrophysics Data System (ADS)

Luhmann, B.; Cheng, P. W.

2014-06-01

A new load reduction concept is being developed for the two-bladed prototype of the Skywind 3.5MW wind turbine. Due to transport and installation advantages both offshore and in complex terrain two-bladed turbine designs are potentially more cost-effective than comparable three-bladed configurations. A disadvantage of two-bladed wind turbines is the increased fatigue loading, which is a result of asymmetrically distributed rotor forces. The innovative load reduction concept of the Skywind prototype consists of a combination of cyclic pitch control and tumbling rotor kinematics to mitigate periodic structural loading. Aerodynamic design tools must be able to model correctly the advanced dynamics of the rotor. In this paper the impact of the aerodynamic modelling approach is investigated for critical operational modes of a two-bladed wind turbine. Using a lifting line free wake vortex code (FVM) the physical limitations of the classical blade element momentum theory (BEM) can be evaluated. During regular operation vertical shear and yawed inflow are the main contributors to periodic blade load asymmetry. It is shown that the near wake interaction of the blades under such conditions is not fully captured by the correction models of BEM approach. The differing prediction of local induction causes a high fatigue load uncertainty especially for two-bladed turbines. The implementation of both cyclic pitch control and a tumbling rotor can mitigate the fatigue loading by increasing the aerodynamic and structural damping. The influence of the time and space variant vorticity distribution in the near wake is evaluated in detail for different cyclic pitch control functions and tumble dynamics respectively. It is demonstrated that dynamic inflow as well as wake blade interaction have a significant impact on the calculated blade forces and need to be accounted for by the aerodynamic modelling approach. Aeroelastic simulations are carried out using the high fidelity multi body simulation software SIMPACK. The aerodynamic loads are calculated using ECN's AeroModule and NREL's BEM code Aerodynl3.

A methodology towards virtualisation-based high performance simulation platform supporting multidisciplinary design of complex products

NASA Astrophysics Data System (ADS)

Ren, Lei; Zhang, Lin; Tao, Fei; (Luke) Zhang, Xiaolong; Luo, Yongliang; Zhang, Yabin

2012-08-01

Multidisciplinary design of complex products leads to an increasing demand for high performance simulation (HPS) platforms. One great challenge is how to achieve high efficient utilisation of large-scale simulation resources in distributed and heterogeneous environments. This article reports a virtualisation-based methodology to realise a HPS platform. This research is driven by the issues concerning large-scale simulation resources deployment and complex simulation environment construction, efficient and transparent utilisation of fine-grained simulation resources and high reliable simulation with fault tolerance. A framework of virtualisation-based simulation platform (VSIM) is first proposed. Then the article investigates and discusses key approaches in VSIM, including simulation resources modelling, a method to automatically deploying simulation resources for dynamic construction of system environment, and a live migration mechanism in case of faults in run-time simulation. Furthermore, the proposed methodology is applied to a multidisciplinary design system for aircraft virtual prototyping and some experiments are conducted. The experimental results show that the proposed methodology can (1) significantly improve the utilisation of fine-grained simulation resources, (2) result in a great reduction in deployment time and an increased flexibility for simulation environment construction and (3)achieve fault tolerant simulation.

The role of riparian vegetation density, channel orientation and water velocity in determining river temperature dynamics

NASA Astrophysics Data System (ADS)

Garner, Grace; Malcolm, Iain A.; Sadler, Jonathan P.; Hannah, David M.

2017-10-01

A simulation experiment was used to understand the importance of riparian vegetation density, channel orientation and flow velocity for stream energy budgets and river temperature dynamics. Water temperature and meteorological observations were obtained in addition to hemispherical photographs along a ∼1 km reach of the Girnock Burn, a tributary of the Aberdeenshire Dee, Scotland. Data from nine hemispherical images (representing different uniform canopy density scenarios) were used to parameterise a deterministic net radiation model and simulate radiative fluxes. For each vegetation scenario, the effects of eight channel orientations were investigated by changing the position of north at 45° intervals in each hemispheric image. Simulated radiative fluxes and observed turbulent fluxes drove a high-resolution water temperature model of the reach. Simulations were performed under low and high water velocity scenarios. Both velocity scenarios yielded decreases in mean (≥1.6 °C) and maximum (≥3.0 °C) temperature as canopy density increased. Slow-flowing water resided longer within the reach, which enhanced heat accumulation and dissipation, and drove higher maximum and lower minimum temperatures. Intermediate levels of shade produced highly variable energy flux and water temperature dynamics depending on the channel orientation and thus the time of day when the channel was shaded. We demonstrate that in many reaches relatively sparse but strategically located vegetation could produce substantial reductions in maximum temperature and suggest that these criteria are used to inform future river management.

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase

PubMed Central

Pisliakov, Andrei V.; Hino, Tomoya; Shiro, Yoshitsugu; Sugita, Yuji

2012-01-01

Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N2O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb 3 oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed. PMID:22956904

Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems.

PubMed

Winkelmann, Stefanie; Schütte, Christof

2017-09-21

Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations.

Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems

NASA Astrophysics Data System (ADS)

Winkelmann, Stefanie; Schütte, Christof

2017-09-01

Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations.

Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: A Raman scattering and molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Lerbret, A.; Affouard, F.; Bordat, P.; Hédoux, A.; Guinet, Y.; Descamps, M.

2009-12-01

The low-frequency (ω <400 cm-1) vibrational properties of lysozyme in aqueous solutions of three well-known protecting sugars, namely, trehalose, maltose, and sucrose, have been investigated by means of complementary Raman scattering experiments and molecular dynamics simulations. The comparison of the Raman susceptibility χ″(ω) of lysozyme/water and lysozyme/sugar/water solutions at a concentration of 40 wt % with the χ″ of dry lysozyme suggests that the protein dynamics mostly appears in the broad peak around 60-80 cm-1 that reflects the vibrations experienced by atoms within the cage formed by their neighbors, whereas the broad shoulder around 170 cm-1 mainly stems from the intermolecular O-H⋯O stretching vibrations of water. The addition of sugars essentially induces a significant high frequency shift and intensity reduction of this band that reveal a slowing down of water dynamics and a distortion of the tetrahedral hydrogen bond network of water, respectively. Furthermore, the lysozyme vibrational densities of states (VDOS) have been determined from simulations of lysozyme in 37-60 wt % disaccharide aqueous solutions. They exhibit an additional broad peak around 290 cm-1, in line with the VDOS of globular proteins obtained in neutron scattering experiments. The influence of sugars on the computed VDOS mostly appears on the first peak as a slight high-frequency shift and intensity reduction in the low-frequency range (ω <50 cm-1), which increase with the sugar concentration and with the exposition of protein residues to the solvent. These results suggest that sugars stiffen the environment experienced by lysozyme atoms, thereby counteracting the softening of protein vibrational modes upon denaturation, observed at high temperature in the Raman susceptibility of the lysozyme/water solution and in the computed VDOS of unfolded lysozyme in water. Finally, the Raman susceptibility of sugar/water solutions and the calculated VDOS of water in the different lysozyme solutions confirm that sugars induce a significant strengthening of the hydrogen bond network of water that may stabilize proteins at high temperatures.

Evaluation of Active Damping for Reduction of Noise, Vibration and Motion of Ground Vehicles by Multibody Simulation

DTIC Science & Technology

2004-10-01

practical applications of the technology in road vehicles. Active dampers based on several mechanical principles are available on the market ...between sportive and comfortable operating modes. A second type is the feedback of vehicle motion and, consequently, a dynamic suspension control...of-the-art in railway and automotive applications and have found an, albeit yet small, market . Typical representatives of semi-active devices are

Solving Operational Models of Interdependent Infrastructure Systems

DTIC Science & Technology

2014-12-01

resilience, getting the biggest “reduction in bang ” for their buck. The most important part of those modeling efforts is the formulation of a mathematical...about the requirements of each system to the model of the other system through shared data. This type of algorithm simulates the dynamic...than just another big project. I found a true interest and excitement working with you both and consider you both the highest caliber faculty I have

Laser interferometer space antenna dynamics and controls model

NASA Astrophysics Data System (ADS)

Maghami, Peiman G.; Tupper Hyde, T.

2003-05-01

A 19 degree-of-freedom (DOF) dynamics and controls model of a laser interferometer space antenna (LISA) spacecraft has been developed. This model is used to evaluate the feasibility of the dynamic pointing and positioning requirements of a typical LISA spacecraft. These requirements must be met for LISA to be able to successfully detect gravitational waves in the frequency band of interest (0.1-100 mHz). The 19-DOF model includes all rigid-body degrees of freedom. A number of disturbance sources, both internal and external, are included. Preliminary designs for the four control systems that comprise the LISA disturbance reduction system (DRS) have been completed and are included in the model. Simulation studies are performed to demonstrate that the LISA pointing and positioning requirements are feasible and can be met.

Active magnetic damper in a power transmission system

NASA Astrophysics Data System (ADS)

Kozanecka, D.; Kozanecki, Z.; Łagodziński, J.

2011-05-01

In rotor dynamics, the bearing characteristics exerts a decisive influence on dynamics of the rotating shaft. The research and application experience have led to active magnetic bearings (AMBs), which allow for unique applications in rotating systems. The paper presents the investigations concerning optimization of the magnetic bearing construction. An active magnetic bearing operates as a radial, auxiliary damper, which cooperates with the long, flexible shaft line (aircraft industry applications) and modifies its dynamic properties. In the developed concept of AMBs for aviation purposes, a necessity of increasing its bearing load capacity and damping has occurred. The second important criterion is a weight reduction. This advanced problem leads to specific requirements on the design and materials for the AMB. To achieve these goals, some simulations have been performed. The experimental results are presented as well.

Cavity hydration dynamics in cytochrome c oxidase and functional implications

PubMed Central

Son, Chang Yun; Cui, Qiang

2017-01-01

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport. PMID:28973914

Dynamic statistical optimization of GNSS radio occultation bending angles: advanced algorithm and performance analysis

NASA Astrophysics Data System (ADS)

Li, Y.; Kirchengast, G.; Scherllin-Pirscher, B.; Norman, R.; Yuan, Y. B.; Fritzer, J.; Schwaerz, M.; Zhang, K.

2015-08-01

We introduce a new dynamic statistical optimization algorithm to initialize ionosphere-corrected bending angles of Global Navigation Satellite System (GNSS)-based radio occultation (RO) measurements. The new algorithm estimates background and observation error covariance matrices with geographically varying uncertainty profiles and realistic global-mean correlation matrices. The error covariance matrices estimated by the new approach are more accurate and realistic than in simplified existing approaches and can therefore be used in statistical optimization to provide optimal bending angle profiles for high-altitude initialization of the subsequent Abel transform retrieval of refractivity. The new algorithm is evaluated against the existing Wegener Center Occultation Processing System version 5.6 (OPSv5.6) algorithm, using simulated data on two test days from January and July 2008 and real observed CHAllenging Minisatellite Payload (CHAMP) and Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) measurements from the complete months of January and July 2008. The following is achieved for the new method's performance compared to OPSv5.6: (1) significant reduction of random errors (standard deviations) of optimized bending angles down to about half of their size or more; (2) reduction of the systematic differences in optimized bending angles for simulated MetOp data; (3) improved retrieval of refractivity and temperature profiles; and (4) realistically estimated global-mean correlation matrices and realistic uncertainty fields for the background and observations. Overall the results indicate high suitability for employing the new dynamic approach in the processing of long-term RO data into a reference climate record, leading to well-characterized and high-quality atmospheric profiles over the entire stratosphere.

A Probabilistic Framework for Constructing Temporal Relations in Replica Exchange Molecular Trajectories.

PubMed

Chattopadhyay, Aditya; Zheng, Min; Waller, Mark Paul; Priyakumar, U Deva

2018-05-23

Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations. However, such methods fall short in analyzing trajectories with partial or no temporal information, for example, replica exchange molecular dynamics or Monte Carlo simulations. In this work we propose a probabilistic algorithm, borrowing concepts from graph theory and machine learning, to extract reactive pathways from molecular trajectories in the absence of temporal data. A suitable vector representation was chosen to represent each frame in the macromolecular trajectory (as a series of interaction and conformational energies) and dimensionality reduction was performed using principal component analysis (PCA). The trajectory was then clustered using a density-based clustering algorithm, where each cluster represents a metastable state on the potential energy surface (PES) of the biomolecule under study. A graph was created with these clusters as nodes with the edges learnt using an iterative expectation maximization algorithm. The most reactive path is conceived as the widest path along this graph. We have tested our method on RNA hairpin unfolding trajectory in aqueous urea solution. Our method makes the understanding of the mechanism of unfolding in RNA hairpin molecule more tractable. As this method doesn't rely on temporal data it can be used to analyze trajectories from Monte Carlo sampling techniques and replica exchange molecular dynamics (REMD).

Revisiting ocean carbon sequestration by direct injection: a global carbon budget perspective

NASA Astrophysics Data System (ADS)

Reith, Fabian; Keller, David P.; Oschlies, Andreas

2016-11-01

In this study we look beyond the previously studied effects of oceanic CO2 injections on atmospheric and oceanic reservoirs and also account for carbon cycle and climate feedbacks between the atmosphere and the terrestrial biosphere. Considering these additional feedbacks is important since backfluxes from the terrestrial biosphere to the atmosphere in response to reducing atmospheric CO2 can further offset the targeted reduction. To quantify these dynamics we use an Earth system model of intermediate complexity to simulate direct injection of CO2 into the deep ocean as a means of emissions mitigation during a high CO2 emission scenario. In three sets of experiments with different injection depths, we simulate a 100-year injection period of a total of 70 GtC and follow global carbon cycle dynamics over another 900 years. In additional parameter perturbation runs, we varied the default terrestrial photosynthesis CO2 fertilization parameterization by ±50 % in order to test the sensitivity of this uncertain carbon cycle feedback to the targeted atmospheric carbon reduction through direct CO2 injections. Simulated seawater chemistry changes and marine carbon storage effectiveness are similar to previous studies. As expected, by the end of the injection period avoided emissions fall short of the targeted 70 GtC by 16-30 % as a result of carbon cycle feedbacks and backfluxes in both land and ocean reservoirs. The target emissions reduction in the parameter perturbation simulations is about 0.2 and 2 % more at the end of the injection period and about 9 % less to 1 % more at the end of the simulations when compared to the unperturbed injection runs. An unexpected feature is the effect of the model's internal variability of deep-water formation in the Southern Ocean, which, in some model runs, causes additional oceanic carbon uptake after injection termination relative to a control run without injection and therefore with slightly different atmospheric CO2 and climate. These results of a model that has very low internal climate variability illustrate that the attribution of carbon fluxes and accounting for injected CO2 may be very challenging in the real climate system with its much larger internal variability.

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

PubMed Central

Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

2013-01-01

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

Final Report. Analysis and Reduction of Complex Networks Under Uncertainty

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

Marzouk, Youssef M.; Coles, T.; Spantini, A.

2013-09-30

The project was a collaborative effort among MIT, Sandia National Laboratories (local PI Dr. Habib Najm), the University of Southern California (local PI Prof. Roger Ghanem), and The Johns Hopkins University (local PI Prof. Omar Knio, now at Duke University). Our focus was the analysis and reduction of large-scale dynamical systems emerging from networks of interacting components. Such networks underlie myriad natural and engineered systems. Examples important to DOE include chemical models of energy conversion processes, and elements of national infrastructure—e.g., electric power grids. Time scales in chemical systems span orders of magnitude, while infrastructure networks feature both local andmore » long-distance connectivity, with associated clusters of time scales. These systems also blend continuous and discrete behavior; examples include saturation phenomena in surface chemistry and catalysis, and switching in electrical networks. Reducing size and stiffness is essential to tractable and predictive simulation of these systems. Computational singular perturbation (CSP) has been effectively used to identify and decouple dynamics at disparate time scales in chemical systems, allowing reduction of model complexity and stiffness. In realistic settings, however, model reduction must contend with uncertainties, which are often greatest in large-scale systems most in need of reduction. Uncertainty is not limited to parameters; one must also address structural uncertainties—e.g., whether a link is present in a network—and the impact of random perturbations, e.g., fluctuating loads or sources. Research under this project developed new methods for the analysis and reduction of complex multiscale networks under uncertainty, by combining computational singular perturbation (CSP) with probabilistic uncertainty quantification. CSP yields asymptotic approximations of reduceddimensionality “slow manifolds” on which a multiscale dynamical system evolves. Introducing uncertainty in this context raised fundamentally new issues, e.g., how is the topology of slow manifolds transformed by parametric uncertainty? How to construct dynamical models on these uncertain manifolds? To address these questions, we used stochastic spectral polynomial chaos (PC) methods to reformulate uncertain network models and analyzed them using CSP in probabilistic terms. Finding uncertain manifolds involved the solution of stochastic eigenvalue problems, facilitated by projection onto PC bases. These problems motivated us to explore the spectral properties stochastic Galerkin systems. We also introduced novel methods for rank-reduction in stochastic eigensystems—transformations of a uncertain dynamical system that lead to lower storage and solution complexity. These technical accomplishments are detailed below. This report focuses on the MIT portion of the joint project.« less

Problem of intensity reduction of acoustic fields generated by gas-dynamic jets of motors of the rocket-launch vehicles at launch

NASA Astrophysics Data System (ADS)

Vorobyov, A. M.; Abdurashidov, T. O.; Bakulev, V. L.; But, A. B.; Kuznetsov, A. B.; Makaveev, A. T.

2015-04-01

The present work experimentally investigates suppression of acoustic fields generated by supersonic jets of the rocket-launch vehicles at the initial period of launch by water injection. Water jets are injected to the combined jet along its perimeter at an angle of 0° and 60°. The solid rocket motor with the rocket-launch vehicles simulator case is used at tests. Effectiveness of reduction of acoustic loads on the rocket-launch vehicles surface by way of creation of water barrier was proved. It was determined that injection angle of 60° has greater effectiveness to reduce pressure pulsation levels.

Rotational relaxation time as unifying time scale for polymer and fiber drag reduction

NASA Astrophysics Data System (ADS)

Boelens, A. M. P.; Muthukumar, M.

2016-05-01

Using hybrid direct numerical simulation plus Langevin dynamics, a comparison is performed between polymer and fiber stress tensors in turbulent flow. The stress tensors are found to be similar, suggesting a common drag reducing mechanism in the onset regime for both flexible polymers and rigid fibers. Since fibers do not have an elastic backbone, this must be a viscous effect. Analysis of the viscosity tensor reveals that all terms are negligible, except the off-diagonal shear viscosity associated with rotation. Based on this analysis, we identify the rotational orientation time as the unifying time scale setting a new time criterion for drag reduction by both flexible polymers and rigid fibers.

Rotational relaxation time as unifying time scale for polymer and fiber drag reduction.

PubMed

Boelens, A M P; Muthukumar, M

2016-05-01

Using hybrid direct numerical simulation plus Langevin dynamics, a comparison is performed between polymer and fiber stress tensors in turbulent flow. The stress tensors are found to be similar, suggesting a common drag reducing mechanism in the onset regime for both flexible polymers and rigid fibers. Since fibers do not have an elastic backbone, this must be a viscous effect. Analysis of the viscosity tensor reveals that all terms are negligible, except the off-diagonal shear viscosity associated with rotation. Based on this analysis, we identify the rotational orientation time as the unifying time scale setting a new time criterion for drag reduction by both flexible polymers and rigid fibers.

Discrete filtering techniques applied to sequential GPS range measurements

NASA Technical Reports Server (NTRS)

Vangraas, Frank

1987-01-01

The basic navigation solution is described for position and velocity based on range and delta range (Doppler) measurements from NAVSTAR Global Positioning System satellites. The application of discrete filtering techniques is examined to reduce the white noise distortions on the sequential range measurements. A second order (position and velocity states) Kalman filter is implemented to obtain smoothed estimates of range by filtering the dynamics of the signal from each satellite separately. Test results using a simulated GPS receiver show a steady-state noise reduction, the input noise variance divided by the output noise variance, of a factor of four. Recommendations for further noise reduction based on higher order Kalman filters or additional delta range measurements are included.

Evaluation of space shuttle main engine fluid dynamic frequency response characteristics

NASA Technical Reports Server (NTRS)

Gardner, T. G.

1980-01-01

In order to determine the POGO stability characteristics of the space shuttle main engine liquid oxygen (LOX) system, the fluid dynamic frequency response functions between elements in the SSME LOX system was evaluated, both analytically and experimentally. For the experimental data evaluation, a software package was written for the Hewlett-Packard 5451C Fourier analyzer. The POGO analysis software is documented and consists of five separate segments. Each segment is stored on the 5451C disc as an individual program and performs its own unique function. Two separate data reduction methods, a signal calibration, coherence or pulser signal based frequency response function blanking, and automatic plotting features are included in the program. The 5451C allows variable parameter transfer from program to program. This feature is used to advantage and requires only minimal user interface during the data reduction process. Experimental results are included and compared with the analytical predictions in order to adjust the general model and arrive at a realistic simulation of the POGO characteristics.

Analysis of Retainer Induced Disturbances of Reaction Wheel

NASA Astrophysics Data System (ADS)

Taniwaki, Shigemune; Kudo, Masahito; Sato, Makoto; Ohkami, Yoshiaki

A ball bearing reaction wheel (RW) is a key attitude control actuator of spacecrafts, but it is also a major source of inner disturbances. Future space mission requires high attitude stability, and disturbance property of the RW must be improved. There are some disturbance sources inside the RW, and abnormal motion of a retainer is one of the most significant ones. The retainer is one of mechanical parts of a ball bearing supporting a rotor spin axis. It is used to keep the ball intervals. Therefore it is nonholonomically constrained with balls, an inner race, and an outer race, and its complex motion causes disturbances which are difficult to be effectively removed. In this paper, dynamics of the retainer is investigated through experimental tests and numerical simulations. Disturbances of normal and abnormal RWs are compared, and relation between retainer mass imbalances and their dynamics are investigated. As results, a trade-off relation between instability reduction and disturbance reduction is verified and one of the criteria to decide the appropriate mass imbalance is proposed.

Low power test architecture for dynamic read destructive fault detection in SRAM

NASA Astrophysics Data System (ADS)

Takher, Vikram Singh; Choudhary, Rahul Raj

2018-06-01

Dynamic Read Destructive Fault (dRDF) is the outcome of resistive open defects in the core cells of static random-access memories (SRAMs). The sensitisation of dRDF involves either performing multiple read operations or creation of number of read equivalent stress (RES), on the core cell under test. Though the creation of RES is preferred over the performing multiple read operation on the core cell, cell dissipates more power during RES than during the read or write operation. This paper focuses on the reduction in power dissipation by optimisation of number of RESs, which are required to sensitise the dRDF during test mode of operation of SRAM. The novel pre-charge architecture has been proposed in order to reduce the power dissipation by limiting the number of RESs to an optimised number of two. The proposed low power architecture is simulated and analysed which shows reduction in power dissipation by reducing the number of RESs up to 18.18%.

Influence of Housing Wall Compliance on Shock Absorbers in the Context of Vehicle Dynamics

NASA Astrophysics Data System (ADS)

Pulvirenti, G.; Faria, C.

2017-10-01

Shock absorbers play a key role in vehicle dynamics. Researchers have spent significant effort in order to understand phenomena associated with this component, but there are still several issues to address, in part because new technology development and design trends continually lead to new challenges, among which weight reduction is crucial. For shock absorbers, weight reduction is related to the use of new materials (e.g. composite) or new design paradigms (e.g. more complex geometry, wall thickness, etc.). All of them are directly linked to wall compliance values higher than the actual ones. The present article proposes a first analysis of the phenomena introduced by a high wall compliance, through a modelling approach and various simulations in order to understand the vehicle behaviour changes. It is shown that high values of wall compliance lead to increased hysteresis in the force-velocity curve. However, comfort, handling and ride performances are not significantly affected by this designing parameter.

Ultra-low Thermal Conductivity in Si/Ge Hierarchical Superlattice Nanowire.

PubMed

Mu, Xin; Wang, Lili; Yang, Xueming; Zhang, Pu; To, Albert C; Luo, Tengfei

2015-11-16

Due to interfacial phonon scattering and nanoscale size effect, silicon/germanium (Si/Ge) superlattice nanowire (SNW) can have very low thermal conductivity, which is very attractive for thermoelectrics. In this paper, we demonstrate using molecular dynamics simulations that the already low thermal conductivity of Si/Ge SNW can be further reduced by introducing hierarchical structure to form Si/Ge hierarchical superlattice nanowire (H-SNW). The structural hierarchy introduces defects to disrupt the periodicity of regular SNW and scatters coherent phonons, which are the key contributors to thermal transport in regular SNW. Our simulation results show that periodically arranged defects in Si/Ge H-SNW lead to a ~38% reduction of the already low thermal conductivity of regular Si/Ge SNW. By randomizing the arrangement of defects and imposing additional surface complexities to enhance phonon scattering, further reduction in thermal conductivity can be achieved. Compared to pure Si nanowire, the thermal conductivity reduction of Si/Ge H-SNW can be as large as ~95%. It is concluded that the hierarchical structuring is an effective way of reducing thermal conductivity significantly in SNW, which can be a promising path for improving the efficiency of Si/Ge-based SNW thermoelectrics.

Ultra-low Thermal Conductivity in Si/Ge Hierarchical Superlattice Nanowire

PubMed Central

Mu, Xin; Wang, Lili; Yang, Xueming; Zhang, Pu; To, Albert C.; Luo, Tengfei

2015-01-01

Due to interfacial phonon scattering and nanoscale size effect, silicon/germanium (Si/Ge) superlattice nanowire (SNW) can have very low thermal conductivity, which is very attractive for thermoelectrics. In this paper, we demonstrate using molecular dynamics simulations that the already low thermal conductivity of Si/Ge SNW can be further reduced by introducing hierarchical structure to form Si/Ge hierarchical superlattice nanowire (H-SNW). The structural hierarchy introduces defects to disrupt the periodicity of regular SNW and scatters coherent phonons, which are the key contributors to thermal transport in regular SNW. Our simulation results show that periodically arranged defects in Si/Ge H-SNW lead to a ~38% reduction of the already low thermal conductivity of regular Si/Ge SNW. By randomizing the arrangement of defects and imposing additional surface complexities to enhance phonon scattering, further reduction in thermal conductivity can be achieved. Compared to pure Si nanowire, the thermal conductivity reduction of Si/Ge H-SNW can be as large as ~95%. It is concluded that the hierarchical structuring is an effective way of reducing thermal conductivity significantly in SNW, which can be a promising path for improving the efficiency of Si/Ge-based SNW thermoelectrics. PMID:26568511

Design of a correlated validated CFD and genetic algorithm model for optimized sensors placement for indoor air quality monitoring

NASA Astrophysics Data System (ADS)

Mousavi, Monireh Sadat; Ashrafi, Khosro; Motlagh, Majid Shafie Pour; Niksokhan, Mohhamad Hosein; Vosoughifar, HamidReza

2018-02-01

In this study, coupled method for simulation of flow pattern based on computational methods for fluid dynamics with optimization technique using genetic algorithms is presented to determine the optimal location and number of sensors in an enclosed residential complex parking in Tehran. The main objective of this research is costs reduction and maximum coverage with regard to distribution of existing concentrations in different scenarios. In this study, considering all the different scenarios for simulation of pollution distribution using CFD simulations has been challenging due to extent of parking and number of cars available. To solve this problem, some scenarios have been selected based on random method. Then, maximum concentrations of scenarios are chosen for performing optimization. CFD simulation outputs are inserted as input in the optimization model using genetic algorithm. The obtained results stated optimal number and location of sensors.

Omnidirectional angle constraint based dynamic six-degree-of-freedom measurement for spacecraft rendezvous and docking simulation

NASA Astrophysics Data System (ADS)

Shi, Shendong; Yang, Linghui; Lin, Jiarui; Ren, Yongjie; Guo, Siyang; Zhu, Jigui

2018-04-01

In this paper we present a novel omnidirectional angle constraint based method for dynamic 6-DOF (six-degree-of-freedom) measurement. A photoelectric scanning measurement network is employed whose photoelectric receivers are fixed on the measured target. They are in a loop distribution and receive signals from rotating transmitters. Each receiver indicates an angle constraint direction. Therefore, omnidirectional angle constraints can be constructed in each rotation cycle. By solving the constrained optimization problem, 6-DOF information can be obtained, which is independent of traditional rigid coordinate system transformation. For the dynamic error caused by the measurement principle, we present an interpolation method for error reduction. Accuracy testing is performed in an 8  ×  8 m measurement area with four transmitters. The experimental results show that the dynamic orientation RMSEs (root-mean-square errors) are reduced from 0.077° to 0.044°, 0.040° to 0.030° and 0.032° to 0.015° in the X, Y, and Z axes, respectively. The dynamic position RMSE is reduced from 0.65 mm to 0.24 mm. This method is applied during the final approach phase in the rendezvous and docking simulation. Experiments under different conditions are performed in a 40  ×  30 m area, and the method is verified to be effective.

Fire modulates climate change response of simulated aspen distribution across topoclimatic gradients in a semi-arid montane landscape

USGS Publications Warehouse

Yang, Jian; Weisberg, Peter J.; Shinneman, Douglas; Dilts, Thomas E.; Earnst, Susan L.; Scheller, Robert M

2015-01-01

Content Changing aspen distribution in response to climate change and fire is a major focus of biodiversity conservation, yet little is known about the potential response of aspen to these two driving forces along topoclimatic gradients. Objective This study is set to evaluate how aspen distribution might shift in response to different climate-fire scenarios in a semi-arid montane landscape, and quantify the influence of fire regime along topoclimatic gradients. Methods We used a novel integration of a forest landscape succession and disturbance model (LANDIS-II) with a fine-scale climatic water deficit approach to simulate dynamics of aspen and associated conifer and shrub species over the next 150 years under various climate-fire scenarios. Results Simulations suggest that many aspen stands could persist without fire for centuries under current climate conditions. However, a simulated 2–5 °C increase in temperature caused a substantial reduction of aspen coverage at lower elevations and a modest increase at upper elevations, leading to an overall reduction of aspen range at the landscape level. Increasing fire activity may favor aspen increase at its upper elevation limits adjacent to coniferous forest, but may also favor reduction of aspen at lower elevation limits adjacent to xeric shrubland. Conclusions Our study highlights the importance of incorporating fine-scale terrain effects on climatic water deficit and ecohydrology when modeling species distribution response to climate change. This modeling study suggests that climate mitigation and adaptation strategies that use fire would benefit from consideration of spatial context at landscape scales.

Principal component analysis on a torus: Theory and application to protein dynamics.

PubMed

Sittel, Florian; Filk, Thomas; Stock, Gerhard

2017-12-28

A dimensionality reduction method for high-dimensional circular data is developed, which is based on a principal component analysis (PCA) of data points on a torus. Adopting a geometrical view of PCA, various distance measures on a torus are introduced and the associated problem of projecting data onto the principal subspaces is discussed. The main idea is that the (periodicity-induced) projection error can be minimized by transforming the data such that the maximal gap of the sampling is shifted to the periodic boundary. In a second step, the covariance matrix and its eigendecomposition can be computed in a standard manner. Adopting molecular dynamics simulations of two well-established biomolecular systems (Aib 9 and villin headpiece), the potential of the method to analyze the dynamics of backbone dihedral angles is demonstrated. The new approach allows for a robust and well-defined construction of metastable states and provides low-dimensional reaction coordinates that accurately describe the free energy landscape. Moreover, it offers a direct interpretation of covariances and principal components in terms of the angular variables. Apart from its application to PCA, the method of maximal gap shifting is general and can be applied to any other dimensionality reduction method for circular data.

A decision-support tool to inform Australian strategies for preventing suicide and suicidal behaviour.

PubMed

Page, Andrew; Atkinson, Jo-An; Heffernan, Mark; McDonnell, Geoff; Hickie, Ian

2017-04-27

Dynamic simulation modelling is increasingly being recognised as a valuable decision-support tool to help guide investments and actions to address complex public health issues such as suicide. In particular, participatory system dynamics (SD) modelling provides a useful tool for asking high-level 'what if' questions, and testing the likely impacts of different combinations of policies and interventions at an aggregate level before they are implemented in the real world. We developed an SD model for suicide prevention in Australia, and investigated the hypothesised impacts over the next 10 years (2015-2025) of a combination of current intervention strategies proposed for population interventions in Australia: 1) general practitioner (GP) training, 2) coordinated aftercare in those who have attempted suicide, 3) school-based mental health literacy programs, 4) brief-contact interventions in hospital settings, and 5) psychosocial treatment approaches. Findings suggest that the largest reductions in suicide were associated with GP training (6%) and coordinated aftercare approaches (4%), with total reductions of 12% for all interventions combined. This paper highlights the value of dynamic modelling methods for managing complexity and uncertainty, and demonstrates their potential use as a decision-support tool for policy makers and program planners for community suicide prevention actions.

Principal component analysis on a torus: Theory and application to protein dynamics

NASA Astrophysics Data System (ADS)

Sittel, Florian; Filk, Thomas; Stock, Gerhard

2017-12-01

A dimensionality reduction method for high-dimensional circular data is developed, which is based on a principal component analysis (PCA) of data points on a torus. Adopting a geometrical view of PCA, various distance measures on a torus are introduced and the associated problem of projecting data onto the principal subspaces is discussed. The main idea is that the (periodicity-induced) projection error can be minimized by transforming the data such that the maximal gap of the sampling is shifted to the periodic boundary. In a second step, the covariance matrix and its eigendecomposition can be computed in a standard manner. Adopting molecular dynamics simulations of two well-established biomolecular systems (Aib9 and villin headpiece), the potential of the method to analyze the dynamics of backbone dihedral angles is demonstrated. The new approach allows for a robust and well-defined construction of metastable states and provides low-dimensional reaction coordinates that accurately describe the free energy landscape. Moreover, it offers a direct interpretation of covariances and principal components in terms of the angular variables. Apart from its application to PCA, the method of maximal gap shifting is general and can be applied to any other dimensionality reduction method for circular data.

CHROTRAN 1.0: A mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

NASA Astrophysics Data System (ADS)

Hansen, Scott K.; Pandey, Sachin; Karra, Satish; Vesselinov, Velimir V.

2017-12-01

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a multi-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, chrotran, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling, and biomass death. Our software implementation handles heterogeneous flow fields, as well as arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.

CHROTRAN: a mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

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

Hansen, Scott; Pandey, Sachin; Karra, Satish

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less

Adaptive Trajectory Prediction Algorithm for Climbing Flights

NASA Technical Reports Server (NTRS)

Schultz, Charles Alexander; Thipphavong, David P.; Erzberger, Heinz

2012-01-01

Aircraft climb trajectories are difficult to predict, and large errors in these predictions reduce the potential operational benefits of some advanced features for NextGen. The algorithm described in this paper improves climb trajectory prediction accuracy by adjusting trajectory predictions based on observed track data. It utilizes rate-of-climb and airspeed measurements derived from position data to dynamically adjust the aircraft weight modeled for trajectory predictions. In simulations with weight uncertainty, the algorithm is able to adapt to within 3 percent of the actual gross weight within two minutes of the initial adaptation. The root-mean-square of altitude errors for five-minute predictions was reduced by 73 percent. Conflict detection performance also improved, with a 15 percent reduction in missed alerts and a 10 percent reduction in false alerts. In a simulation with climb speed capture intent and weight uncertainty, the algorithm improved climb trajectory prediction accuracy by up to 30 percent and conflict detection performance, reducing missed and false alerts by up to 10 percent.

CHROTRAN: a mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

DOE PAGES

Hansen, Scott; Pandey, Sachin; Karra, Satish; ...

2017-04-25

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less

Finite element dynamic analysis of soft tissues using state-space model.

PubMed

Iorga, Lucian N; Shan, Baoxiang; Pelegri, Assimina A

2009-04-01

A finite element (FE) model is employed to investigate the dynamic response of soft tissues under external excitations, particularly corresponding to the case of harmonic motion imaging. A solid 3D mixed 'u-p' element S8P0 is implemented to capture the near-incompressibility inherent in soft tissues. Two important aspects in structural modelling of these tissues are studied; these are the influence of viscous damping on the dynamic response and, following FE-modelling, a developed state-space formulation that valuates the efficiency of several order reduction methods. It is illustrated that the order of the mathematical model can be significantly reduced, while preserving the accuracy of the observed system dynamics. Thus, the reduced-order state-space representation of soft tissues for general dynamic analysis significantly reduces the computational cost and provides a unitary framework for the 'forward' simulation and 'inverse' estimation of soft tissues. Moreover, the results suggest that damping in soft-tissue is significant, effectively cancelling the contribution of all but the first few vibration modes.

Canonical formalism for modelling and control of rigid body dynamics.

PubMed

Gurfil, P

2005-12-01

This paper develops a new paradigm for stabilization of rigid-body dynamics. The state-space model is formulated using canonical elements, known as the Serret-Andoyer (SA) variables, thus far scarcely used for engineering applications. The main feature of the SA formalism is the reduction of the dynamics via the underlying symmetry stemming from conservation of angular momentum and rotational kinetic energy. The controllability of the system model is examined using the notion of accessibility, and is shown to be accessible from all points. Based on the accessibility proof, two nonlinear asymptotic feedback stabilizers are developed: a damping feedback is designed based on the Jurdjevic-Quinn method, and a Hamiltonian controller is derived by using the Hamiltonian as a natural Lyapunov function for the closed-loop dynamics. It is shown that the Hamiltonian control is both passive and inverse optimal with respect to a meaningful performance index. The performance of the new controllers is examined and compared using simulations of realistic scenarios from the satellite attitude dynamics field.

Ozone impact minimization through coordinated scheduling of turnaround operations from multiple olefin plants in an ozone nonattainment area

NASA Astrophysics Data System (ADS)

Ge, Sijie; Wang, Sujing; Xu, Qiang; Ho, Thomas

2018-03-01

Turnaround operations (start-up and shutdown) are critical operations in olefin plants, which emit large quantities of VOCs, NOx and CO. The emission has great potentials to impact the ozone level in ozone nonattainment areas. This study demonstrates a novel practice to minimize the ozone impact through coordinated scheduling of turnaround operations from multiple olefin plants located in Houston, Texas, an ozone nonattainment area. The study considered two olefin plants scheduled to conduct turnaround operations: one start-up and one shutdown, simultaneously on the same day within a five-hour window. Through dynamic simulations of the turnaround operations using ASPEN Plus Dynamics and air quality simulations using CAMx, the study predicts the ozone impact from the combined effect of the two turnaround operations under different starting-time scenarios. The simulations predict that the ozone impact from planned turnaround operations ranges from a maximum of 11.4 ppb to a minimum of 1.4 ppb. Hence, a reduction of up to 10.0 ppb can be achieved on a single day based on the selected two simulation days. This study demonstrates a cost-effective and environmentally benign ozone control practice for relevant stakeholders, including environmental agencies, regional plant operators, and local communities.

Adaptive sampling strategies with high-throughput molecular dynamics

NASA Astrophysics Data System (ADS)

Clementi, Cecilia

Despite recent significant hardware and software developments, the complete thermodynamic and kinetic characterization of large macromolecular complexes by molecular simulations still presents significant challenges. The high dimensionality of these systems and the complexity of the associated potential energy surfaces (creating multiple metastable regions connected by high free energy barriers) does not usually allow to adequately sample the relevant regions of their configurational space by means of a single, long Molecular Dynamics (MD) trajectory. Several different approaches have been proposed to tackle this sampling problem. We focus on the development of ensemble simulation strategies, where data from a large number of weakly coupled simulations are integrated to explore the configurational landscape of a complex system more efficiently. Ensemble methods are of increasing interest as the hardware roadmap is now mostly based on increasing core counts, rather than clock speeds. The main challenge in the development of an ensemble approach for efficient sampling is in the design of strategies to adaptively distribute the trajectories over the relevant regions of the systems' configurational space, without using any a priori information on the system global properties. We will discuss the definition of smart adaptive sampling approaches that can redirect computational resources towards unexplored yet relevant regions. Our approaches are based on new developments in dimensionality reduction for high dimensional dynamical systems, and optimal redistribution of resources. NSF CHE-1152344, NSF CHE-1265929, Welch Foundation C-1570.

Hydrogen-vacancy-dislocation interactions in α-Fe

NASA Astrophysics Data System (ADS)

Tehranchi, A.; Zhang, X.; Lu, G.; Curtin, W. A.

2017-02-01

Atomistic simulations of the interactions between dislocations, hydrogen atoms, and vacancies are studied to assess the viability of a recently proposed mechanism for the formation of nanoscale voids in Fe-based steels in the presence of hydrogen. Quantum-mechanics/molecular-mechanics method calculations confirm molecular statics simulations based on embedded atom method (EAM) potential showing that individual vacancies on the compressive side of an edge dislocation can be transported with the dislocation as it glides. Molecular dynamics simulations based on EAM potential then show, however, that vacancy clusters in the glide plane of an approaching dislocation are annihilated or reduced in size by the creation of a double-jog/climb process that is driven by the huge reduction in energy accompanying vacancy annihilation. The effectiveness of annihilation/reduction processes is not reduced by the presence of hydrogen in the vacancy clusters because typical V-H cluster binding energies are much lower than the vacancy formation energy, except at very high hydrogen content in the cluster. Analysis of a range of configurations indicates that hydrogen plays no special role in stabilizing nanovoids against jog formation processes that shrink voids. Experimental observations of nanovoids on the fracture surfaces of steels must be due to as-yet undetermined processes.

Foreign Object Damage Prediction in Ceramic Matrix Composites

DTIC Science & Technology

2011-02-28

Management and Budget. Paperwork Reduction Project (0704-0188) Washington, DC 20503 PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD...has been utilized successf ul I y f or damage predi cti on i n many probl ems In a peri dynamic simulation, the distances between points in the...this model as suits their needs, with N& R Engineering and UofA providing tool support/development as required. A marketing study will be conducted

Insight into the molecular mechanism of the sulfur oxidation process by reverse sulfite reductase (rSiR) from sulfur oxidizer Allochromatium vinosum.

PubMed

Ghosh, Semanti; Bagchi, Angshuman

2018-04-26

Sulfur metabolism is one of the oldest known biochemical processes. Chemotrophic or phototrophic proteobacteria, through the dissimilatory pathway, use sulfate, sulfide, sulfite, thiosulfate or elementary sulfur by either reductive or oxidative mechanisms. During anoxygenic photosynthesis, anaerobic sulfur oxidizer Allochromatium vinosum forms sulfur globules that are further oxidized by dsr operon. One of the key redox enzymes in reductive or oxidative sulfur metabolic pathways is the DsrAB protein complex. However, there are practically no reports to elucidate the molecular mechanism of the sulfur oxidation process by the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum. In the present context, we tried to analyze the structural details of the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum by molecular dynamics simulations. The molecular dynamics simulation results revealed the various types of molecular interactions between DsrA and DsrB proteins during the formation of DsrAB protein complex. We, for the first time, predicted the mode of binding interactions between the co-factor and DsrAB protein complex from Allochromatium vinosum. We also compared the binding interfaces of DsrAB from sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris. This study is the first to provide a comparative aspect of binding modes of sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris.

Reduction of community alcohol problems: computer simulation experiments in three counties.

PubMed

Holder, H D; Blose, J O

1987-03-01

A series of alcohol abuse prevention strategies was evaluated using computer simulation for three counties in the United States: Wake County, North Carolina, Washington County, Vermont and Alameda County, California. A system dynamics model composed of a network of interacting variables was developed for the pattern of alcoholic beverage consumption in a community. The relationship of community drinking patterns to various stimulus factors was specified in the model based on available empirical research. Stimulus factors included disposable income, alcoholic beverage prices, advertising exposure, minimum drinking age and changes in cultural norms. After a generic model was developed and validated on the national level, a computer-based system dynamics model was developed for each county, and a series of experiments was conducted to project the potential impact of specific prevention strategies. The project concluded that prevention efforts can both lower current levels of alcohol abuse and reduce projected increases in alcohol-related problems. Without such efforts, already high levels of alcohol-related family disruptions in the three counties could be expected to rise an additional 6% and drinking-related work problems 1-5%, over the next 10 years after controlling for population growth. Of the strategies tested, indexing the price of alcoholic beverages to the consumer price index in conjunction with the implementation of a community educational program with well-defined target audiences has the best potential for significant problem reduction in all three counties.

Mechanistic Insights into Xenon Inhibition of NMDA Receptors from MD Simulations

PubMed Central

Liu, Lu Tian; Xu, Yan; Tang, Pei

2010-01-01

Inhibition of N-methyl-D-aspartate (NMDA) receptors has been viewed as a primary cause of xenon anesthesia, yet the mechanism is unclear. Here, we investigated interactions between xenon and the ligand-binding domain (LBD) of a NMDA receptor and examined xenon-induced structural and dynamical changes that are relevant to functional changes of the NMDA receptor. Several comparative molecular dynamics simulations were performed on two X-ray structures representing the open- and closed-cleft LBD of the NMDA receptor. We identified plausible xenon action sites in the LBD, including those nearby agonist sites, in the hinge region, and at the interface between two subunits. The xenon binding energy varies from −5.3 to −0.7 kcal/mol. Xenon's effect on the NMDA receptor is conformation-dependent and is produced through both competitive and non-competitive mechanisms. Xenon can promote cleft opening in the absence of agonists and consequently stabilizes the closed channel. Xenon can also bind at the interface of two subunits, alter the inter-subunit interaction, and lead to a reduction of the distance between GT-links. This reduction corresponds to a rearrangement of the channel toward a direction of pore size decreasing, implying a closed or desensitized channel. In addition to these non-competitive actions, xenon was found to weaken the glutamate binding, which could lead to low agonist efficacy and appear as competitive inhibition. PMID:20560662

Locomotive dynamic performance under traction/braking conditions considering effect of gear transmissions

NASA Astrophysics Data System (ADS)

Chen, Zaigang; Zhai, Wanming; Wang, Kaiyun

2018-07-01

Traction or braking operations are usually applied to trains or locomotives for acceleration, speed adjustment, and stopping. During these operations, gear transmission equipment plays a very significant role in the delivery of traction or electrical braking power. Failures of the gear transmissions are likely to cause power loses and even threaten the operation safety of the train. Its dynamic performance is closely related to the normal operation and service safety of the entire train, especially under some emergency braking conditions. In this paper, a locomotive-track coupled vertical-longitudinal dynamics model is employed with considering the dynamic action from the gear transmissions. This dynamics model enables the detailed analysis and more practical simulation on the characteristics of power transmission path, namely motor-gear transmission-wheelset-longitudinal motion of locomotive, especially for traction or braking conditions. Multi-excitation sources, such as time-varying mesh stiffness and nonlinear wheel-rail contact excitations, are considered in this study. This dynamics model is then validated by comparing the simulated results with the experimental test results under braking conditions. The calculated results indicate that involvement of gear transmission could reveal the load reduction of the wheelset due to transmitted forces. Vibrations of the wheelset and the motor are dominated by variation of the gear dynamic mesh forces in the low speed range and by rail geometric irregularity in the higher speed range. Rail vertical geometric irregularity could also cause wheelset longitudinal vibrations, and do modulations to the gear dynamic mesh forces. Besides, the hauling weight has little effect on the locomotive vibrations and the dynamic mesh forces of the gear transmissions for both traction and braking conditions under the same running speed.

Drag reduction strategies

NASA Technical Reports Server (NTRS)

Hill, D. Christopher

1994-01-01

previously a description was given of an active control scheme using wall transpiration that leads to a 15% reduction in surface skin friction beneath a turbulent boundary layer, according to direct numerical simulation. In this research brief further details of that scheme and its variants are given together with some suggestions as to how sensor/actuator arrays could be configured to reduce surface drag. The research which is summarized here was performed during the first half of 1994. This research is motivated by the need to understand better how the dynamics of near-wall turbulent flow can be modified so that skin friction is reduced. The reduction of turbulent skin friction is highly desirable in many engineering applications. Experiments and direct numerical simulations have led to an increased understanding of the cycle of turbulence production and transport in the boundary layer and raised awareness of the possibility of disrupting the process with a subsequent reduction in turbulent skin friction. The implementation of active feedback control in a computational setting is a viable approach for the investigation of the modifications to the flow physics that can be achieved. Bewley et al. and Hill describe how ideas from optimal control theory are employed to give 'sub-optimal' drag reduction schemes. The objectives of the work reported here is to investigate in greater detail the assumptions implicit within such schemes and their limitations. It is also our objective to describe how an array of sensors and actuators could be arranged and interconnected to form a 'smart' surface which has low skin friction.

Measurement of the mechanical properties of car body sheet steels at high strain rates and non ambient temperature

NASA Astrophysics Data System (ADS)

Bleck, W.; Larour, P.

2003-09-01

Crash behaviour and light weight have become the major design criteria for car bodies. Modem high strength steels offer appropriate solutions for these requirements. The prediction of the crash behaviour in simulation programs requires the information on materials behaviour during dynamic testing. The reduction of the signal waviness and the inertia effects at strain rates above 50s^{-1} are major issues in dynamic tensile testing. Damping techniques or load measurement on the sample itself are the common way to reduce oscillations. Strain measurement from the piston displacement or from optical devices on the specimen itself are also compared. Advantages and drawbacks of those various measurement techniques are presented.

Simulation of salinity intrusion along the Georgia and South Carolina coasts using climate-change scenarios

USGS Publications Warehouse

Conrads, Paul; Roehl, Edwin A.; Daamen, Ruby C.; Cook, John B.

2013-01-01

Potential changes in climate could alter interactions between environmental and societal systems and adversely affect the availability of water resources in many coastal communities. Changes in streamflow patterns in conjunction with sea-level rise may change the salinity-intrusion dynamics of coastal rivers. Several municipal water-supply intakes are located along the Georgia and South Carolina coast that are proximal to the present day saltwater-freshwater interface of tidal rivers. Increases in the extent of salinity intrusion resulting from climate change could threaten the availability of freshwater supplies in the vicinity of these intakes. To effectively manage these supplies, water-resource managers need estimates of potential changes in the frequency, duration, and magnitude of salinity intrusion near their water-supply intakes that may occur as a result of climate change. This study examines potential effects of climate change, including altered streamflow and sea-level rise, on the dynamics of saltwater intrusion near municipal water-supply intakes in two coastal areas. One area consists of the Atlantic Intracoastal Waterway (AIW) and the Waccamaw River near Myrtle Beach along the Grand Strand of the South Carolina Coast, and the second area is on or near the lower Savannah River near Savannah, Georgia. The study evaluated how future sea-level rise and a reduction in streamflows can potentially affect salinity intrusion and threaten municipal water supplies and the biodiversity of freshwater tidal marshes in these two areas. Salinity intrusion occurs as a result of the interaction between three principal forces—streamflow, mean coastal water levels, and tidal range. To analyze and simulate salinity dynamics at critical coastal gaging stations near four municipal water-supply intakes, various data-mining techniques, including artificial neural network (ANN) models, were used to evaluate hourly streamflow, salinity, and coastal water-level data collected over a period exceeding 10 years. The ANN models were trained (calibrated) to learn the specific interactions that cause salinity intrusions, and resulting models were able to accurately simulate historical salinity dynamics in both study areas. Changes in sea level and streamflow quantity and timing can be simulated by the salinity intrusion models to evaluate various climate-change scenarios. The salinity intrusion models for the study areas are deployed in a decision support system to facilitate the use of the models for management decisions by coastal water-resource managers. The report describes the use of the salinity-intrusion models decision support system to evaluate salinity-intrusion dynamics for various climate-change scenarios, including incremental increases in sea level in combination with incremental decreases in streamflow. Operation of municipal water-treatment plants is problematic when the specific-conductance values for source water are greater than 1,000 to 2,000 microsiemens per centimeter (µS/cm). High specific-conductance values contribute to taste problems that require treatment. Data from a gage downstream from a municipal water intake indicate specific conductance exceeded 1,000 µS/cm about 5.4 percent of the time over the 14-year period from August 1995 to August 2008. Simulations of specific conductance at this gaging station that incorporates sea-level rises resulted in a doubling of the exceedances to 11.0 percent for a 1-foot increase and 17.6 percent for a 2-foot increase. The frequency of intrusion of water with specific conductance values of 1,000 µS/cm was less sensitive to incremental reductions in streamflow than to incremental increases in sea level. Simulations of conditions associated with a 10-percent reduction in streamflow, in combination with a 1-foot rise in sea level, increased the percentage of time specific conductance exceeded 1,000 µS/cm at this site from 11.0 to 13.3 percent, and a 20-percent reduction in streamflow increased the percentage of time to 16.6 percent. Precipitation and temperature data from a global circulation model were used, after scale adjustments, as input to a watershed model of the Yadkin-Pee Dee River basin, which flows into the Waccamaw River and Atlantic Intracoastal Waterway study area in South Carolina. The simulated streamflow for historical conditions and projected climate change in the future was used as input for the ANN model in decision support system. Results of simulations incorporating climate-change projections for alterations in streamflow indicate an increase in the frequency of salinity-intrusion events and a shift in the seasonal occurrence of the intrusion events from the summer to the fall.

Suppression of Biodynamic Interference by Adaptive Filtering

NASA Technical Reports Server (NTRS)

Velger, M.; Merhav, S. J.; Grunwald, A. J.

1984-01-01

Preliminary experimental results obtained in moving base simulator tests are presented. Both for pursuit and compensatory tracking tasks, a strong deterioration in tracking performance due to biodynamic interference is found. The use of adaptive filtering is shown to substantially alleviate these effects, resulting in a markedly improved tracking performance and reduction in task difficulty. The effect of simulator motion and of adaptive filtering on human operator describing functions is investigated. Adaptive filtering is found to substantially increase pilot gain and cross-over frequency, implying a more tight tracking behavior. The adaptive filter is found to be effective in particular for high-gain proportional dynamics, low display forcing function power and for pursuit tracking task configurations.

Integration of Linear Dynamic Emission and Climate Models with Air Traffic Simulations

NASA Technical Reports Server (NTRS)

Sridhar, Banavar; Ng, Hok K.; Chen, Neil Y.

2012-01-01

Future air traffic management systems are required to balance the conflicting objectives of maximizing safety and efficiency of traffic flows while minimizing the climate impact of aviation emissions and contrails. Integrating emission and climate models together with air traffic simulations improve the understanding of the complex interaction between the physical climate system, carbon and other greenhouse gas emissions and aviation activity. This paper integrates a national-level air traffic simulation and optimization capability with simple climate models and carbon cycle models, and climate metrics to assess the impact of aviation on climate. The capability can be used to make trade-offs between extra fuel cost and reduction in global surface temperature change. The parameters in the simulation can be used to evaluate the effect of various uncertainties in emission models and contrails and the impact of different decision horizons. Alternatively, the optimization results from the simulation can be used as inputs to other tools that monetize global climate impacts like the FAA s Aviation Environmental Portfolio Management Tool for Impacts.

Living with a large reduction in permited loading by using a hydrograph-controlled release scheme

USGS Publications Warehouse

Conrads, P.A.; Martello, W.P.; Sullins, N.R.

2003-01-01

The Total Maximum Daily Load (TMDL) for ammonia and biochemical oxygen demand for the Pee Dee, Waccamaw, and Atlantic Intracoastal Waterway system near Myrtle Beach, South Carolina, mandated a 60-percent reduction in point-source loading. For waters with a naturally low background dissolved-oxygen concentrations, South Carolina anti-degradation rules in the water-quality regulations allows a permitted discharger a reduction of dissolved oxygen of 0.1 milligrams per liter (mg/L). This is known as the "0.1 rule." Permitted dischargers within this region of the State operate under the "0.1 rule" and cannot cause a cumulative impact greater than 0.1 mg/L on dissolved-oxygen concentrations. For municipal water-reclamation facilities to serve the rapidly growing resort and retirement community near Myrtle Beach, a variable loading scheme was developed to allow dischargers to utilize increased assimilative capacity during higher streamflow conditions while still meeting the requirements of a recently established TMDL. As part of the TMDL development, an extensive real-time data-collection network was established in the lower Waccamaw and Pee Dee River watershed where continuous measurements of streamflow, water level, dissolved oxygen, temperature, and specific conductance are collected. In addition, the dynamic BRANCH/BLTM models were calibrated and validated to simulate the water quality and tidal dynamics of the system. The assimilative capacities for various streamflows were also analyzed. The variable-loading scheme established total loadings for three streamflow levels. Model simulations show the results from the additional loading to be less than a 0.1 mg/L reduction in dissolved oxygen. As part of the loading scheme, the real-time network was redesigned to monitor streamflow entering the study area and water-quality conditions in the location of dissolved-oxygen "sags." The study reveals how one group of permit holders used a variable-loading scheme to implement restrictive permit limits without experiencing prohibitive capital expenditures or initiating a lengthy appeals process.

The dynamics of human-water systems: comparing observations and simulations

NASA Astrophysics Data System (ADS)

Di Baldassarre, G.; Ciullo, A.; Castellarin, A.; Viglione, A.

2016-12-01

Real-word data of human-flood interactions are compared to the results of stylized socio-hydrological models. These models build on numerous examples from different parts of the world and consider two main prototypes of floodplain systems. Green systems, whereby societies cope with flood risk via non-structural measures, e.g. resettling out of floodplain areas ("living with floods" approach); and Technological systems, whereby societies cope with flood risk by also via structural measures, e.g. building levees ("fighting floods" approach). The floodplain systems of the Tiber River in Rome and the Ganges-Brahmaputra-Meghna Rivers in Bangladesh systems are used as case studies. The comparison of simulations and observations shows the potential of socio-hydrological models in capturing the dynamics of risk emerging from the interactions and feedbacks between social and hydrological processes, such as learning and forgetting effects. It is then discussed how the proposed approach can contribute to a better understanding of flood risk changes and therefore support the process of disaster risk reduction.

Probing energetics of Abeta fibril elongation by molecular dynamics simulations.

PubMed

Takeda, Takako; Klimov, Dmitri K

2009-06-03

Using replica exchange molecular dynamics simulations and an all-atom implicit solvent model, we probed the energetics of Abeta(10-40) fibril growth. The analysis of the interactions between incoming Abeta peptides and the fibril led us to two conclusions. First, considerable variations in fibril binding propensities are observed along the Abeta sequence. The peptides in the fibril and those binding to its edge interact primarily through their N-termini. Therefore, the mutations affecting the Abeta positions 10-23 are expected to have the largest impact on fibril elongation compared with those occurring in the C-terminus and turn. Second, we performed weak perturbations of the binding free energy landscape by scanning partial deletions of side-chain interactions at various Abeta sequence positions. The results imply that strong side-chain interactions--in particular, hydrophobic contacts--impede fibril growth by favoring disordered docking of incoming peptides. Therefore, fibril elongation may be promoted by moderate reduction of Abeta hydrophobicity. The comparison with available experimental data is presented.

Molecular dynamics simulations of polyelectrolyte brushes under poor solvent conditions: origins of bundle formation.

PubMed

He, Gui-Li; Merlitz, Holger; Sommer, Jens-Uwe

2014-03-14

Molecular dynamics simulations are applied to investigate salt-free planar polyelectrolyte brushes under poor solvent conditions. Starting above the Θ-point with a homogeneous brush and then gradually reducing the temperature, the polymers initially display a lateral structure formation, forming vertical bundles of chains. A further reduction of the temperature (or solvent quality) leads to a vertical collapse of the brush. By varying the size and selectivity of the counterions, we show that lateral structure formation persists and therefore demonstrate that the entropy of counterions being the dominant factor for the formation of the bundle phase. By applying an external compression force on the brush we calculate the minimal work done on the polymer phase only and prove that the entropy gain of counterions in the bundle state, as compared to the homogeneously collapsed state at the same temperature, is responsible for the lateral microphase segregation. As a consequence, the observed lateral structure formation has to be regarded universal for osmotic polymer brushes below the Θ-point.

Reducing Visual Discomfort with HMDs Using Dynamic Depth of Field.

PubMed

Carnegie, Kieran; Rhee, Taehyun

2015-01-01

Although head-mounted displays (HMDs) are ideal devices for personal viewing of immersive stereoscopic content, exposure to VR applications on them results in significant discomfort for the majority of people, with symptoms including eye fatigue, headaches, nausea, and sweating. A conflict between accommodation and vergence depth cues on stereoscopic displays is a significant cause of visual discomfort. This article describes the results of an evaluation used to judge the effectiveness of dynamic depth-of-field (DoF) blur in an effort to reduce discomfort caused by exposure to stereoscopic content on HMDs. Using a commercial game engine implementation, study participants report a reduction of visual discomfort on a simulator sickness questionnaire when DoF blurring is enabled. The study participants reported a decrease in symptom severity caused by HMD exposure, indicating that dynamic DoF can effectively reduce visual discomfort.

Dynamical buoyancy of hydrodynamic eddies. [in solar atmosphere

NASA Technical Reports Server (NTRS)

Parker, E. N.

1991-01-01

The dynamical pressure reduction within a vortex tube produces both a tension along the tube and a general buoyancy, analogous to magnetic flux tubes. The dynamical buoyancy causes convective cells to rise at speeds comparable to the rms fluid velocity within the cell. Consequently, the convective cells in a stratified atmosphere are more active than indicated by the standard anelastic approximation. The coherent convective cells at each level actively crowd upward into the convective cells above, elbowing weaker cells out of the way and flattening themselves and others against the upper surface of the convective region. These effects can be seen in the recent SOUP observations of the solar granulation. Deeper in the convective zone the inhomogeneity of the buoyancy may explain the random character of the convective motions that turns up in recent numerical simulations.

A simulation model for designing effective interventions in early childhood caries.

PubMed

Hirsch, Gary B; Edelstein, Burton L; Frosh, Marcy; Anselmo, Theresa

2012-01-01

Early childhood caries (ECC)--tooth decay among children younger than 6 years--is prevalent and consequential, affecting nearly half of US 5-year-olds, despite being highly preventable. Various interventions have been explored to limit caries activity leading to cavities, but little is known about the long-term effects and costs of these interventions. We developed a system dynamics model to determine which interventions, singly and in combination, could have the greatest effect in reducing caries experience and cost in a population of children aged birth to 5 years. System dynamics is a computer simulation technique useful to policy makers in choosing the most appropriate interventions for their populations. This study of Colorado preschool children models 6 categories of ECC intervention--applying fluorides, limiting cariogenic bacterial transmission from mothers to children, using xylitol directly with children, clinical treatment, motivational interviewing, and combinations of these--to compare their relative effect and cost. The model projects 10-year intervention costs ranging from $6 million to $245 million and relative reductions in cavity prevalence ranging from none to 79.1% from the baseline. Interventions targeting the youngest children take 2 to 4 years longer to affect the entire population of preschool-age children but ultimately exert a greater benefit in reducing ECC; interventions targeting the highest-risk children provide the greatest return on investment, and combined interventions that target ECC at several stages of its natural history have the greatest potential for cavity reduction. Some interventions save more in dental repair than their cost; all produce substantial reductions in repair cost. By using data relevant to any geographic area, this system model can provide policy makers with information to maximize the return on public health and clinical care investments.

High-Speed Rotor Analytical Dynamics on Flexible Foundation Subjected to Internal and External Excitation

NASA Astrophysics Data System (ADS)

Jivkov, Venelin S.; Zahariev, Evtim V.

2016-12-01

The paper presents a geometrical approach to dynamics simulation of a rigid and flexible system, compiled of high speed rotating machine with eccentricity and considerable inertia and mass. The machine is mounted on a vertical flexible pillar with considerable height. The stiffness and damping of the column, as well as, of the rotor bearings and the shaft are taken into account. Non-stationary vibrations and transitional processes are analyzed. The major frequency and modal mode of the flexible column are used for analytical reduction of its mass, stiffness and damping properties. The rotor and the foundation are modelled as rigid bodies, while the flexibility of the bearings is estimated by experiments and the requirements of the manufacturer. The transition effects as a result of limited power are analyzed by asymptotic methods of averaging. Analytical expressions for the amplitudes and unstable vibrations throughout resonance are derived by quasi-static approach increasing and decreasing of the exciting frequency. Analytical functions give the possibility to analyze the influence of the design parameter of many structure applications as wind power generators, gas turbines, turbo-generators, and etc. A numerical procedure is applied to verify the effectiveness and precision of the simulation process. Nonlinear and transitional effects are analyzed and compared to the analytical results. External excitations, as wave propagation and earthquakes, are discussed. Finite elements in relative and absolute coordinates are applied to model the flexible column and the high speed rotating machine. Generalized Newton - Euler dynamics equations are used to derive the precise dynamics equations. Examples of simulation of the system vibrations and nonstationary behaviour are presented.

Energy and wear optimisation of train longitudinal dynamics and of traction and braking systems

NASA Astrophysics Data System (ADS)

Conti, R.; Galardi, E.; Meli, E.; Nocciolini, D.; Pugi, L.; Rindi, A.

2015-05-01

Traction and braking systems deeply affect longitudinal train dynamics, especially when an extensive blending phase among different pneumatic, electric and magnetic devices is required. The energy and wear optimisation of longitudinal vehicle dynamics has a crucial economic impact and involves several engineering problems such as wear of braking friction components, energy efficiency, thermal load on components, level of safety under degraded or adhesion conditions (often constrained by the current regulation in force on signalling or other safety-related subsystem). In fact, the application of energy storage systems can lead to an efficiency improvement of at least 10% while, as regards the wear reduction, the improvement due to distributed traction systems and to optimised traction devices can be quantified in about 50%. In this work, an innovative integrated procedure is proposed by the authors to optimise longitudinal train dynamics and traction and braking manoeuvres in terms of both energy and wear. The new approach has been applied to existing test cases and validated with experimental data provided by Breda and, for some components and their homologation process, the results of experimental activities derive from cooperation performed with relevant industrial partners such as Trenitalia and Italcertifer. In particular, simulation results are referred to the simulation tests performed on a high-speed train (Ansaldo Breda Emu V250) and on a tram (Ansaldo Breda Sirio Tram). The proposed approach is based on a modular simulation platform in which the sub-models corresponding to different subsystems can be easily customised, depending on the considered application, on the availability of technical data and on the homologation process of different components.

LES of a Jet Excited by the Localized Arc Filament Plasma Actuators

NASA Technical Reports Server (NTRS)

Brown, Clifford A.

2011-01-01

The fluid dynamics of a high-speed jet are governed by the instability waves that form in the free-shear boundary layer of the jet. Jet excitation manipulates the growth and saturation of particular instability waves to control the unsteady flow structures that characterize the energy cascade in the jet.The results may include jet noise mitigation or a reduction in the infrared signature of the jet. The Localized Arc Filament Plasma Actuators (LAFPA) have demonstrated the ability to excite a high-speed jets in laboratory experiments. Extending and optimizing this excitation technology, however, is a complex process that will require many tests and trials. Computational simulations can play an important role in understanding and optimizing this actuator technology for real-world applications. Previous research has focused on developing a suitable actuator model and coupling it with the appropriate computational fluid dynamics (CFD) methods using two-dimensional spatial flow approximations. This work is now extended to three-dimensions (3-D) in space. The actuator model is adapted to a series of discrete actuators and a 3-D LES simulation of an excited jet is run. The results are used to study the fluid dynamics near the actuator and in the jet plume.

Investigation of the external flow analysis for density measurements at high altitude

NASA Technical Reports Server (NTRS)

Bienkowski, G. K.

1984-01-01

The results of analysis performed on the external flow around the shuttle orbiter nose regions at the Shuttle Upper Atmosphere Mass Spectrometer (SUMS) inlet orifice are presented. The purpose of the analysis is to quantitatively characterize the flow conditions to facilitate SUMS flight data reduction and subsequent determination of orbiter aerodynamic force coefficients in the hypersonic rarefied flow regime. Experimental determination of aerodynamic force coefficients requires accurate simultaneous measurement of forces (or acceleration) and dynamic pressure along with independent knowledge of density and velocity. The SUMS provides independent measurement of dynamic pressure; however, it does so indirectly and requires knowledge of the relationship between measured orifice conditions and the dynamic pressure which can only be determined on the basis of molecule or theory for a winged configuration. Monte Carlo direct simulation computer codes were developed for both the flow field solution at the orifice and for the internal orifice flow. These codes were used to study issues associated with geometric modeling of the orbiter nose geometry and the modeling of intermolecular collisions including rotational energy exchange and a preliminary analysis of vibrational excitation and dissociation effects. Data obtained from preliminary simulation runs are presented.

Improvement on Fermionic properties and new isotope production in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Wang, Ning; Wu, Tong; Zeng, Jie; Yang, Yongxu; Ou, Li

2016-06-01

By considering momentum transfer in the Fermi constraint procedure, the stability of the initial nuclei and fragments produced in heavy-ion collisions can be further improved in quantum molecular dynamics simulations. The case of a phase-space occupation probability larger than one is effectively reduced with the proposed procedure. Simultaneously, the energy conservation can be better described for both individual nuclei and heavy-ion reactions. With the revised version of the improved quantum molecular dynamics model, the fusion excitation functions of 16O+186W and the central collisions of Au+Au at 35 AMeV are re-examined. The fusion cross sections at sub-barrier energies and the charge distribution of fragments are relatively better reproduced due to the reduction of spurious nucleon emission. The charge and isotope distribution of fragments in Xe+Sn, U+U and Zr+Sn at intermediate energies are also predicted. More unmeasured extremely neutron-rich fragments with Z = 16-28 are observed in the central collisions of 238U+238U than that of 96Zr+124Sn, which indicates that multi-fragmentation of U+U may offer a fruitful pathway to new neutron-rich isotopes.

General Trends of Dihedral Conformational Transitions in a Globular Protein

PubMed Central

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; McCammon, J. Andrew

2017-01-01

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and Adaptive Biasing Force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions ~2 times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the Bend, Coil and Turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein sidechains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Sidechains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. PMID:26799251

Insights into proton translocation in cbb3 oxidase from MD simulations.

PubMed

Carvalheda, Catarina A; Pisliakov, Andrei V

2017-05-01

Heme-copper oxidases are membrane protein complexes that catalyse the final step of the aerobic respiration, namely the reduction of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochemical gradient that is used for ATP synthesis. The distinctive C-type (or cbb 3 ) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a number of unique structural and functional features, including high catalytic activity at low oxygen concentrations. At the moment, the functioning mechanism of C-type oxidases, in particular the proton transfer/pumping mechanism presumably via a single proton channel, is still poorly understood. In this work we used all-atom molecular dynamics simulations and continuum electrostatics calculations to obtain atomic-level insights into the hydration and dynamics of a cbb 3 oxidase. We provide the details of the water dynamics and proton transfer pathways for both the "chemical" and "pumped" protons, and show that formation of protonic connections is strongly affected by the protonation state of key residues, namely H243, E323 and H337. Copyright © 2017 Elsevier B.V. All rights reserved.

Firing rate dynamics in recurrent spiking neural networks with intrinsic and network heterogeneity.

PubMed

Ly, Cheng

2015-12-01

Heterogeneity of neural attributes has recently gained a lot of attention and is increasing recognized as a crucial feature in neural processing. Despite its importance, this physiological feature has traditionally been neglected in theoretical studies of cortical neural networks. Thus, there is still a lot unknown about the consequences of cellular and circuit heterogeneity in spiking neural networks. In particular, combining network or synaptic heterogeneity and intrinsic heterogeneity has yet to be considered systematically despite the fact that both are known to exist and likely have significant roles in neural network dynamics. In a canonical recurrent spiking neural network model, we study how these two forms of heterogeneity lead to different distributions of excitatory firing rates. To analytically characterize how these types of heterogeneities affect the network, we employ a dimension reduction method that relies on a combination of Monte Carlo simulations and probability density function equations. We find that the relationship between intrinsic and network heterogeneity has a strong effect on the overall level of heterogeneity of the firing rates. Specifically, this relationship can lead to amplification or attenuation of firing rate heterogeneity, and these effects depend on whether the recurrent network is firing asynchronously or rhythmically firing. These observations are captured with the aforementioned reduction method, and furthermore simpler analytic descriptions based on this dimension reduction method are developed. The final analytic descriptions provide compact and descriptive formulas for how the relationship between intrinsic and network heterogeneity determines the firing rate heterogeneity dynamics in various settings.

Optimizing Controlling-Value-Based Power Gating with Gate Count and Switching Activity

NASA Astrophysics Data System (ADS)

Chen, Lei; Kimura, Shinji

In this paper, a new heuristic algorithm is proposed to optimize the power domain clustering in controlling-value-based (CV-based) power gating technology. In this algorithm, both the switching activity of sleep signals (p) and the overall numbers of sleep gates (gate count, N) are considered, and the sum of the product of p and N is optimized. The algorithm effectively exerts the total power reduction obtained from the CV-based power gating. Even when the maximum depth is kept to be the same, the proposed algorithm can still achieve power reduction approximately 10% more than that of the prior algorithms. Furthermore, detailed comparison between the proposed heuristic algorithm and other possible heuristic algorithms are also presented. HSPICE simulation results show that over 26% of total power reduction can be obtained by using the new heuristic algorithm. In addition, the effect of dynamic power reduction through the CV-based power gating method and the delay overhead caused by the switching of sleep transistors are also shown in this paper.

Molecular dynamics simulation of interactions between a sodium dodecyl sulfate micelle and a poly(ethylene oxide) polymer.

PubMed

Shang, Barry Z; Wang, Zuowei; Larson, Ronald G

2008-03-13

We have performed atomistic molecular dynamics simulations of an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. The micelle consisted of 60 surfactant molecules, and the polymer chain lengths varied from 20 to 40 monomers. The force field parameters for PEO were adjusted by using 1,2-dimethoxymethane (DME) as a model compound and matching its hydration enthalpy and conformational behavior to experiment. Excellent agreement with previous experimental and simulation work was obtained through these modifications. The simulated scaling behavior of the PEO radius of gyration was also in close agreement with experimental results. The SDS-PEO simulations show that the polymer resides on the micelle surface and at the hydrocarbon-water interface, leading to a selective reduction in the hydrophobic contribution to the solvent-accessible surface area of the micelle. The association is mainly driven by hydrophobic interactions between the polymer and surfactant tails, while the interaction between the polymer and sulfate headgroups on the micelle surface is weak. The 40-monomer chain is mostly wrapped around the micelle, and nearly 90% of the monomers are adsorbed at low PEO concentration. Simulations were also performed with multiple 20-monomer chains, and gradual addition of polymer indicates that about 120 monomers are required to saturate the micelle surface. The stoichiometry of the resulting complex is in close agreement with experimental results, and the commonly accepted "beaded necklace" structure of the SDS-PEO complex is recovered by our simulations.

Estimation of absolute solvent and solvation shell entropies via permutation reduction

NASA Astrophysics Data System (ADS)

Reinhard, Friedemann; Grubmüller, Helmut

2007-01-01

Despite its prominent contribution to the free energy of solvated macromolecules such as proteins or DNA, and although principally contained within molecular dynamics simulations, the entropy of the solvation shell is inaccessible to straightforward application of established entropy estimation methods. The complication is twofold. First, the configurational space density of such systems is too complex for a sufficiently accurate fit. Second, and in contrast to the internal macromolecular dynamics, the configurational space volume explored by the diffusive motion of the solvent molecules is too large to be exhaustively sampled by current simulation techniques. Here, we develop a method to overcome the second problem and to significantly alleviate the first one. We propose to exploit the permutation symmetry of the solvent by transforming the trajectory in a way that renders established estimation methods applicable, such as the quasiharmonic approximation or principal component analysis. Our permutation-reduced approach involves a combinatorial problem, which is solved through its equivalence with the linear assignment problem, for which O(N3) methods exist. From test simulations of dense Lennard-Jones gases, enhanced convergence and improved entropy estimates are obtained. Moreover, our approach renders diffusive systems accessible to improved fit functions.

A significant reduction of ice adhesion on nanostructured surfaces that consist of an array of single-walled carbon nanotubes: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Bao, Luyao; Huang, Zhaoyuan; Priezjev, Nikolai V.; Chen, Shaoqiang; Luo, Kai; Hu, Haibao

2018-04-01

It is well recognized that excessive ice accumulation at low-temperature conditions can cause significant damage to civil infrastructure. The passive anti-icing surfaces provide a promising solution to suppress ice nucleation and enhance ice removal. However, despite extensive efforts, it remains a challenge to design anti-icing surfaces with low ice adhesion. Using all-atom molecular dynamics (MD) simulations, we show that surfaces with single-walled carbon nanotube array (CNTA) significantly reduce ice adhesion due to the extremely low solid areal fraction. It was found that the CNTA surface exhibits up to a 45% decrease in the ice adhesion strength in comparison with the atomically smooth graphene surface. The details of the ice detachment from the CNTA surface were examined for different water-carbon interaction energies and temperatures of the ice cube. Remarkably, the results of MD simulations demonstrate that the ice detaching strength depends linearly on the ratio of the ice-surface interaction energy and the ice temperature. These results open the possibility for designing novel robust surfaces with low ice adhesion for passive anti-icing applications.

Proposal for a new mass distribution control system and its simulation for vibration reduction on rotating machinery

NASA Astrophysics Data System (ADS)

Enginoglu, Ozan; Ozturk, Hasan

2016-12-01

This study presents a new mass distribution control system (MDCS) along with its analysis and simulation. It is aimed to balance a system containing rotating parts in order to minimize the dynamic vibration on it. For this purpose, a test mechanism rotating with an angular velocity of ω is simulated. The mechanism consists of a pair of MDCS, each containing three flaps connected to the shaft. The flaps rotate in relation to the shaft's plane of rotation. The center of gravity (COG) of the MDCS is concentric with the shaft axis when all three flaps are stretched out but the COG changes as the flaps rotate. By adjusting the orientations of the flaps in both systems, it is possible to create a counterforce which suppresses the imbalance force, reducing the vibration to a minimum.

Computer simulation of the matrix-inclusion interphase in bulk metallic glass based nanocomposites

NASA Astrophysics Data System (ADS)

Kokotin, V.; Hermann, H.; Eckert, J.

2011-10-01

Atomistic models for matrix-inclusion systems are generated. Analyses of the systems show that interphase layers of finite thickness appear interlinking the surface of the nanocrystalline inclusion and the embedding amorphous matrix. In a first approximation, the interphase is characterized as an amorphous structure with a density slightly reduced compared to that of the matrix. This result holds for both monatomic hard sphere systems and a Cu47.5Zr47.5Al5 alloy simulated by molecular dynamics (MD). The elastic shear and bulk modulus of the interphase are calculated by simulated deformation of the MD systems. Both moduli diminish with decreasing density but the shear modulus is more sensitive against density reduction by one order of magnitude. This result explains recent observations of shear band initiation at the amorphous-crystalline interface during plastic deformation.

Thermal transport in UO 2 with defects and fission products by molecular dynamics simulations

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

Liu, Xiang-Yang; Cooper, Michael William Donald; Mcclellan, Kenneth James

2015-10-14

The importance of the thermal transport in nuclear fuel has motivated a wide range of experimental and modelling studies. In this report, the reduction of thermal transport in UO 2 due to defects and fission products has been investigated using non-equilibrium MD simulations, with two sets of empirical potentials for studying the degregation of UO 2 thermal conductivity including a Buckingham type interatomic potential and a recently developed EAM type interatomic potential. Additional parameters for U 5+ and Zr 4+ in UO 2 have been developed for the EAM potential. The thermal conductivity results from MD simulations are then correctedmore » for the spin-phonon scattering through Callaway model formulations. To validate the modelling results, comparison was made with experimental measurements on single crystal hyper-stoichiometric UO 2+x samples.« less

The Societal Costs and Benefits of Commuter Bicycling: Simulating the Effects of Specific Policies Using System Dynamics Modeling

PubMed Central

Connor, Jennie; Witten, Karen; Kearns, Robin; Rees, David; Woodward, Alistair

2014-01-01

Background: Shifting to active modes of transport in the trip to work can achieve substantial co-benefits for health, social equity, and climate change mitigation. Previous integrated modeling of transport scenarios has assumed active transport mode share and has been unable to incorporate acknowledged system feedbacks. Objectives: We compared the effects of policies to increase bicycle commuting in a car-dominated city and explored the role of participatory modeling to support transport planning in the face of complexity. Methods: We used system dynamics modeling (SDM) to compare realistic policies, incorporating feedback effects, nonlinear relationships, and time delays between variables. We developed a system dynamics model of commuter bicycling through interviews and workshops with policy, community, and academic stakeholders. We incorporated best available evidence to simulate five policy scenarios over the next 40 years in Auckland, New Zealand. Injury, physical activity, fuel costs, air pollution, and carbon emissions outcomes were simulated. Results: Using the simulation model, we demonstrated the kinds of policies that would likely be needed to change a historical pattern of decline in cycling into a pattern of growth that would meet policy goals. Our model projections suggest that transforming urban roads over the next 40 years, using best practice physical separation on main roads and bicycle-friendly speed reduction on local streets, would yield benefits 10–25 times greater than costs. Conclusions: To our knowledge, this is the first integrated simulation model of future specific bicycling policies. Our projections provide practical evidence that may be used by health and transport policy makers to optimize the benefits of transport bicycling while minimizing negative consequences in a cost-effective manner. The modeling process enhanced understanding by a range of stakeholders of cycling as a complex system. Participatory SDM can be a helpful method for integrating health and environmental outcomes in transport and urban planning. Citation: Macmillan A, Connor J, Witten K, Kearns R, Rees D, Woodward A. 2014. The societal costs and benefits of commuter bicycling: simulating the effects of specific policies using system dynamics modeling. Environ Health Perspect 122:335–344; http://dx.doi.org/10.1289/ehp.1307250 PMID:24496244

Evaluation of low emission zone policy on vehicle emission reduction in Beijing, China

NASA Astrophysics Data System (ADS)

Zhang, Yi; Andre, Michel; Liu, Yao; Wu, Lin; Jing, Boyu; Mao, Hongjun

2018-02-01

This study evaluates the effect of the LEZ in Beijing from the perspective of vehicle emission reduction based on developing an urban street-scale vehicle emission inventory on the basis of the local emission factors and the dynamic or static traffic data via a bottom-up approach. In 2016, before the implementation of the LEZ, the vehicle emission of CO, HC, NOx, and PM were 49.01×104, 6.31×104, 5.96×104, and 0.12×104 t, respectively. According to the simulation results, the LEZ policy would have an obviously positive effect on emission reduction, especially for CO and HC. In order to realize the long-term mitigation target, it is necessary to update and amend the detailed terms of the LEZ policy regularly according to the traffic development and vehicle emission change.

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0059: Molecular Dynamics Modeling Support

DTIC Science & Technology

2008-03-01

Molecular Dynamics Simulations 5 Theory: Equilibrium Molecular Dynamics Simulations 6 Theory: Non...Equilibrium Molecular Dynamics Simulations 8 Carbon Nanotube Simulations : Approach and results from equilibrium and non-equilibrium molecular dynamics ...touched from the perspective of molecular dynamics simulations . However, ordered systems such as “Carbon Nanotubes” have been investigated in terms

Antimicrobial Properties of Selected Copper Alloys on Staphylococcus aureus and Escherichia coli in Different Simulations of Environmental Conditions: With vs. without Organic Contamination

PubMed Central

Różańska, Anna; Chmielarczyk, Agnieszka; Romaniszyn, Dorota; Sroka-Oleksiak, Agnieszka; Bulanda, Małgorzata; Walkowicz, Monika; Osuch, Piotr; Knych, Tadeusz

2017-01-01

Background: Hospital equipment made from copper alloys can play an important role in complementing traditional methods of disinfection. Aims of the study: The aim of this study was to assess the dynamics of the antimicrobial properties of selected copper alloys in different simulations of environmental conditions (with organic contamination vs. without organic contamination), and to test alternatives to the currently used testing methods. Materials and Methods: A modification of Japanese standard JIS Z 2801 as well as Staphylococcus aureus (SA) and Escherichia coli (EC) suspended in NaCl vs. tryptic soy broth (TSB) were used in tests performed on seven commonly used copper alloys, copper, and stainless steel. Results: A much faster reduction of the bacterial suspension was observed for the inoculum prepared in NaCl than in TSB. A faster reduction for EC than for SA was observed in the inoculum prepared in NaCl. The opposite results were found for the inoculum based on TSB. A significant correlation between the copper concentration in the copper alloys and the time and degree of bacterial suspension reduction was only observed in the case of EC. Conclusions: This study confirmed the antimicrobial properties of copper alloys, and additionally showed that Staphylococcus aureus was more resistant than Escherichia coli in the variant of the experiment without organic contamination. However, even for SA, a total reduction of the bacterial inoculum’s density took no longer than 2 h. Under conditions simulating organic contamination, all of the tested alloys were shown to have bactericidal or bacteriostatic properties, which was contrary to the results from stainless steel. PMID:28726753

Antimicrobial Properties of Selected Copper Alloys on Staphylococcus aureus and Escherichia coli in Different Simulations of Environmental Conditions: With vs. without Organic Contamination.

PubMed

Różańska, Anna; Chmielarczyk, Agnieszka; Romaniszyn, Dorota; Sroka-Oleksiak, Agnieszka; Bulanda, Małgorzata; Walkowicz, Monika; Osuch, Piotr; Knych, Tadeusz

2017-07-20

Background: Hospital equipment made from copper alloys can play an important role in complementing traditional methods of disinfection. Aims of the study: The aim of this study was to assess the dynamics of the antimicrobial properties of selected copper alloys in different simulations of environmental conditions (with organic contamination vs. without organic contamination), and to test alternatives to the currently used testing methods. Materials and Methods: A modification of Japanese standard JIS Z 2801 as well as Staphylococcus aureus (SA) and Escherichia coli (EC) suspended in NaCl vs. tryptic soy broth (TSB) were used in tests performed on seven commonly used copper alloys, copper, and stainless steel. Results: A much faster reduction of the bacterial suspension was observed for the inoculum prepared in NaCl than in TSB. A faster reduction for EC than for SA was observed in the inoculum prepared in NaCl. The opposite results were found for the inoculum based on TSB. A significant correlation between the copper concentration in the copper alloys and the time and degree of bacterial suspension reduction was only observed in the case of EC. Conclusions: This study confirmed the antimicrobial properties of copper alloys, and additionally showed that Staphylococcus aureus was more resistant than Escherichia coli in the variant of the experiment without organic contamination. However, even for SA, a total reduction of the bacterial inoculum's density took no longer than 2 h. Under conditions simulating organic contamination, all of the tested alloys were shown to have bactericidal or bacteriostatic properties, which was contrary to the results from stainless steel.

Top-down constraints on disturbance dynamics in the terrestrial carbon cycle: effects at global and regional scales

NASA Astrophysics Data System (ADS)

Bloom, A. A.; Exbrayat, J. F.; van der Velde, I.; Peters, W.; Williams, M.

2014-12-01

Large uncertainties preside over terrestrial carbon flux estimates on a global scale. In particular, the strongly coupled dynamics between net ecosystem productivity and disturbance C losses are poorly constrained. To gain an improved understanding of ecosystem C dynamics from regional to global scale, we apply a Markov Chain Monte Carlo based model-data-fusion approach into the CArbon DAta-MOdel fraMework (CARDAMOM). We assimilate MODIS LAI and burned area, plant-trait data, and use the Harmonized World Soil Database (HWSD) and maps of above ground biomass as prior knowledge for initial conditions. We optimize model parameters based on (a) globally spanning observations and (b) ecological and dynamic constraints that force single parameter values and parameter inter-dependencies to be representative of real world processes. We determine the spatial and temporal dynamics of major terrestrial C fluxes and model parameter values on a global scale (GPP = 123 +/- 8 Pg C yr-1 & NEE = -1.8 +/- 2.7 Pg C yr-1). We further show that the incorporation of disturbance fluxes, and accounting for their instantaneous or delayed effect, is of critical importance in constraining global C cycle dynamics, particularly in the tropics. In a higher resolution case study centred on the Amazon Basin we show how fires not only trigger large instantaneous emissions of burned matter, but also how they are responsible for a sustained reduction of up to 50% in plant uptake following the depletion of biomass stocks. The combination of these two fire-induced effects leads to a 1 g C m-2 d-1reduction in the strength of the net terrestrial carbon sink. Through our simulations at regional and global scale, we advocate the need to assimilate disturbance metrics in global terrestrial carbon cycle models to bridge the gap between globally spanning terrestrial carbon cycle data and the full dynamics of the ecosystem C cycle. Disturbances are especially important because their quick occurrence may have long-term effects on ecosystems. Our synthetic simulations show that while tropical ecosystems uptake may reach pre-disturbance level after a decade, biomass stocks would most likely need more than a century to recover from a single extreme disturbance event.

Silicon material task. Part 3: Low-cost silicon solar array project

NASA Technical Reports Server (NTRS)

Roques, R. A.; Coldwell, D. M.

1977-01-01

The feasibility of a process for carbon reduction of low impurity silica in a plasma heat source was investigated to produce low-cost solar-grade silicon. Theoretical aspects of the reaction chemistry were studied with the aid of a computer program using iterative free energy minimization. These calculations indicate a threshold temperature exists at 2400 K below which no silicon is formed. The computer simulation technique of molecular dynamics was used to study the quenching of product species.

Zonal flow dynamics and control of turbulent transport in stellarators.

PubMed

Xanthopoulos, P; Mischchenko, A; Helander, P; Sugama, H; Watanabe, T-H

2011-12-09

The relation between magnetic geometry and the level of ion-temperature-gradient (ITG) driven turbulence in stellarators is explored through gyrokinetic theory and direct linear and nonlinear simulations. It is found that the ITG radial heat flux is sensitive to details of the magnetic configuration that can be understood in terms of the linear behavior of zonal flows. The results throw light on the question of how the optimization of neoclassical confinement is related to the reduction of turbulence.

Noise analysis for near field 3-D FM-CW radar imaging systems

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

Sheen, David M.

2015-06-19

Near field radar imaging systems are used for several applications including concealed weapon detection in airports and other high-security venues. Despite the near-field operation, phase noise and thermal noise can limit the performance in several ways including reduction in system sensitivity and reduction of image dynamic range. In this paper, the effects of thermal noise, phase noise, and processing gain are analyzed in the context of a near field 3-D FM-CW imaging radar as might be used for concealed weapon detection. In addition to traditional frequency domain analysis, a time-domain simulation is employed to graphically demonstrate the effect of thesemore » noise sources on a fast-chirping FM-CW system.« less

Significant reduction of thermal conductivity in Si/Ge core-shell nanowires.

PubMed

Hu, Ming; Giapis, Konstantinos P; Goicochea, Javier V; Zhang, Xiaoliang; Poulikakos, Dimos

2011-02-09

We report on the effect of germanium (Ge) coatings on the thermal transport properties of silicon (Si) nanowires using nonequilibrium molecular dynamics simulations. Our results show that a simple deposition of a Ge shell of only 1 to 2 unit cells in thickness on a single crystalline Si nanowire can lead to a dramatic 75% decrease in thermal conductivity at room temperature compared to an uncoated Si nanowire. By analyzing the vibrational density states of phonons and the participation ratio of each specific mode, we demonstrate that the reduction in the thermal conductivity of Si/Ge core-shell nanowire stems from the depression and localization of long-wavelength phonon modes at the Si/Ge interface and of high frequency nonpropagating diffusive modes.

Phase-contrast MRI versus numerical simulation to quantify hemodynamical changes in cerebral aneurysms after flow diverter treatment

PubMed Central

Frolov, Sergey; Prothmann, Sascha; Liepsch, Dieter; Balasso, Andrea; Berg, Philipp; Kaczmarz, Stephan; Kirschke, Jan Stefan

2018-01-01

Cerebral aneurysms are a major risk factor for intracranial bleeding with devastating consequences for the patient. One recently established treatment is the implantation of flow-diverters (FD). Methods to predict their treatment success before or directly after implantation are not well investigated yet. The aim of this work was to quantitatively study hemodynamic parameters in patient-specific models of treated cerebral aneurysms and its correlation with the clinical outcome. Hemodynamics were evaluated using both computational fluid dynamics (CFD) and phase contrast (PC) MRI. CFD simulations and in vitro MRI measurements were done under similar flow conditions and results of both methods were comparatively analyzed. For preoperative and postoperative distribution of hemodynamic parameters, CFD simulations and PC-MRI velocity measurements showed similar results. In both cases where no occlusion of the aneurysm was observed after six months, a flow reduction of about 30-50% was found, while in the clinically successful case with complete occlusion of the aneurysm after 6 months, the flow reduction was about 80%. No vortex was observed in any of the three models after treatment. The results are in agreement with recent studies suggesting that CFD simulations can predict post-treatment aneurysm flow alteration already before implantation of a FD and PC-MRI could validate the predicted hemodynamic changes right after implantation of a FD. PMID:29304062

Variance-reduced simulation of lattice discrete-time Markov chains with applications in reaction networks

NASA Astrophysics Data System (ADS)

Maginnis, P. A.; West, M.; Dullerud, G. E.

2016-10-01

We propose an algorithm to accelerate Monte Carlo simulation for a broad class of stochastic processes. Specifically, the class of countable-state, discrete-time Markov chains driven by additive Poisson noise, or lattice discrete-time Markov chains. In particular, this class includes simulation of reaction networks via the tau-leaping algorithm. To produce the speedup, we simulate pairs of fair-draw trajectories that are negatively correlated. Thus, when averaged, these paths produce an unbiased Monte Carlo estimator that has reduced variance and, therefore, reduced error. Numerical results for three example systems included in this work demonstrate two to four orders of magnitude reduction of mean-square error. The numerical examples were chosen to illustrate different application areas and levels of system complexity. The areas are: gene expression (affine state-dependent rates), aerosol particle coagulation with emission and human immunodeficiency virus infection (both with nonlinear state-dependent rates). Our algorithm views the system dynamics as a ;black-box;, i.e., we only require control of pseudorandom number generator inputs. As a result, typical codes can be retrofitted with our algorithm using only minor changes. We prove several analytical results. Among these, we characterize the relationship of covariances between paths in the general nonlinear state-dependent intensity rates case, and we prove variance reduction of mean estimators in the special case of affine intensity rates.

Incorporating human-water dynamics in a hyper-resolution land surface model

NASA Astrophysics Data System (ADS)

Vergopolan, N.; Chaney, N.; Wanders, N.; Sheffield, J.; Wood, E. F.

2017-12-01

The increasing demand for water, energy, and food is leading to unsustainable groundwater and surface water exploitation. As a result, the human interactions with the environment, through alteration of land and water resources dynamics, need to be reflected in hydrologic and land surface models (LSMs). Advancements in representing human-water dynamics still leave challenges related to the lack of water use data, water allocation algorithms, and modeling scales. This leads to an over-simplistic representation of human water use in large-scale models; this is in turn leads to an inability to capture extreme events signatures and to provide reliable information at stakeholder-level spatial scales. The emergence of hyper-resolution models allows one to address these challenges by simulating the hydrological processes and interactions with the human impacts at field scales. We integrated human-water dynamics into HydroBlocks - a hyper-resolution, field-scale resolving LSM. HydroBlocks explicitly solves the field-scale spatial heterogeneity of land surface processes through interacting hydrologic response units (HRUs); and its HRU-based model parallelization allows computationally efficient long-term simulations as well as ensemble predictions. The implemented human-water dynamics include groundwater and surface water abstraction to meet agricultural, domestic and industrial water demands. Furthermore, a supply-demand water allocation scheme based on relative costs helps to determine sectoral water use requirements and tradeoffs. A set of HydroBlocks simulations over the Midwest United States (daily, at 30-m spatial resolution for 30 years) are used to quantify the irrigation impacts on water availability. The model captures large reductions in total soil moisture and water table levels, as well as spatiotemporal changes in evapotranspiration and runoff peaks, with their intensity related to the adopted water management strategy. By incorporating human-water dynamics in a hyper-resolution LSM this work allows for progress on hydrological monitoring and predictions, as well as drought preparedness and water impact assessments at relevant decision-making scales.

Repetition-related reductions in neural activity reveal component processes of mental simulation.

PubMed

Szpunar, Karl K; St Jacques, Peggy L; Robbins, Clifford A; Wig, Gagan S; Schacter, Daniel L

2014-05-01

In everyday life, people adaptively prepare for the future by simulating dynamic events about impending interactions with people, objects and locations. Previous research has consistently demonstrated that a distributed network of frontal-parietal-temporal brain regions supports this ubiquitous mental activity. Nonetheless, little is known about the manner in which specific regions of this network contribute to component features of future simulation. In two experiments, we used a functional magnetic resonance (fMR)-repetition suppression paradigm to demonstrate that distinct frontal-parietal-temporal regions are sensitive to processing the scenarios or what participants imagined was happening in an event (e.g., medial prefrontal, posterior cingulate, temporal-parietal and middle temporal cortices are sensitive to the scenarios associated with future social events), people (medial prefrontal cortex), objects (inferior frontal and premotor cortices) and locations (posterior cingulate/retrosplenial, parahippocampal and posterior parietal cortices) that typically constitute simulations of personal future events. This pattern of results demonstrates that the neural substrates of these component features of event simulations can be reliably identified in the context of a task that requires participants to simulate complex, everyday future experiences.

Development of a large-scale, outdoor, ground-based test capability for evaluating the effect of rain on airfoil lift

NASA Technical Reports Server (NTRS)

Bezos, Gaudy M.; Campbell, Bryan A.

1993-01-01

A large-scale, outdoor, ground-based test capability for acquiring aerodynamic data in a simulated rain environment was developed at the Langley Aircraft Landing Dynamics Facility (ALDF) to assess the effect of heavy rain on airfoil performance. The ALDF test carriage was modified to transport a 10-ft-chord NACA 64210 wing section along a 3000-ft track at full-scale aircraft approach speeds. An overhead rain simulation system was constructed along a 525-ft section of the track with the capability of producing simulated rain fields of 2, 10, 30, and 40 in/hr. The facility modifications, the aerodynamic testing and rain simulation capability, the design and calibration of the rain simulation system, and the operational procedures developed to minimize the effect of wind on the simulated rain field and aerodynamic data are described in detail. The data acquisition and reduction processes are also presented along with sample force data illustrating the environmental effects on data accuracy and repeatability for the 'rain-off' test condition.

Model and Data Reduction for Control, Identification and Compressed Sensing

NASA Astrophysics Data System (ADS)

Kramer, Boris

This dissertation focuses on problems in design, optimization and control of complex, large-scale dynamical systems from different viewpoints. The goal is to develop new algorithms and methods, that solve real problems more efficiently, together with providing mathematical insight into the success of those methods. There are three main contributions in this dissertation. In Chapter 3, we provide a new method to solve large-scale algebraic Riccati equations, which arise in optimal control, filtering and model reduction. We present a projection based algorithm utilizing proper orthogonal decomposition, which is demonstrated to produce highly accurate solutions at low rank. The method is parallelizable, easy to implement for practitioners, and is a first step towards a matrix free approach to solve AREs. Numerical examples for n ≥ 106 unknowns are presented. In Chapter 4, we develop a system identification method which is motivated by tangential interpolation. This addresses the challenge of fitting linear time invariant systems to input-output responses of complex dynamics, where the number of inputs and outputs is relatively large. The method reduces the computational burden imposed by a full singular value decomposition, by carefully choosing directions on which to project the impulse response prior to assembly of the Hankel matrix. The identification and model reduction step follows from the eigensystem realization algorithm. We present three numerical examples, a mass spring damper system, a heat transfer problem, and a fluid dynamics system. We obtain error bounds and stability results for this method. Chapter 5 deals with control and observation design for parameter dependent dynamical systems. We address this by using local parametric reduced order models, which can be used online. Data available from simulations of the system at various configurations (parameters, boundary conditions) is used to extract a sparse basis to represent the dynamics (via dynamic mode decomposition). Subsequently, a new, compressed sensing based classification algorithm is developed which incorporates the extracted dynamic information into the sensing basis. We show that this augmented classification basis makes the method more robust to noise, and results in superior identification of the correct parameter. Numerical examples consist of a Navier-Stokes, as well as a Boussinesq flow application.

Dynamical downscaling with the fifth-generation Canadian regional climate model (CRCM5) over the CORDEX Arctic domain: effect of large-scale spectral nudging and of empirical correction of sea-surface temperature

NASA Astrophysics Data System (ADS)

Takhsha, Maryam; Nikiéma, Oumarou; Lucas-Picher, Philippe; Laprise, René; Hernández-Díaz, Leticia; Winger, Katja

2017-10-01

As part of the CORDEX project, the fifth-generation Canadian Regional Climate Model (CRCM5) is used over the Arctic for climate simulations driven by reanalyses and by the MPI-ESM-MR coupled global climate model (CGCM) under the RCP8.5 scenario. The CRCM5 shows adequate skills capturing general features of mean sea level pressure (MSLP) for all seasons. Evaluating 2-m temperature (T2m) and precipitation is more problematic, because of inconsistencies between observational reference datasets over the Arctic that suffer of a sparse distribution of weather stations. In our study, we additionally investigated the effect of large-scale spectral nudging (SN) on the hindcast simulation driven by reanalyses. The analysis shows that SN is effective in reducing the spring MSLP bias, but otherwise it has little impact. We have also conducted another experiment in which the CGCM-simulated sea-surface temperature (SST) is empirically corrected and used as lower boundary conditions over the ocean for an atmosphere-only global simulation (AGCM), which in turn provides the atmospheric lateral boundary conditions to drive the CRCM5 simulation. This approach, so-called 3-step approach of dynamical downscaling (CGCM-AGCM-RCM), which had considerably improved the CRCM5 historical simulations over Africa, exhibits reduced impact over the Arctic domain. The most notable positive effect over the Arctic is a reduction of the T2m bias over the North Pacific Ocean and the North Atlantic Ocean in all seasons. Future projections using this method are compared with the results obtained with the traditional 2-step dynamical downscaling (CGCM-RCM) to assess the impact of correcting systematic biases of SST upon future-climate projections. The future projections are mostly similar for the two methods, except for precipitation.

A Dynamical Downscaling Approach with GCM Bias Corrections and Spectral Nudging

NASA Astrophysics Data System (ADS)

Xu, Z.; Yang, Z.

2013-12-01

To reduce the biases in the regional climate downscaling simulations, a dynamical downscaling approach with GCM bias corrections and spectral nudging is developed and assessed over North America. Regional climate simulations are performed with the Weather Research and Forecasting (WRF) model embedded in the National Center for Atmospheric Research (NCAR) Community Atmosphere Model (CAM). To reduce the GCM biases, the GCM climatological means and the variances of interannual variations are adjusted based on the National Centers for Environmental Prediction-NCAR global reanalysis products (NNRP) before using them to drive WRF which is the same as our previous method. In this study, we further introduce spectral nudging to reduce the RCM-based biases. Two sets of WRF experiments are performed with and without spectral nudging. All WRF experiments are identical except that the initial and lateral boundary conditions are derived from the NNRP, the original GCM output, and the bias corrected GCM output, respectively. The GCM-driven RCM simulations with bias corrections and spectral nudging (IDDng) are compared with those without spectral nudging (IDD) and North American Regional Reanalysis (NARR) data to assess the additional reduction in RCM biases relative to the IDD approach. The results show that the spectral nudging introduces the effect of GCM bias correction into the RCM domain, thereby minimizing the climate drift resulting from the RCM biases. The GCM bias corrections and spectral nudging significantly improve the downscaled mean climate and extreme temperature simulations. Our results suggest that both GCM bias corrections or spectral nudging are necessary to reduce the error of downscaled climate. Only one of them does not guarantee better downscaling simulation. The new dynamical downscaling method can be applied to regional projection of future climate or downscaling of GCM sensitivity simulations. Annual mean RMSEs. The RMSEs are computed over the verification region by monthly mean data over 1981-2010. Experimental design

Influence of polymer-surfactant aggregates on fluid flow.

PubMed

Malcher, Tadeusz; Gzyl-Malcher, Barbara

2012-10-01

This paper describes the influence of interactions of poly(ethylene oxide) (PEO) with cationic cetyltrimethylammonium bromide (CTAB) micelles on drag reduction. Since the interactions between PEO and CTAB micelles alone are weak, salicylate ions were used as CTAB counterions. They facilitate formation of polymer-micelle aggregates by screening the electrostatic repulsions between the charged surfactant headgroups. The influence of polymer-surfactant interactions on drag reduction is of biomedical engineering importance. Drag reducing additives introduced to blood produce beneficial effects on blood circulation, representing a novel way to treat cardiovascular disorders. PEO is a blood-compatible polymer. However, it quickly mechanically degrades when subjected to high shear stresses. Thus, there is a need to search for other additives able to reduce drag, which would be more mechanically stable, e.g. polymer-surfactant aggregates. Numerical simulations of the flow were performed using the CFX software. Based on the internal structure of the polymer-surfactant solution, a hypothesis explaining the reason of increase of drag reduction and decrease in dynamic viscosity with increasing shear rate was proposed. It was suggested that the probable reason for the abrupt increase in friction factor, observed when the critical Reynolds number was exceeded, was the disappearance of the difference in the dynamic viscosity. Copyright © 2012 Elsevier B.V. All rights reserved.

Practical recipes for the model order reduction, dynamical simulation and compressive sampling of large-scale open quantum systems

NASA Astrophysics Data System (ADS)

Sidles, John A.; Garbini, Joseph L.; Harrell, Lee E.; Hero, Alfred O.; Jacky, Jonathan P.; Malcomb, Joseph R.; Norman, Anthony G.; Williamson, Austin M.

2009-06-01

Practical recipes are presented for simulating high-temperature and nonequilibrium quantum spin systems that are continuously measured and controlled. The notion of a spin system is broadly conceived, in order to encompass macroscopic test masses as the limiting case of large-j spins. The simulation technique has three stages: first the deliberate introduction of noise into the simulation, then the conversion of that noise into an equivalent continuous measurement and control process, and finally, projection of the trajectory onto state-space manifolds having reduced dimensionality and possessing a Kähler potential of multilinear algebraic form. These state-spaces can be regarded as ruled algebraic varieties upon which a projective quantum model order reduction (MOR) is performed. The Riemannian sectional curvature of ruled Kählerian varieties is analyzed, and proved to be non-positive upon all sections that contain a rule. These manifolds are shown to contain Slater determinants as a special case and their identity with Grassmannian varieties is demonstrated. The resulting simulation formalism is used to construct a positive P-representation for the thermal density matrix. Single-spin detection by magnetic resonance force microscopy (MRFM) is simulated, and the data statistics are shown to be those of a random telegraph signal with additive white noise. Larger-scale spin-dust models are simulated, having no spatial symmetry and no spatial ordering; the high-fidelity projection of numerically computed quantum trajectories onto low dimensionality Kähler state-space manifolds is demonstrated. The reconstruction of quantum trajectories from sparse random projections is demonstrated, the onset of Donoho-Stodden breakdown at the Candès-Tao sparsity limit is observed, a deterministic construction for sampling matrices is given and methods for quantum state optimization by Dantzig selection are given.

Maximum height and minimum time vertical jumping.

PubMed

Domire, Zachary J; Challis, John H

2015-08-20

The performance criterion in maximum vertical jumping has typically been assumed to simply raise the center of mass as high as possible. In many sporting activities minimizing movement time during the jump is likely also critical to successful performance. The purpose of this study was to examine maximum height jumps performed while minimizing jump time. A direct dynamics model was used to examine squat jump performance, with dual performance criteria: maximize jump height and minimize jump time. The muscle model had activation dynamics, force-length, force-velocity properties, and a series of elastic component representing the tendon. The simulations were run in two modes. In Mode 1 the model was placed in a fixed initial position. In Mode 2 the simulation model selected the initial squat configuration as well as the sequence of muscle activations. The inclusion of time as a factor in Mode 1 simulations resulted in a small decrease in jump height and moderate time savings. The improvement in time was mostly accomplished by taking off from a less extended position. In Mode 2 simulations, more substantial time savings could be achieved by beginning the jump in a more upright posture. However, when time was weighted more heavily in these simulations, there was a more substantial reduction in jump height. Future work is needed to examine the implications for countermovement jumping and to examine the possibility of minimizing movement time as part of the control scheme even when the task is to jump maximally. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impacts of aerosol direct effects on tropospheric ozone through changes in atmospheric dynamics and photolysis rates

NASA Astrophysics Data System (ADS)

Xing, Jia; Wang, Jiandong; Mathur, Rohit; Wang, Shuxiao; Sarwar, Golam; Pleim, Jonathan; Hogrefe, Christian; Zhang, Yuqiang; Jiang, Jingkun; Wong, David C.; Hao, Jiming

2017-08-01

Aerosol direct effects (ADEs), i.e., scattering and absorption of incoming solar radiation, reduce radiation reaching the ground and the resultant photolysis attenuation can decrease ozone (O3) formation in polluted areas. One the other hand, evidence also suggests that ADE-associated cooling suppresses atmospheric ventilation, thereby enhancing surface-level O3. Assessment of ADE impacts is thus important for understanding emission reduction strategies that seek co-benefits associated with reductions in both particulate matter and O3 levels. This study quantifies the impacts of ADEs on tropospheric ozone by using a two-way online coupled meteorology and atmospheric chemistry model, WRF-CMAQ, using a process analysis methodology. Two manifestations of ADE impacts on O3 including changes in atmospheric dynamics (ΔDynamics) and changes in photolysis rates (ΔPhotolysis) were assessed separately through multiple scenario simulations for January and July of 2013 over China. Results suggest that ADEs reduced surface daily maxima 1 h O3 (DM1O3) in China by up to 39 µg m-3 through the combination of ΔDynamics and ΔPhotolysis in January but enhanced surface DM1O3 by up to 4 µg m-3 in July. Increased O3 in July is largely attributed to ΔDynamics, which causes a weaker O3 sink of dry deposition and a stronger O3 source of photochemistry due to the stabilization of the atmosphere. Meanwhile, surface OH is also enhanced at noon in July, though its daytime average values are reduced in January. An increased OH chain length and a shift towards more volatile organic compound (VOC)-limited conditions are found due to ADEs in both January and July. This study suggests that reducing ADEs may have the potential risk of increasing O3 in winter, but it will benefit the reduction in maxima O3 in summer.

Forest fuel reduction alters fire severity and long-term carbon storage in three Pacific Northwest ecosystems.

PubMed

Mitchell, Stephen R; Harmon, Mark E; O'Connell, Kari E B

2009-04-01

Two forest management objectives being debated in the context of federally managed landscapes in the U.S. Pacific Northwest involve a perceived trade-off between fire restoration and carbon sequestration. The former strategy would reduce fuel (and therefore C) that has accumulated through a century of fire suppression and exclusion which has led to extreme fire risk in some areas. The latter strategy would manage forests for enhanced C sequestration as a method of reducing atmospheric CO2 and associated threats from global climate change. We explored the trade-off between these two strategies by employing a forest ecosystem simulation model, STANDCARB, to examine the effects of fuel reduction on fire severity and the resulting long-term C dynamics among three Pacific Northwest ecosystems: the east Cascades ponderosa pine forests, the west Cascades western hemlock-Douglas-fir forests, and the Coast Range western hemlock-Sitka spruce forests. Our simulations indicate that fuel reduction treatments in these ecosystems consistently reduced fire severity. However, reducing the fraction by which C is lost in a wildfire requires the removal of a much greater amount of C, since most of the C stored in forest biomass (stem wood, branches, coarse woody debris) remains unconsumed even by high-severity wildfires. For this reason, all of the fuel reduction treatments simulated for the west Cascades and Coast Range ecosystems as well as most of the treatments simulated for the east Cascades resulted in a reduced mean stand C storage. One suggested method of compensating for such losses in C storage is to utilize C harvested in fuel reduction treatments as biofuels. Our analysis indicates that this will not be an effective strategy in the west Cascades and Coast Range over the next 100 years. We suggest that forest management plans aimed solely at ameliorating increases in atmospheric CO2 should forgo fuel reduction treatments in these ecosystems, with the possible exception of some east Cascades ponderosa pine stands with uncharacteristic levels of understory fuel accumulation. Balancing a demand for maximal landscape C storage with the demand for reduced wildfire severity will likely require treatments to be applied strategically throughout the landscape rather than indiscriminately treating all stands.

Communication: Hot-atom abstraction dynamics of hydrogen from tungsten surfaces: The role of surface structure

NASA Astrophysics Data System (ADS)

Galparsoro, Oihana; Busnengo, Heriberto Fabio; Juaristi, Joseba Iñaki; Crespos, Cédric; Alducin, Maite; Larregaray, Pascal

2017-09-01

Adiabatic and non-adiabatic quasiclassical molecular dynamics simulations are performed to investigate the role of the crystal face on hot-atom abstraction of H adsorbates by H scattering from covered W(100) and W(110). On both cases, hyperthermal diffusion is strongly affected by the energy dissipated into electron-hole pair excitations. As a result, the hot-atom abstraction is highly reduced in favor of adsorption at low incidence energy and low coverages, i.e., when the mean free path of the hyperthermal H is typically larger. Qualitatively, this reduction is rather similar on both surfaces, despite at such initial conditions, the abstraction process involves more subsurface penetration on W(100) than on W(110).

Viscoelastic and elastomeric active matter: linear instability and nonlinear dynamics

NASA Astrophysics Data System (ADS)

Hemingway, Ewan J.; Cates, M. E.; Marchetti, M. C.; Fielding, S. M.

We consider a continuum model of active viscoelastic matter, whereby a model of an active nematic liquid-crystal is coupled to a minimal model of polymer dynamics with a viscoelastic relaxation time τc. To explore the resulting interplay between active and polymeric dynamics, we first generalise a linear stability analysis (from earlier studies without polymer) to derive criteria for the onset of spontaneous flow. Perhaps surprisingly, our results show that the spontaneous flow instability persists even for divergent polymer relaxation times. We explore the novel dynamical states to which these instabilities lead by means of nonlinear numerical simulations. This reveals oscillatory shear-banded states in 1D, and activity-driven turbulence in 2D, even in the limit τc --> ∞ . Adding polymer can also have calming effects, increasing the net throughput of spontaneous flow along a channel in a new type of ''drag-reduction'', an effect that may have implications for cytoplasmic streaming processes within the cell.

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

Romera, M.; Monteblanco, E.; Garcia-Sanchez, F.

The influence of dynamic coupling in between magnetic layers of a standard spin torque nano-oscillator composed of a synthetic antiferromagnet (SyF) as a polarizer and an in-plane magnetized free layer has been investigated. Experiments on spin valve nanopillars reveal non-continuous features such as kinks in the frequency field dependence that cannot be explained without such interactions. Comparison of experiments to numerical macrospin simulations shows that this is due to non-linear interaction between the spin torque (STT) driven mode and a damped mode that is mediated via the third harmonics of the STT mode. It only occurs at large applied currentsmore » and thus at large excitation amplitudes of the STT mode. Under these conditions, a hybridized mode characterized by a strong reduction of the linewidth appears. The reduced linewidth can be explained by a reduction of the non-linear contribution to the linewidth via an enhanced effective damping. Interestingly, the effect depends also on the exchange interaction within the SyF. An enhancement of the current range of reduced linewidth by a factor of two and a reduction of the minimum linewidth by a factor of two are predicted from simulation when the exchange interaction strength is reduced by 30%. These results open directions to optimize the design and microwave performances of spin torque nano-oscillators taking advantage of the coupling mechanisms.« less

Space Shuttle main engine nozzle-steerhorn dynamics

NASA Technical Reports Server (NTRS)

Kiefling, L.

1981-01-01

On two occasions during the Space Shuttle main engine development, the LH2 feedline (called the steerhorn, because of its shape) failed during the cutoff transient. A dynamic test was undertaken, and an analytical model was developed and correlated to the dynamic test. Detailed models of the tube bundle were required to obtain the equivalent shell coefficients. All-shell models of the nozzle wall were found better than beam-shell models. The most difficult part of the structure to simulate was the felt-metal pad between the feedline and its mount, which introduced nonlinear stiffness and damping and led to the use of separate low amplitude and high amplitude models. The total structure was found to have 400 modes in the frequency range of interest, 0 to 500 Hz. Good test analysis correlation was obtained and a modified feedline configuration was found to demonstrate a 40% reduction of response stress from the original configuration.

Experimental investigation of active loads control for aircraft landing gear

NASA Technical Reports Server (NTRS)

Mcgehee, J. R.; Dreher, R. C.

1982-01-01

Aircraft dynamic loads and vibrations resulting from landing impact and from runway and taxiway unevenness are recognized as significant in causing fatigue damage, dynamic stress on the airframe, crew and passenger discomfort, and reduction of the pilot's ability to control the aircraft during ground operations. One potential method for improving operational characteistics of aircraft on the ground is the application of active control technology to the landing gears to reduce ground loads applied to the airframe. An experimental investigation was conducted which simulated the landing dynamics of a light airplane to determine the feasibility and potential of a series hydraulic active control main landing gear. The experiments involved a passive gear and an active control gear. Results of this investigation show that a series hydraulically controlled gear is feasible and that such a gear is very effective in reducing the loads transmitted by the gear to the airframe during ground operations.

Life and dynamic capacity modeling for aircraft transmissions

NASA Technical Reports Server (NTRS)

Savage, Michael

1991-01-01

A computer program to simulate the dynamic capacity and life of parallel shaft aircraft transmissions is presented. Five basic configurations can be analyzed: single mesh, compound, parallel, reverted, and single plane reductions. In execution, the program prompts the user for the data file prefix name, takes input from a ASCII file, and writes its output to a second ASCII file with the same prefix name. The input data file includes the transmission configuration, the input shaft torque and speed, and descriptions of the transmission geometry and the component gears and bearings. The program output file describes the transmission, its components, their capabilities, locations, and loads. It also lists the dynamic capability, ninety percent reliability, and mean life of each component and the transmission as a system. Here, the program, its input and output files, and the theory behind the operation of the program are described.

An improved low-voltage ride-through performance of DFIG based wind plant using stator dynamic composite fault current limiter.

PubMed

Gayen, P K; Chatterjee, D; Goswami, S K

2016-05-01

In this paper, an enhanced low-voltage ride-through (LVRT) performance of a grid connected doubly fed induction generator (DFIG) has been presented with the usage of stator dynamic composite fault current limiter (SDCFCL). This protection circuit comprises of a suitable series resistor-inductor combination and parallel bidirectional semiconductor switch. The SDCFCL facilitates double benefits such as reduction of rotor induced open circuit voltage due to increased value of stator total inductance and concurrent increase of rotor impedance. Both effects will limit rotor circuit over current and over voltage situation more secured way in comparison to the conventional scheme like the dynamic rotor current limiter (RCL) during any type of fault situation. The proposed concept is validated through the simulation study of the grid integrated 2.0MW DFIG. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Reduced Dynamics of the Non-holonomic Whipple Bicycle

NASA Astrophysics Data System (ADS)

Boyer, Frédéric; Porez, Mathieu; Mauny, Johan

2018-06-01

Though the bicycle is a familiar object of everyday life, modeling its full nonlinear three-dimensional dynamics in a closed symbolic form is a difficult issue for classical mechanics. In this article, we address this issue without resorting to the usual simplifications on the bicycle kinematics nor its dynamics. To derive this model, we use a general reduction-based approach in the principal fiber bundle of configurations of the three-dimensional bicycle. This includes a geometrically exact model of the contacts between the wheels and the ground, the explicit calculation of the kernel of constraints, along with the dynamics of the system free of any external forces, and its projection onto the kernel of admissible velocities. The approach takes benefits of the intrinsic formulation of geometric mechanics. Along the path toward the final equations, we show that the exact model of the bicycle dynamics requires to cope with a set of non-symmetric constraints with respect to the structural group of its configuration fiber bundle. The final reduced dynamics are simulated on several examples representative of the bicycle. As expected the constraints imposed by the ground contacts, as well as the energy conservation, are satisfied, while the dynamics can be numerically integrated in real time.

Dimensionality reduction in epidemic spreading models

NASA Astrophysics Data System (ADS)

Frasca, M.; Rizzo, A.; Gallo, L.; Fortuna, L.; Porfiri, M.

2015-09-01

Complex dynamical systems often exhibit collective dynamics that are well described by a reduced set of key variables in a low-dimensional space. Such a low-dimensional description offers a privileged perspective to understand the system behavior across temporal and spatial scales. In this work, we propose a data-driven approach to establish low-dimensional representations of large epidemic datasets by using a dimensionality reduction algorithm based on isometric features mapping (ISOMAP). We demonstrate our approach on synthetic data for epidemic spreading in a population of mobile individuals. We find that ISOMAP is successful in embedding high-dimensional data into a low-dimensional manifold, whose topological features are associated with the epidemic outbreak. Across a range of simulation parameters and model instances, we observe that epidemic outbreaks are embedded into a family of closed curves in a three-dimensional space, in which neighboring points pertain to instants that are close in time. The orientation of each curve is unique to a specific outbreak, and the coordinates correlate with the number of infected individuals. A low-dimensional description of epidemic spreading is expected to improve our understanding of the role of individual response on the outbreak dynamics, inform the selection of meaningful global observables, and, possibly, aid in the design of control and quarantine procedures.

Spacecraft Formation Flying Maneuvers Using Linear Quadratic Regulation With No Radial Axis Inputs

NASA Technical Reports Server (NTRS)

Starin, Scott R.; Yedavalli, R. K.; Sparks, Andrew G.; Bauer, Frank H. (Technical Monitor)

2001-01-01

Regarding multiple spacecraft formation flying, the observation has been made that control thrust need only be applied coplanar to the local horizon to achieve complete controllability of a two-satellite (leader-follower) formation. A formulation of orbital dynamics using the state of one satellite relative to another is used. Without the need for thrust along the radial (zenith-nadir) axis of the relative reference frame, propulsion system simplifications and weight reduction may be accomplished. This work focuses on the validation of this control system on its own merits, and in comparison to a related system which does provide thrust along the radial axis of the relative frame. Maneuver simulations are performed using commercial ODE solvers to propagate the Keplerian dynamics of a controlled satellite relative to an uncontrolled leader. These short maneuver simulations demonstrate the capacity of the controller to perform changes from one formation geometry to another. Control algorithm performance is evaluated based on measures such as the fuel required to complete a maneuver and the maximum acceleration required by the controller. Based on this evaluation, the exclusion of the radial axis of control still allows enough control authority to use Linear Quadratic Regulator (LQR) techniques to design a gain matrix of adequate performance over finite maneuvers. Additional simulations are conducted including perturbations and using no radial control inputs. A major conclusion presented is that control inputs along the three axes have significantly different relationships to the governing orbital dynamics that may be exploited using LQR.

Molecular docking and dynamic simulation studies evidenced plausible immunotherapeutic anticancer property by Withaferin A targeting indoleamine 2,3-dioxygenase.

PubMed

Reddy, S V G; Reddy, K Thammi; Kumari, V Valli; Basha, Syed Hussain

2015-01-01

Indoleamine 2,3-dioxygenase (IDO) is emerging as an important new therapeutic drug target for the treatment of cancer characterized by pathological immune suppression. IDO catalyzes the rate-limiting step of tryptophan degradation along the kynurenine pathway. Reduction in local tryptophan concentration and the production of immunomodulatory tryptophan metabolites contribute to the immunosuppressive effects of IDO. Presence of IDO on dentritic cells in tumor-draining lymph nodes leading to the activation of T cells toward forming immunosuppressive microenvironment for the survival of tumor cells has confirmed the importance of IDO as a promising novel anticancer immunotherapy drug target. On the other hand, Withaferin A (WA) - active constituent of Withania Somnifera ayurvedic herb has shown to be having a wide range of targeted anticancer properties. In the present study conducted here is an attempt to explore the potential of WA in attenuating IDO for immunotherapeutic tumor arresting activity and to elucidate the underlying mode of action in a computational approach. Our docking and molecular dynamic simulation results predict high binding affinity of the ligand to the receptor with up to -11.51 kcal/mol of energy and 3.63 nM of IC50 value. Further, de novo molecular dynamic simulations predicted stable ligand interactions with critically important residues SER167; ARG231; LYS377, and heme moiety involved in IDO's activity. Conclusively, our results strongly suggest WA as a valuable small ligand molecule with strong binding affinity toward IDO.

Drag Reduction of an Airfoil Using Deep Learning

NASA Astrophysics Data System (ADS)

Jiang, Chiyu; Sun, Anzhu; Marcus, Philip

2017-11-01

We reduced the drag of a 2D airfoil by starting with a NACA-0012 airfoil and used deep learning methods. We created a database which consists of simulations of 2D external flow over randomly generated shapes. We then developed a machine learning framework for external flow field inference given input shapes. Past work which utilized machine learning in Computational Fluid Dynamics focused on estimations of specific flow parameters, but this work is novel in the inference of entire flow fields. We further showed that learned flow patterns are transferable to cases that share certain similarities. This study illustrates the prospects of deeper integration of data-based modeling into current CFD simulation frameworks for faster flow inference and more accurate flow modeling.

New modeling method for the dielectric relaxation of a DRAM cell capacitor

NASA Astrophysics Data System (ADS)

Choi, Sujin; Sun, Wookyung; Shin, Hyungsoon

2018-02-01

This study proposes a new method for automatically synthesizing the equivalent circuit of the dielectric relaxation (DR) characteristic in dynamic random access memory (DRAM) without frequency dependent capacitance measurement. Charge loss due to DR can be observed by a voltage drop at the storage node and this phenomenon can be analyzed by an equivalent circuit. The Havariliak-Negami model is used to accurately determine the electrical characteristic parameters of an equivalent circuit. The DRAM sensing operation is performed in HSPICE simulations to verify this new method. The simulation demonstrates that the storage node voltage drop resulting from DR and the reduction in the sensing voltage margin, which has a critical impact on DRAM read operation, can be accurately estimated using this new method.

Design and cost analysis of rapid aquifer restoration systems using flow simulation and quadratic programming.

USGS Publications Warehouse

Lefkoff, L.J.; Gorelick, S.M.

1986-01-01

Detailed two-dimensional flow simulation of a complex ground-water system is combined with quadratic and linear programming to evaluate design alternatives for rapid aquifer restoration. Results show how treatment and pumping costs depend dynamically on the type of treatment process, and capacity of pumping and injection wells, and the number of wells. The design for an inexpensive treatment process minimizes pumping costs, while an expensive process results in the minimization of treatment costs. Substantial reductions in pumping costs occur with increases in injection capacity or in the number of wells. Treatment costs are reduced by expansions in pumping capacity or injecion capacity. The analysis identifies maximum pumping and injection capacities.-from Authors

Effect of two imidazolium derivatives of ionic liquids on the structure and activity of adenosine deaminase.

PubMed

Ajloo, Davood; Sangian, Masoomeh; Ghadamgahi, Maryam; Evini, Mina; Saboury, Ali Akbar

2013-04-01

The effect of two ionic liquids, 1-allyl 3-methyl-imidazolium (IL1) and 1-octhyl 3-methyl-imidozolium chlorides (IL2), on the structure and activity of adenosine deaminase (ADA) were described by UV-vis and fluorescence spectrophotometry in phosphate buffer and results were compared with docking and molecular dynamics (MD) simulation studies. All results showed that inhibition of activity and reduction of enzyme tertiary structure are more for octhyl than allyl derivative due to the more hydrophobic property of it. Finally structure parameters obtained from MD simulation showed that ionic liquid reduces intermolecular hydrogen bond and unfold enzyme structure. Calculation results are in good agreement with spectrophotometric studies. Copyright © 2013 Elsevier B.V. All rights reserved.

Application of a dynamic population-based model for evaluation of exposure reduction strategies in the baking industry

NASA Astrophysics Data System (ADS)

Meijster, Tim; Warren, Nick; Heederik, Dick; Tielemans, Erik

2009-02-01

Recently a dynamic population model was developed that simulates a population of bakery workers longitudinally through time and tracks the development of work-related sensitisation and respiratory symptoms in each worker. Input for this model comes from cross-sectional and longitudinal epidemiological studies which allowed estimation of exposure response relationships and disease transition probabilities This model allows us to study the development of diseases and transitions between disease states over time in relation to determinants of disease including flour dust and/or allergen exposure. Furthermore it enables more realistic modelling of the health impact of different intervention strategies at the workplace (e.g. changes in exposure may take several years to impact on ill-health and often occur as a gradual trend). A large dataset of individual full-shift exposure measurements and real-time exposure measurements were used to obtain detailed insight into the effectiveness of control measures and other determinants of exposure. Given this information a population wide reduction of the median exposure with 50% was evaluated in this paper.

Boattail juncture shaping for spin-stabilized rounds in supersonic flight

NASA Astrophysics Data System (ADS)

Jiajan, W.; Chue, R. S. M.; Nguyen, T.; Yu, S. C. M.

2015-03-01

In this paper, the effects of boattail junction shaping on aerodynamic drag and stability of supersonic spin-stabilized rounds are investigated using computational fluid dynamics. For a generic round body comprising of a secant-ogive nose, a cylindrical body and a conical boattail, the shaping technique was achieved by adding a convex surface of varying degrees of radius of curvature to the junction between the cylindrical body and the boattail. It was shown through numerical simulations that this shaping technique can provide a reduction in aerodynamic drag of up to 5.4 % without destabilizing the round bodies when the radius of curvature is less than 8.8 times the diameter of the cylindrical body. The more gradual change of the flow characteristics, e.g., the pressure over the convex surface, was identified as the main reason for the drag reduction. A unique aspect of the current work is that stability is treated as an integral part of the performance assessment. It was also found that the dynamic instability encountered at large radii of curvature is due to the Magnus effects.

Molecular dynamics simulation study of the structure of poly(ethylene oxide) brushes on nonpolar surfaces in aqueous solution.

PubMed

Bedrov, Dmitry; Smith, Grant D

2006-07-04

The structure of poly(ethylene oxide) (PEO, M(w) = 526) brushes of various grafting density (sigma) on nonpolar graphite and hydrophobic (oily) surfaces in aqueous solution has been studied using atomistic molecular dynamics simulations. Additionally, the influence of PEO-surface interactions on the brush structure was investigated by systematically reducing the strength of the (dispersion) attraction between PEO and the surfaces. PEO chains were found to adsorb strongly to the graphite surface due primarily to the relative strength of dispersion interactions between PEO and the atomically dense graphite compared to those between water and graphite. For the oily surface, PEO-surface and water-surface dispersion interactions are much weaker, greatly reducing the energetic driving force for PEO adsorption. This reduction is mediated to some extent by a hydrophobic driving force for PEO adsorption on the oily surface. Reduction in the strength of PEO-surface attraction results in reduced adsorption of PEO for both surfaces, with the effect being much greater for the graphite surface where the strong PEO-surface dispersion interactions dominate. At high grafting density (sigma approximately 1/R(g)(2)), the PEO density profiles exhibited classical brush behavior and were largely independent of the strength of the PEO-surface interaction. With decreasing grafting density (sigma < 1/R(g)(2)), coverage of the surface by PEO requires an increasingly large fraction of PEO segments resulting in a strong dependence of the PEO density profile on the nature of the PEO-surface interaction.

Developing parallel GeoFEST(P) using the PYRAMID AMR library

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Tisdale, Robert E.

2004-01-01

The PYRAMID parallel unstructured adaptive mesh refinement (AMR) library has been coupled with the GeoFEST geophysical finite element simulation tool to support parallel active tectonics simulations. Specifically, we have demonstrated modeling of coseismic and postseismic surface displacement due to a simulated Earthquake for the Landers system of interacting faults in Southern California. The new software demonstrated a 25-times resolution improvement and a 4-times reduction in time to solution over the sequential baseline milestone case. Simulations on workstations using a few tens of thousands of stress displacement finite elements can now be expanded to multiple millions of elements with greater than 98% scaled efficiency on various parallel platforms over many hundreds of processors. Our most recent work has demonstrated that we can dynamically adapt the computational grid as stress grows on a fault. In this paper, we will describe the major issues and challenges associated with coupling these two programs to create GeoFEST(P). Performance and visualization results will also be described.

Addressing Control Research Issues Leading to Piloted Simulations in Support of the IFCS F-15

NASA Technical Reports Server (NTRS)

Napolitano, Marcello; Perhinschi, Mario; Campa, Giampiero; Seanor, Brad

2004-01-01

This report summarizes the research effort by a team of researchers at West Virginia University in support of the NASA Intelligent Flight Control System (IFCS) F-15 program. In particular, WVU researchers assisted NASA Dryden researchers in the following technical tasks leading to piloted simulation of the 'Gen_2' IFCS control laws. Task #1- Performance comparison of different neural network (NN) augmentation for the Dynamic Inversion (DI) -based VCAS 'Gen_2' control laws. Task #2- Development of safety monitor criteria for transition to research control laws with and without failure during flight test. Task #3- Fine-tuning of the 'Gen_2' control laws for cross-coupling reduction at post-failure conditions. Matlab/Simulink-based simulation codes were provided to the technical monitor on a regular basis throughout the duration of the project. Additional deliverables for the project were Power Point-based slides prepared for different project meetings. This document provides a description of the methodology and discusses the general conclusions from the simulation results.

Dynamic Modeling, Controls, and Testing for Electrified Aircraft

NASA Technical Reports Server (NTRS)

Connolly, Joseph; Stalcup, Erik

2017-01-01

Electrified aircraft have the potential to provide significant benefits for efficiency and emissions reductions. To assess these potential benefits, modeling tools are needed to provide rapid evaluation of diverse concepts and to ensure safe operability and peak performance over the mission. The modeling challenge for these vehicles is the ability to show significant benefits over the current highly refined aircraft systems. The STARC-ABL (single-aisle turbo-electric aircraft with an aft boundary layer propulsor) is a new test proposal that builds upon previous N3-X team hybrid designs. This presentation describes the STARC-ABL concept, the NASA Electric Aircraft Testbed (NEAT) which will allow testing of the STARC-ABL powertrain, and the related modeling and simulation efforts to date. Modeling and simulation includes a turbofan simulation, Numeric Propulsion System Simulation (NPSS), which has been integrated with NEAT; and a power systems and control model for predicting testbed performance and evaluating control schemes. Model predictions provide good comparisons with testbed data for an NPSS-integrated test of the single-string configuration of NEAT.

Simulating drought impacts on energy balance in an Amazonian rainforest

NASA Astrophysics Data System (ADS)

Imbuzeiro, H. A.; Costa, M. H.; Galbraith, D.; Christoffersen, B. O.; Powell, T.; Harper, A. B.; Levine, N. M.; Rowland, L.; Moorcroft, P. R.; Benezoli, V. H.; Meir, P.; da Costa, A. C. L.; Brando, P. M.; Malhi, Y.; Saleska, S. R.; Williams, M. D.

2014-12-01

The studies of the interaction between vegetation and climate change in the Amazon Basin indicate that up to half of the region's forests may be displaced by savanna vegetation by the end of the century. Additional analyses suggest that complex interactions among land use, fire-frequency, and episodic drought are driving an even more rapid process of the forest impoverishment and displacement referred here as "savannization". But it is not clear whether surface/ecosystem models are suitable to analyze extreme events like a drought. Long-term simulations of throughfall exclusion experiments has provided unique insights into the energy dynamics of Amazonian rainforests during drought conditions. In this study, we evaluate how well six surface/ecosystem models quantify the energy dynamics from two Amazonian throughfall exclusion experiments. All models were run for the Tapajós and Caxiuanã sites with one control plot using normal precipitation (i.e. do not impose a drought) and then the drought manipulation was imposed for several drought treatments (10 to 90% rainfall exclusion). The sap flow, net radiation (Rn), sensible (H), latent (LE) and ground (G) heat flux are used to analyze if the models are able to capture the dynamics of water stress and what the implications for the energy dynamics are. With respect to the model validation, when we compare the sap flow observed and transpiration simulated, models are more accurate to simulate control plots than drought treatments (50% rainfall exclusion). The results show that the models overestimate the sap flow data during the drought conditions, but they were able to capture the changes in the main energy balance components for different drought treatments. The Rn and LE decreased and H increased with more intensity of drought. The models sensitivity analysis indicate that models are more sensitive to drought when rainfall is excluded for more than 60% and when this reduction occurs during the dry season.

Predicting Large Deflections of Multiplate Fuel Elements Using a Monolithic FSI Approach

DOE PAGES

Curtis, Franklin G.; Freels, James D.; Ekici, Kivanc

2017-10-26

As part of the Global Threat Reduction Initiative, the Oak Ridge National Laboratory is evaluating conversion of fuel for the High Flux Isotope Reactor (HFIR) from high-enriched uranium to low-enriched uranium. Currently, multiphysics simulations that model fluid-structure interaction phenomena are being performed to ensure the safety of the reactor with the new fuel type. A monolithic solver that fully couples fluid and structural dynamics is used to model deflections in the new design. A classical experiment is chosen to validate the capabilities of the current solver and the method. Here, a single-plate simulation with various boundary conditions as well asmore » a five-plate simulation are presented. Finally, use of the monolithic solver provides stable solutions for the large deflections and the tight coupling of the fluid and structure and the maximum deflections are captured accurately.« less

Determination of the oil distribution in a hermetic compressor using numerical simulation

NASA Astrophysics Data System (ADS)

Posch, S.; Hopfgartner, J.; Berger, E.; Zuber, B.; Almbauer, R.; Schöllauf, P.

2017-08-01

In addition to the reduction of friction the oil in a hermetic compressor is very important for the transfer of heat from hot parts to the compressor shell. The simulation of the oil distribution in a hermetic reciprocating compressor for refrigeration application is shown in the present work. Using the commercial Computational Fluid Dynamics (CFD) software ANSYS Fluent, the oil flow inside the compressor shell from the oil pump outlet to the oil sump is calculated. A comprehensive overview of the used models and the boundary conditions is given. After reaching steady-state conditions the oil covered surfaces are analysed concerning heat transfer coefficients. The gained heat transfer coefficients are used as input parameters for a thermal model of a hermetic compressor. An increase in accuracy of the thermal model with the simulated heat transfer coefficients compared to values from literature is shown by model validation with experimental data.

Lap time simulation and design optimisation of a brushed DC electric motorcycle for the Isle of Man TT Zero Challenge

NASA Astrophysics Data System (ADS)

Dal Bianco, N.; Lot, R.; Matthys, K.

2018-01-01

This works regards the design of an electric motorcycle for the annual Isle of Man TT Zero Challenge. Optimal control theory was used to perform lap time simulation and design optimisation. A bespoked model was developed, featuring 3D road topology, vehicle dynamics and electric power train, composed of a lithium battery pack, brushed DC motors and motor controller. The model runs simulations over the entire ? or ? of the Snaefell Mountain Course. The work is validated using experimental data from the BX chassis of the Brunel Racing team, which ran during the 2009 to 2015 TT Zero races. Optimal control is used to improve drive train and power train configurations. Findings demonstrate computational efficiency, good lap time prediction and design optimisation potential, achieving a 2 minutes reduction of the reference lap time through changes in final drive gear ratio, battery pack size and motor configuration.

Airflow Hazard Visualization for Helicopter Pilots: Flight Simulation Study Results

NASA Technical Reports Server (NTRS)

Aragon, Cecilia R.; Long, Kurtis R.

2005-01-01

Airflow hazards such as vortices or low level wind shear have been identified as a primary contributing factor in many helicopter accidents. US Navy ships generate airwakes over their decks, creating potentially hazardous conditions for shipboard rotorcraft launch and recovery. Recent sensor developments may enable the delivery of airwake data to the cockpit, where visualizing the hazard data may improve safety and possibly extend ship/helicopter operational envelopes. A prototype flight-deck airflow hazard visualization system was implemented on a high-fidelity rotorcraft flight dynamics simulator. Experienced helicopter pilots, including pilots from all five branches of the military, participated in a usability study of the system. Data was collected both objectively from the simulator and subjectively from post-test questionnaires. Results of the data analysis are presented, demonstrating a reduction in crash rate and other trends that illustrate the potential of airflow hazard visualization to improve flight safety.

gpuSPHASE-A shared memory caching implementation for 2D SPH using CUDA

NASA Astrophysics Data System (ADS)

Winkler, Daniel; Meister, Michael; Rezavand, Massoud; Rauch, Wolfgang

2017-04-01

Smoothed particle hydrodynamics (SPH) is a meshless Lagrangian method that has been successfully applied to computational fluid dynamics (CFD), solid mechanics and many other multi-physics problems. Using the method to solve transport phenomena in process engineering requires the simulation of several days to weeks of physical time. Based on the high computational demand of CFD such simulations in 3D need a computation time of years so that a reduction to a 2D domain is inevitable. In this paper gpuSPHASE, a new open-source 2D SPH solver implementation for graphics devices, is developed. It is optimized for simulations that must be executed with thousands of frames per second to be computed in reasonable time. A novel caching algorithm for Compute Unified Device Architecture (CUDA) shared memory is proposed and implemented. The software is validated and the performance is evaluated for the well established dambreak test case.

A probabilistic approach to examine the impacts of mitigation policies on future global PM emissions from on-road vehicles

NASA Astrophysics Data System (ADS)

Yan, F.; Winijkul, E.; Bond, T. C.; Streets, D. G.

2012-12-01

There is deficiency in the determination of emission reduction potential in the future, especially with consideration of uncertainty. Mitigation measures for some economic sectors have been proposed, but few studies provide an evaluation of the amount of PM emission reduction that can be obtained in future years by different emission reduction strategies. We attribute the absence of helpful mitigation strategy analysis to limitations in the technical detail of future emission scenarios, which result in the inability to relate technological or regulatory intervention to emission changes. The purpose of this work is to provide a better understanding of the potential benefits of mitigation policies in addressing global and regional emissions. In this work, we introduce a probabilistic approach to explore the impacts of retrofit and scrappage on global PM emissions from on-road vehicles in the coming decades. This approach includes scenario analysis, sensitivity analysis and Monte Carlo simulations. A dynamic model of vehicle population linked to emission characteristics, SPEW-Trend, is used to estimate future emissions and make policy evaluations. Three basic questions will be answered in this work: (1) what contribution can these two programs make to improve global emissions in the future? (2) in which regions are such programs most and least effective in reducing emissions and what features of the vehicle fleet cause these results? (3) what is the level of confidence in the projected emission reductions, given uncertain parameters in describing the dynamic vehicle fleet?

Simulated effects of recruitment variability, exploitation, and reduced habitat area on the muskellunge population in Shoepack Lake, Voyageurs National Park, Minnesota

USGS Publications Warehouse

Frohnauer, N.K.; Pierce, C.L.; Kallemeyn, L.W.

2007-01-01

The genetically unique population of muskellunge Esox masquinongy inhabiting Shoepack Lake in Voyageurs National Park, Minnesota, is potentially at risk for loss of genetic variability and long-term viability. Shoepack Lake has been subject to dramatic surface area changes from the construction of an outlet dam by beavers Castor canadensis and its subsequent failure. We simulated the long-term dynamics of this population in response to recruitment variation, increased exploitation, and reduced habitat area. We then estimated the effective population size of the simulated population and evaluated potential threats to long-term viability, based on which we recommend management actions to help preserve the long-term viability of the population. Simulations based on the population size and habitat area at the beginning of a companion study resulted in an effective population size that was generally above the threshold level for risk of loss of genetic variability, except when fishing mortality was increased. Simulations based on the reduced habitat area after the beaver dam failure and our assumption of a proportional reduction in population size resulted in an effective population size that was generally below the threshold level for risk of loss of genetic variability. Our results identified two potential threats to the long-term viability of the Shoepack Lake muskellunge population, reduction in habitat area and exploitation. Increased exploitation can be prevented through traditional fishery management approaches such as the adoption of no-kill, barbless hook, and limited entry regulations. Maintenance of the greatest possible habitat area and prevention of future habitat area reductions will require maintenance of the outlet dam built by beavers. Our study should enhance the long-term viability of the Shoepack Lake muskellunge population and illustrates a useful approach for other unique populations. ?? Copyright by the American Fisheries Society 2007.

Simulation of Sound Waves Using the Lattice Boltzmann Method for Fluid Flow: Benchmark Cases for Outdoor Sound Propagation

PubMed Central

Salomons, Erik M.; Lohman, Walter J. A.; Zhou, Han

2016-01-01

Propagation of sound waves in air can be considered as a special case of fluid dynamics. Consequently, the lattice Boltzmann method (LBM) for fluid flow can be used for simulating sound propagation. In this article application of the LBM to sound propagation is illustrated for various cases: free-field propagation, propagation over porous and non-porous ground, propagation over a noise barrier, and propagation in an atmosphere with wind. LBM results are compared with solutions of the equations of acoustics. It is found that the LBM works well for sound waves, but dissipation of sound waves with the LBM is generally much larger than real dissipation of sound waves in air. To circumvent this problem it is proposed here to use the LBM for assessing the excess sound level, i.e. the difference between the sound level and the free-field sound level. The effect of dissipation on the excess sound level is much smaller than the effect on the sound level, so the LBM can be used to estimate the excess sound level for a non-dissipative atmosphere, which is a useful quantity in atmospheric acoustics. To reduce dissipation in an LBM simulation two approaches are considered: i) reduction of the kinematic viscosity and ii) reduction of the lattice spacing. PMID:26789631

Simulation of Sound Waves Using the Lattice Boltzmann Method for Fluid Flow: Benchmark Cases for Outdoor Sound Propagation.

PubMed

Salomons, Erik M; Lohman, Walter J A; Zhou, Han

2016-01-01

Propagation of sound waves in air can be considered as a special case of fluid dynamics. Consequently, the lattice Boltzmann method (LBM) for fluid flow can be used for simulating sound propagation. In this article application of the LBM to sound propagation is illustrated for various cases: free-field propagation, propagation over porous and non-porous ground, propagation over a noise barrier, and propagation in an atmosphere with wind. LBM results are compared with solutions of the equations of acoustics. It is found that the LBM works well for sound waves, but dissipation of sound waves with the LBM is generally much larger than real dissipation of sound waves in air. To circumvent this problem it is proposed here to use the LBM for assessing the excess sound level, i.e. the difference between the sound level and the free-field sound level. The effect of dissipation on the excess sound level is much smaller than the effect on the sound level, so the LBM can be used to estimate the excess sound level for a non-dissipative atmosphere, which is a useful quantity in atmospheric acoustics. To reduce dissipation in an LBM simulation two approaches are considered: i) reduction of the kinematic viscosity and ii) reduction of the lattice spacing.

Computer simulation of vasectomy for wolf control

USGS Publications Warehouse

Haight, R.G.; Mech, L.D.

1997-01-01

Recovering gray wolf (Canis lupus) populations in the Lake Superior region of the United States are prompting state management agencies to consider strategies to control population growth. In addition to wolf removal, vasectomy has been proposed. To predict the population effects of different sterilization and removal strategies, we developed a simulation model of wolf dynamics using simple rules for demography and dispersal. Simulations suggested that the effects of vasectomy and removal in a disjunct population depend largely on the degree of annual immigration. With low immigration, periodic sterilization reduced pup production and resulted in lower rates of territory recolonization. Consequently, average pack size, number of packs, and population size were significantly less than those for an untreated population. Periodically removing a proportion of the population produced roughly the same trends as did sterilization; however, more than twice as many wolves had to be removed than sterilized. With high immigration, periodic sterilization reduced pup production but not territory recolonization and produced only moderate reductions in population size relative to an untreated population. Similar reductions in population size were obtained by periodically removing large numbers of wolves. Our analysis does not address the possible effects of vasectomy on larger wolf populations, but it suggests that the subject should be considered through modeling or field testing.

High frequency dynamic engine simulation. [TF-30 engine

NASA Technical Reports Server (NTRS)

Schuerman, J. A.; Fischer, K. E.; Mclaughlin, P. W.

1977-01-01

A digital computer simulation of a mixed flow, twin spool turbofan engine was assembled to evaluate and improve the dynamic characteristics of the engine simulation to disturbance frequencies of at least 100 Hz. One dimensional forms of the dynamic mass, momentum and energy equations were used to model the engine. A TF30 engine was simulated so that dynamic characteristics could be evaluated against results obtained from testing of the TF30 engine at the NASA Lewis Research Center. Dynamic characteristics of the engine simulation were improved by modifying the compression system model. Modifications to the compression system model were established by investigating the influence of size and number of finite dynamic elements. Based on the results of this program, high frequency engine simulations using finite dynamic elements can be assembled so that the engine dynamic configuration is optimum with respect to dynamic characteristics and computer execution time. Resizing of the compression systems finite elements improved the dynamic characteristics of the engine simulation but showed that additional refinements are required to obtain close agreement simulation and actual engine dynamic characteristics.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

PubMed

Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

2017-08-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

PubMed Central

Sing-Long, Carlos A.

2017-01-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates. PMID:28989618

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

DOE PAGES

Yang, Qian; Sing-Long, Carlos A.; Reed, Evan J.

2017-06-19

Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our methodmore » on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. Furthermore, we describe a framework in this work that paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.« less

Optimal Ge/SiGe nanofin geometries for hole mobility enhancement: Technology limit from atomic simulations

NASA Astrophysics Data System (ADS)

Vedula, Ravi Pramod; Mehrotra, Saumitra; Kubis, Tillmann; Povolotskyi, Michael; Klimeck, Gerhard; Strachan, Alejandro

2015-05-01

We use first principles simulations to engineer Ge nanofins for maximum hole mobility by controlling strain tri-axially through nano-patterning. Large-scale molecular dynamics predict fully relaxed, atomic structures for experimentally achievable nanofins, and orthogonal tight binding is used to obtain the corresponding electronic structure. Hole transport properties are then obtained via a linearized Boltzmann formalism. This approach explicitly accounts for free surfaces and associated strain relaxation as well as strain gradients which are critical for quantitative predictions in nanoscale structures. We show that the transverse strain relaxation resulting from the reduction in the aspect ratio of the fins leads to a significant enhancement in phonon limited hole mobility (7× over unstrained, bulk Ge, and 3.5× over biaxially strained Ge). Maximum enhancement is achieved by reducing the width to be approximately 1.5 times the height and further reduction in width does not result in additional gains. These results indicate significant room for improvement over current-generation Ge nanofins, provide geometrical guidelines to design optimized geometries and insight into the physics behind the significant mobility enhancement.

Numerical Simulations for Turbulent Drag Reduction Using Liquid Infused Surfaces

NASA Astrophysics Data System (ADS)

Arenas-Navarro, Isnardo

Numerical simulations of the turbulent flow over Super Hydrophobic and Liquid Infused Surfaces have been performed in this work. Three different textured surfaces have been considered: longitudinal square bars, transversal square bars and staggered cubes. The numerical code combines an immersed boundary method to mimic the substrate and a level set method to track the interface. Liquid Infused Surfaces reduce the drag by locking a lubricant within structured roughness to facilitate a slip velocity at the surface interface. The conceptual idea is similar to Super Hydrophobic Surfaces, which rely on a lubricant air layer, whereas liquid-infused surfaces use a preferentially wetting liquid lubricant to create a fluid-fluid interface. This slipping interface has been shown to be an effective method of passively reducing skin friction drag in turbulent flows. Details are given on the effect of the viscosity ratio between the two fluids and the dynamics of the interface on drag reduction. An attempt has been made to reconcile Super-Hydrophobic, Liquid Infused and rough wall under the same framework by correlating the drag to the wall normal velocity fluctuations.

Project ARGO: Gas phase formation in simulated microgravity

NASA Technical Reports Server (NTRS)

Powell, Michael R.; Waligora, James M.; Norfleet, William T.; Kumar, K. Vasantha

1993-01-01

The ARGO study investigated the reduced incidence of joint pain decompression sickness (DCS) encountered in microgravity as compared with an expected incidence of joint pain DCS experienced by test subjects in Earth-based laboratories (unit gravity) with similar protocols. Individuals who are decompressed from saturated conditions usually acquire joint pain DCS in the lower extremities. Our hypothesis is that the incidence of joint pain DCS can be limited by a significant reduction in the tissue gas micronuclei formed by stress-assisted nucleation. Reductions in dynamic and kinetic stresses in vivo are linked to hypokinetic and adynamic conditions of individuals in zero g. We employed the Doppler ultrasound bubble detection technique in simulated microgravity studies to determine quantitatively the degree of gas phase formation in the upper and lower extremities of test subjects during decompression. We found no evidence of right-to-left shunting through pulmonary vasculature. The volume of gas bubble following decompression was examined and compared with the number following saline contrast injection. From this, we predict a reduced incidence of DCS on orbit, although the incidence of predicted mild DCS still remains larger than that encountered on orbit.

cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems

PubMed Central

Besozzi, Daniela; Pescini, Dario; Mauri, Giancarlo

2014-01-01

Tau-leaping is a stochastic simulation algorithm that efficiently reconstructs the temporal evolution of biological systems, modeled according to the stochastic formulation of chemical kinetics. The analysis of dynamical properties of these systems in physiological and perturbed conditions usually requires the execution of a large number of simulations, leading to high computational costs. Since each simulation can be executed independently from the others, a massive parallelization of tau-leaping can bring to relevant reductions of the overall running time. The emerging field of General Purpose Graphic Processing Units (GPGPU) provides power-efficient high-performance computing at a relatively low cost. In this work we introduce cuTauLeaping, a stochastic simulator of biological systems that makes use of GPGPU computing to execute multiple parallel tau-leaping simulations, by fully exploiting the Nvidia's Fermi GPU architecture. We show how a considerable computational speedup is achieved on GPU by partitioning the execution of tau-leaping into multiple separated phases, and we describe how to avoid some implementation pitfalls related to the scarcity of memory resources on the GPU streaming multiprocessors. Our results show that cuTauLeaping largely outperforms the CPU-based tau-leaping implementation when the number of parallel simulations increases, with a break-even directly depending on the size of the biological system and on the complexity of its emergent dynamics. In particular, cuTauLeaping is exploited to investigate the probability distribution of bistable states in the Schlögl model, and to carry out a bidimensional parameter sweep analysis to study the oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae. PMID:24663957

Effect of vorticity on polycrystalline ice deformation

NASA Astrophysics Data System (ADS)

Llorens, Maria-Gema; Griera, Albert; Steinbach, Florian; Bons, Paul D.; Gomez-Rivas, Enrique; Jansen, Daniela; Lebensohn, Ricardo A.; Weikusat, Ilka

2017-04-01

Understanding ice sheet dynamics requires a good knowledge of how dynamic recrystallisation controls ice microstructures and rheology at different boundary conditions. In polar ice sheets, pure shear flattening typically occurs at the top of the sheets, while simple shearing dominates near their base. We present a series of two-dimensional microdynamic numerical simulations that couple ice deformation with dynamic recrystallisation of various intensities, paying special attention to the effect of boundary conditions. The viscoplastic full-field numerical modelling approach (VPFFT) (Lebensohn, 2001) is used to calculate the response of a polycrystalline aggregate that deforms purely by dislocation glide. This code is coupled with the ELLE microstructural modelling platform that includes recrystallisation in the aggregate by intracrystalline recovery, nucleation by polygonisation, as well as grain boundary migration driven by the reduction of surface and strain energies (Llorens et al., 2016a, 2016b, 2017). The results reveal that regardless the amount of DRX and ice flow a single c-axes maximum develops all simulations. This maximum is oriented approximately parallel to the maximum finite shortening direction and rotates in simple shear towards the normal to the shear plane. This leads to a distinctly different behaviour in pure and simple shear. In pure shear, the lattice preferred orientation (LPO) and shape-preferred orientation (SPO) are increasingly unfavourable for deformation, leading to hardening and an increased activity of non-basal slip. The opposite happens in simple shear, where the imposed vorticity causes rotation of the LPO and SPO to a favourable orientation, leading to strain softening. An increase of recrystallisation enhances the activity of the non-basal slip, due to the reduction of deformation localisation. In pure shear conditions, the pyramidal slip activity is thus even more enhanced and can become higher than the basal-slip activity. Our results further show that subgrain boundaries can be developed by the activity of the non-basal slip systems. The implementation of the polygonisation routine reduces grain size and SPO, but does not significantly change the final LPO, because newly nucleated grains approximately keep the c-axis orientations of their parental grains. However, it enables the establishment of an equilibrium grain size, and therefore the differential stress reaches a steady-state. Lebensohn. 2001 N-site modelling of a 3D viscoplastic polycrystal using fast Fourier transform. Acta Materialia, 49(14), 2723-2737. Llorens, et al., 2016a. Dynamic recrystallisation of ice aggregates during co-axial viscoplastic deformation: a numerical approach. Journal of Glaciology, 62(232), 359-377. Llorens, et al., 2016b. Full-field predictions of ice dynamic recrystallisation under simple shear conditions, Earth and Planetary Science Letters, 450, 233-242. Llorens, et al., 2017. Dynamic recrystallisation during deformation of polycrystalline ice: insights from numerical simulations, Philosophical Transactions of the Royal Society A, 375 (2086), 20150346.

Reduction of Large Dynamical Systems by Minimization of Evolution Rate

NASA Technical Reports Server (NTRS)

Girimaji, Sharath S.

1999-01-01

Reduction of a large system of equations to a lower-dimensional system of similar dynamics is investigated. For dynamical systems with disparate timescales, a criterion for determining redundant dimensions and a general reduction method based on the minimization of evolution rate are proposed.

Partial scan artifact reduction (PSAR) for the assessment of cardiac perfusion in dynamic phase-correlated CT.

PubMed

Stenner, Philip; Schmidt, Bernhard; Bruder, Herbert; Allmendinger, Thomas; Haberland, Ulrike; Flohr, Thomas; Kachelriess, Marc

2009-12-01

Cardiac CT achieves its high temporal resolution by lowering the scan range from 2pi to pi plus fan angle (partial scan). This, however, introduces CT-value variations, depending on the angular position of the pi range. These partial scan artifacts are of the order of a few HU and prevent the quantitative evaluation of perfusion measurements. The authors present the new algorithm partial scan artifact reduction (PSAR) that corrects a dynamic phase-correlated scan without a priori information. In general, a full scan does not suffer from partial scan artifacts since all projections in [0, 2pi] contribute to the data. To maintain the optimum temporal resolution and the phase correlation, PSAR creates an artificial full scan pn(AF) by projectionwise averaging a set of neighboring partial scans pn(P) from the same perfusion examination (typically N approximately 30 phase-correlated partial scans distributed over 20 s and n = 1, ..., N). Corresponding to the angular range of each partial scan, the authors extract virtual partial scans pn(V) from the artificial full scan pn(AF). A standard reconstruction yields the corresponding images fn(P), fn(AF), and fn(V). Subtracting the virtual partial scan image fn(V) from the artificial full scan image fn(AF) yields an artifact image that can be used to correct the original partial scan image: fn(C) = fn(P) - fn(V) + fn(AF), where fn(C) is the corrected image. The authors evaluated the effects of scattered radiation on the partial scan artifacts using simulated and measured water phantoms and found a strong correlation. The PSAR algorithm has been validated with a simulated semianthropomorphic heart phantom and with measurements of a dynamic biological perfusion phantom. For the stationary phantoms, real full scans have been performed to provide theoretical reference values. The improvement in the root mean square errors between the full and the partial scans with respect to the errors between the full and the corrected scans is up to 54% for the simulations and 90% for the measurements. The phase-correlated data now appear accurate enough for a quantitative analysis of cardiac perfusion.

Kinetics of triscarbonato uranyl reduction by aqueous ferrous iron: a theoretical study.

PubMed

Wander, Matthew C F; Kerisit, Sebastien; Rosso, Kevin M; Schoonen, Martin A A

2006-08-10

Uranium is a pollutant whose mobility is strongly dependent on its oxidation state. While U(VI) in the form of the uranyl cation is readily reduced by a range of natural reductants, by contrast complexation of uranyl by carbonate greatly reduces its reduction potential and imposes increased electron transfer (ET) distances. Very little is known about the elementary processes involved in uranium reduction from U(VI) to U(V) to U(IV) in general. In this study, we examine the theoretical kinetics of ET from ferrous iron to triscarbonato uranyl in aqueous solution. A combination of molecular dynamics (MD) simulations and density functional theory (DFT) electronic structure calculations is employed to compute the parameters that enter into Marcus' ET model, including the thermodynamic driving forces, reorganization energies, and electronic coupling matrix elements. MD simulations predict that two ferrous iron atoms will bind in an inner-sphere fashion to the three-membered carbonate ring of triscarbonato uranyl, forming the charge-neutral ternary Fe(2)UO(2)(CO(3))(3)(H(2)O)(8) complex. Through a sequential proton-coupled electron-transfer mechanism (PCET), the first ET step converting U(VI) to U(V) is predicted by DFT to occur with an electronic barrier that corresponds to a rate on the order of approximately 1 s(-1). The second ET step converting U(V) to U(IV) is predicted to be significantly endergonic. Therefore, U(V) is a stabilized end product in this ET system, in agreement with experiment.

Structural Dependence of the Sulfur Reduction Mechanism in Carbon-Based Cathodes for Lithium–Sulfur Batteries

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

Burgos, Juan C.; Balbuena, Perla B.; Montoya, Javier A.

We report lithium-sulfur batteries are promising non-conventional sources of energy due to their high theoretical capacity and energy density. However, the successful implementation of this technology has been hindered due to the low cycling life of the battery, caused by long chain polysulfide shuttling between electrodes during charge/discharge, among other issues. Quantum chemical calculations are used to study the reactivity of sulfur in the porous cathode of lithium-sulfur batteries, and the retention capabilities of porous carbon materials to avoid long chain polysulfide diffusion. Ab initio molecular dynamics (AIMD) simulations are initially employed to evaluate sulfur reduction mechanisms and kinetics, andmore » to identify main reduction products. A porous cathode architecture is modeled through parallel graphene layers with elemental sulfur rings in the interlayer, and filled with 1,3-dioxolane (DOL) organic solvent and lithium ions. AIMD simulations showed fast reduction of elemental sulfur and formation of short chain polysulfide. Furthermore, the effect of dangling carbon bonds of graphene on the reactivity of the cathode was confirmed. Adsorption calculations through density functional theory (DFT) proved the capacity of small pores to retain long polysulfide chains. An analysis of the effect of the specific current on the chemical behavior of sulfur reveals an influence of current on the amount of sulfur utilization and practical specific capacity of the battery. In conclusion, this work illustrates the physical-chemical behavior of the sulfur/polysulfide in the porous cathode system at atomistic level.« less

Structural Dependence of the Sulfur Reduction Mechanism in Carbon-Based Cathodes for Lithium–Sulfur Batteries

DOE PAGES

Burgos, Juan C.; Balbuena, Perla B.; Montoya, Javier A.

2017-08-17

We report lithium-sulfur batteries are promising non-conventional sources of energy due to their high theoretical capacity and energy density. However, the successful implementation of this technology has been hindered due to the low cycling life of the battery, caused by long chain polysulfide shuttling between electrodes during charge/discharge, among other issues. Quantum chemical calculations are used to study the reactivity of sulfur in the porous cathode of lithium-sulfur batteries, and the retention capabilities of porous carbon materials to avoid long chain polysulfide diffusion. Ab initio molecular dynamics (AIMD) simulations are initially employed to evaluate sulfur reduction mechanisms and kinetics, andmore » to identify main reduction products. A porous cathode architecture is modeled through parallel graphene layers with elemental sulfur rings in the interlayer, and filled with 1,3-dioxolane (DOL) organic solvent and lithium ions. AIMD simulations showed fast reduction of elemental sulfur and formation of short chain polysulfide. Furthermore, the effect of dangling carbon bonds of graphene on the reactivity of the cathode was confirmed. Adsorption calculations through density functional theory (DFT) proved the capacity of small pores to retain long polysulfide chains. An analysis of the effect of the specific current on the chemical behavior of sulfur reveals an influence of current on the amount of sulfur utilization and practical specific capacity of the battery. In conclusion, this work illustrates the physical-chemical behavior of the sulfur/polysulfide in the porous cathode system at atomistic level.« less

Implications of Lagrangian transport for coupled chemistry-climate simulations

NASA Astrophysics Data System (ADS)

Stenke, A.; Dameris, M.; Grewe, V.; Garny, H.

2008-10-01

For the first time a purely Lagrangian transport algorithm is applied in a fully coupled chemistry-climate model (CCM). We use the Lagrangian scheme ATTILA for the transport of water vapour, cloud water and chemical trace species in the ECHAM4.L39(DLR)/CHEM (E39C) CCM. The advantage of the Lagrangian approach is that it is numerically non-diffusive and therefore maintains steeper and more realistic gradients than the operational semi-Lagrangian transport scheme. In case of radiatively active species changes in the simulated distributions feed back to model dynamics which in turn affect the modelled transport. The implications of the Lagrangian transport scheme for stratospheric model dynamics and tracer distributions in the upgraded model version E39C-ATTILA (E39C-A) are evaluated by comparison with observations and results of the E39C model with the operational semi-Lagrangian advection scheme. We find that several deficiencies in stratospheric dynamics in E39C seem to originate from a pronounced modelled wet bias and an associated cold bias in the extra-tropical lowermost stratosphere. The reduction of the simulated moisture and temperature bias in E39C-A leads to a significant advancement of stratospheric dynamics in terms of the mean state as well as annual and interannual variability. As a consequence of the favourable numerical characteristics of the Lagrangian transport scheme and the improved model dynamics, E39C-A generally shows more realistic stratospheric tracer distributions: Compared to E39C high stratospheric chlorine (Cly) concentrations extend further downward and agree now well with analyses derived from observations. Therefore E39C-A realistically covers the altitude of maximum ozone depletion in the stratosphere. The location of the ozonopause, i.e. the transition from low tropospheric to high stratospheric ozone values, is also clearly improved in E39C-A. Furthermore, the simulated temporal evolution of stratospheric Cly in the past is realistically reproduced which is an important step towards a more reliable projection of future changes, especially of stratospheric ozone.

Modelling derecho dynamics and the direct radiative effect of wildfire smoke upon it with NWP model HARMONIE

NASA Astrophysics Data System (ADS)

Toll, Velle; Männik, Aarne

2014-05-01

Convection permitting numerical weather prediction model HARMONIE was used to simulate the dynamics of the derecho that swept over Eastern Europe on August 8, 2010. The storm moved over Belarus, Lithuania, Latvia, Estonia and Finland and the strongest wind gusts (up to 36.5 m/s) were measured in Estonia. The storm path is recorded on the radar images where characteristic bow echo was observed. The model setup was similar to near-future operational, nearly kilometre-scale environments in European national weather services. Hindcast experiments show the ability of the HARMONIE model to predict the severe convective storm and forecast concurrent strong wind gusts. Wind gusts with very similar intensity to observed ones were simulated by the HARMONIE model and 2.5-km horizontal resolution appears sufficient for reliable forecast of the derecho event. The timing of the modelled storm was in good agreement with the observations. The simulated average storm propagation speed was 25 m/s, similar to the radar observations. Hindcast experiments suggest that more precise warning for the storm could have been issued if the HARMONIE model would have been utilised. The derecho event was accompanied by the remarkable smoke aerosol concentrations (maximum total aerosol optical depth more than 4 at 550 nm) originating from the wildfires from Russia. Smoke plume travelled clockwise around Moscow from August 5 to 9. On August 8, 2010, smoke plume was situated on the Eastern border of Estonia. The derecho occurred on the western side of the smoke plume path. HARMONIE experiments were performed to study the direct radiative effect of wildfire smoke on a severe convective storm. The impact of smoke aerosol on the derecho dynamics was investigated. Reduction in the shortwave radiation flux at the surface resulting from aerosol influence simulated by the HARMONIE model is up to 200 W/m2 in the area with the highest aerosol concentrations. This causes near surface cooling of up to 3 ºC. The direct radiative effect of aerosol increases the stability of the atmospheric boundary layer and this had influence on the simulated derecho dynamics.

A numerical model of a HIL scaled roller rig for simulation of wheel-rail degraded adhesion condition

NASA Astrophysics Data System (ADS)

Conti, Roberto; Meli, Enrico; Pugi, Luca; Malvezzi, Monica; Bartolini, Fabio; Allotta, Benedetto; Rindi, Andrea; Toni, Paolo

2012-05-01

Scaled roller rigs used for railway applications play a fundamental role in the development of new technologies and new devices, combining the hardware in the loop (HIL) benefits with the reduction of the economic investments. The main problem of the scaled roller rig with respect to the full scale ones is the improved complexity due to the scaling factors. For this reason, before building the test rig, the development of a software model of the HIL system can be useful to analyse the system behaviour in different operative conditions. One has to consider the multi-body behaviour of the scaled roller rig, the controller and the model of the virtual vehicle, whose dynamics has to be reproduced on the rig. The main purpose of this work is the development of a complete model that satisfies the previous requirements and in particular the performance analysis of the controller and of the dynamical behaviour of the scaled roller rig when some disturbances are simulated with low adhesion conditions. Since the scaled roller rig will be used to simulate degraded adhesion conditions, accurate and realistic wheel-roller contact model also has to be included in the model. The contact model consists of two parts: the contact point detection and the adhesion model. The first part is based on a numerical method described in some previous studies for the wheel-rail case and modified to simulate the three-dimensional contact between revolute surfaces (wheel-roller). The second part consists in the evaluation of the contact forces by means of the Hertz theory for the normal problem and the Kalker theory for the tangential problem. Some numerical tests were performed, in particular low adhesion conditions were simulated, and bogie hunting and dynamical imbalance of the wheelsets were introduced. The tests were devoted to verify the robustness of control system with respect to some of the more frequent disturbances that may influence the roller rig dynamics. In particular we verified that the wheelset imbalance could significantly influence system performance, and to reduce the effect of this disturbance a multistate filter was designed.

Evaluation of the flame propagation within an SI engine using flame imaging and LES

NASA Astrophysics Data System (ADS)

He, Chao; Kuenne, Guido; Yildar, Esra; van Oijen, Jeroen; di Mare, Francesca; Sadiki, Amsini; Ding, Carl-Philipp; Baum, Elias; Peterson, Brian; Böhm, Benjamin; Janicka, Johannes

2017-11-01

This work shows experiments and simulations of the fired operation of a spark ignition engine with port-fuelled injection. The test rig considered is an optically accessible single cylinder engine specifically designed at TU Darmstadt for the detailed investigation of in-cylinder processes and model validation. The engine was operated under lean conditions using iso-octane as a substitute for gasoline. Experiments have been conducted to provide a sound database of the combustion process. A planar flame imaging technique has been applied within the swirl- and tumble-planes to provide statistical information on the combustion process to complement a pressure-based comparison between simulation and experiments. This data is then analysed and used to assess the large eddy simulation performed within this work. For the simulation, the engine code KIVA has been extended by the dynamically thickened flame model combined with chemistry reduction by means of pressure dependent tabulation. Sixty cycles have been simulated to perform a statistical evaluation. Based on a detailed comparison with the experimental data, a systematic study has been conducted to obtain insight into the most crucial modelling uncertainties.

Modelling the aqueous and nonaqueous interfaces for CO2 electro-reduction over Sn catalysts

NASA Astrophysics Data System (ADS)

Sheng, Tian; Sun, Shi-Gang

2018-01-01

In CO2 electroreduction, Sn catalysts with a high overpotential for hydrogen evolution reaction and a high selectivity towards formic acid formation are very attractive. Many efforts have been made for improving the catalytic performance and for understanding the mechanisms. In electrochemistry, the role of solvents for surface reactions was deserved to be investigated, in particular for some nonaqueous solvents. Here, we have modeled the aqueous (water) and nonaqueous (acetonitrile and dichloromethane) for investigation of CO2 electroreduction on Sn surface, by constrained ab initio molecular dynamics simulations and thermodynamic integrations, including a number of explicit solvent molecules in computational models. It was found that CO2 reduction is initiated from formate formation and solvents, in particular, water can effectively facilitate the reaction.

Natural and anthropogenic perturbations of the stratospheric ozone layer

NASA Technical Reports Server (NTRS)

Brasseur, Guy P.

1992-01-01

The paper reviews potential causes for reduction in the ozone abundance. The response of stratospheric ozone to solar activity is discussed. Ozone changes are simulated in relation with the potential development of a fleet of high-speed stratospheric aircraft and the release in the atmosphere of chlorofluorocarbons. The calculations are performed by a two-dimensional chemical-radiative-dynamical model. The importance of heterogeneous chemistry in polar stratospheric clouds and in the Junge layer (sulfate aerosol) is emphasized. The recently reported ozone trend over the last decade is shown to have been largely caused by the simultaneous effects of increasing concentrations of chlorofluorocarbons and heterogeneous chemistry. The possibility for a reduction in stratospheric ozone following a large volcanic eruption such as that of Mount Pinatubo in 1991 is discussed.

Reduction of Electrolyte Components on a Coated Si Anode of Lithium-Ion Batteries.

PubMed

Gomez-Ballesteros, Jose L; Balbuena, Perla B

2017-07-20

Surface modification of Si anodes in Li-ion batteries by deposition of a thin alucone coating has demonstrated an effective way to help maintain a stable anode/electrolyte interface and good battery performance. In this work, we investigate the interactions and reactivity of the film with electrolyte components using ab initio molecular dynamics simulations. Adsorption of solvent molecules (ethylene carbonate, EC) and salt (LiPF 6 ) and reduction by two mechanisms depending on the Li content of the film (yielding open EC adsorbed on the film or C 2 H 4 + CO 3 2- ) take place near the film/electrolyte and film/anode interfaces. Reaction products incorporate into the structure of the film and create a new kind of solid-electrolyte interphase layer.

Reduction of Electrolyte Components on a Coated Si Anode of Lithium-Ion Batteries

DOE PAGES

Gomez-Ballesteros, Jose L.; Balbuena, Perla B.

2017-07-07

Surface modification of Si anodes in Li-ion batteries by deposition of a thin alucone coating has demonstrated an effective way to help maintain a stable anode/electrolyte interface and good battery performance. In this paper, we investigate the interactions and reactivity of the film with electrolyte components using ab initio molecular dynamics simulations. Adsorption of solvent molecules (ethylene carbonate, EC) and salt (LiPF 6), and reduction by two mechanisms depending on the Li content of the film (yielding open EC adsorbed on the film or C 2H 4 + CO 3 2-) take place near the film/electrolyte and film/anode interfaces. Finally,more » reactions products incorporate to the structure of the film and create a new kind of solid-electrolyte interphase layer.« less

The influence of cations on lithium ion coordination and transport in ionic liquid electrolytes: a MD simulation study.

PubMed

Lesch, Volker; Li, Zhe; Bedrov, Dmitry; Borodin, Oleg; Heuer, Andreas

2016-01-07

The dynamical and structural properties in two ionic liquid electrolytes (ILEs) based on 1-ethyl-3-methylimidazolium bis-(trifluoromethanesulfonyl)-imide ([emim][TFSI]) and N-methyl-N-propylpyrrolidinium bis-(trifluoromethanesulfonyl)imide([pyr13][TFSI]) were compared as a function of lithium bis-(trifluoromethanesulfonyl)-imide (LiTFSI) salt concentrations using atomistic molecular dynamics (MD) simulations. The many-body polarizable APPLE&P force field has been utilized. The influence of anion polarization on the structure of the first coordination shell of Li(+) was examined. In particular, the reduction of the oxygen of the TFSI anion (OTFSI) polarizability from 1.36 Å(3) to 1.00 Å(3) resulted in an increased fraction of the TFSI anion bidentate coordination to the Li(+). While the overall dynamics in [pyr13][TFSI]-based ILEs was slower than in [emim][TFSI]-based ILEs, the exchange of TFSI anions in and out of the first coordination shell of Li(+) was found to be faster in pyr13-based systems. The Li(+) ion transference number is higher for these systems as well. These trends can be related to the difference in interaction of TFSI with the IL cation which is stronger for pyr13 than for emim.

Solvent Dependence of Double Proton Transfer in the Formic Acid-Formamidine Complex: Path Integral Molecular Dynamics Investigation.

PubMed

Kungwan, Nawee; Ngaojampa, Chanisorn; Ogata, Yudai; Kawatsu, Tsutomu; Oba, Yuki; Kawashima, Yukio; Tachikawa, Masanori

2017-10-05

Solvent dependence of double proton transfer in the formic acid-formamidine (FA-FN) complex at room temperature was investigated by means of ab initio path integral molecular dynamics (AIPIMD) simulation with taking nuclear quantum and thermal effects into account. The conductor-like screening model (COSMO) was applied for solvent effect. In comparison with gas phase, double proton delocalization between two heavy atoms (O and N) in FA-FN were observed with reduced proton transfer barrier height in low dielectric constant medium (<4.8). For dielectric constant medium at 4.8, the chance of finding these two protons are more pronounced due to the solvent effect which completely washes out the proton transfer barrier. In the case of higher dielectric constant medium (>4.8), the ionic species becomes more stable than the neutral ones and the formate anion and formamidium cation are thermodynamically stable. For ab initio molecular dynamics simulation, in low dielectric constant medium (<4.8) a reduction of proton transfer barrier with solvent effect is found to be less pronounced than the AIPIMD due to the absence of nuclear quantum effect. Moreover, the motions of FA-FN complex are significantly different with increasing dielectric constant medium. Such a difference is revealed in detail by the principal component analysis.

Study of the flow field past dimpled aerodynamic surfaces: numerical simulation and experimental verification

NASA Astrophysics Data System (ADS)

Binci, L.; Clementi, G.; D'Alessandro, V.; Montelpare, S.; Ricci, R.

2017-11-01

This work presents the study of the flow field past of dimpled laminar airfoil. Fluid dynamic behaviour of these elements has been not still deeply studied in the scientific community. Therefore Computational Fluid-Dynamics (CFD) is here used to analyze the flow field induced by dimples on the NACA 64-014A laminar airfoil at Re = 1.75 · 105 at α = 0°. Reynolds Averaged Navier-Stokes (RANS) equations and Large-Eddy Simulations (LES) were compared with wind tunnel measurements in order to evaluate their effectiveness in the modeling this kind of flow field. LES equations were solved using a specifically developed OpenFOAM solver adopting an L-stable Singly Diagonally Implicit Runge-Kutta (SDIRK) technique with an iterated PISO-like procedure for handling pressure-velocity coupling within each RK stage. Dynamic Smagorinsky subgrid model was employed. LES results provided good agreement with experimental data, while RANS equations closed with \\[k-ω -γ -\\overset{}{\\mathop{{{\\operatorname{Re}}θ, \\text{t}}}} \\] approach overstimates laminar separation bubble (LSB) extension of dimpled and un-dimpled configurations. Moreover, through skin friction coefficient analysis, we found a different representation of the turbulent zone between the numerical models; indeed, with RANS model LSB seems to be divided in two different parts, meanwhile LES model shows a LSB global reduction.

General trends of dihedral conformational transitions in a globular protein.

PubMed

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C; McCammon, J Andrew

2016-04-01

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. © 2016 Wiley Periodicals, Inc.

General trends of dihedral conformational transitions in a globular protein

DOE PAGES

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; ...

2016-02-15

In this paper, dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed bymore » the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. In conclusion, these general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.« less

Insights into the effects of mutations on Cren7-DNA binding using molecular dynamics simulations and free energy calculations.

PubMed

Chen, Lin; Zheng, Qing-Chuan; Zhang, Hong-Xing

2015-02-28

A novel, highly conserved chromatin protein, Cren7 is involved in regulating essential cellular processes such as transcription, replication and repair. Although mutations in the DNA-binding loop of Cren7 destabilize the structure and reduce DNA-binding activity, the details are not very clear. Focusing on the specific Cren7-dsDNA complex (PDB code ), we applied molecular dynamics (MD) simulations and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculations to explore the structural and dynamic effects of W26A, L28A, and K53A mutations in comparison to the wild-type protein. The energetic analysis indicated that the intermolecular van der Waals interaction and nonpolar solvation energy play an important role in the binding process of Cren7 and dsDNA. Compared with the wild type Cren7, all the studied mutants W26A, L28A, and K53A have obviously reduced binding free energies with dsDNA in the reduction of the polar and/or nonpolar interactions. These results further elucidated the previous experiments to understand the Cren7-DNA interaction comprehensively. Our work also would provide support for an understanding of the interactions of proteins with nucleic acids.

Impacts of aerosol direct effects on tropospheric ozone ...

EPA Pesticide Factsheets

Aerosol direct effects (ADE), i.e., scattering and absorption of incoming solar radiation, reduce radiation reaching the ground and the resultant photolysis attenuation can decrease O3 formation in polluted areas. One the other hand, evidence also suggests that ADE associated cooling suppresses atmospheric ventilation thereby enhancing surface-level O3. Assessment of ADE impacts is thus important for understanding emission reduction strategies that seek co-benefits associated with reductions in both particulate matter and O3 levels. This study quantifies the impacts of ADE on tropospheric ozone by using a two-way online coupled meteorology and atmospheric chemistry model, WRF-CMAQ, instrumented with process analysis methodology. Two manifestations of ADE impacts on O3 including changes in atmospheric dynamics (∆Dynamics) and changes in photolysis rates (∆Photolysis) were assessed separately through multiple scenario simulations for January and July of 2013 over China. Results suggest that ADE reduced surface daily maxima 1h O3 (DM1O3) in China by up to 39 µg m-3 1 through the combination of ∆Dynamics and ∆Photolysis in January, but enhanced surface DM1O3 by up to 4 µg m-3 in July. Increased O3 in July is largely attributed to ∆Dynamics which causes a weaker O3 sink of dry deposition and a stronger O3 source of photochemistry due to the stabilization of atmosphere. Meanwhile, surface OH is also enhanced at noon in July, though its daytime average valu

Sensitivity and requirement of improvements of four soybean crop simulation models for climate change studies in Southern Brazil

NASA Astrophysics Data System (ADS)

Battisti, R.; Sentelhas, P. C.; Boote, K. J.

2017-12-01

Crop growth models have many uncertainties that affect the yield response to climate change. Based on that, the aim of this study was to evaluate the sensitivity of crop models to systematic changes in climate for simulating soybean attainable yield in Southern Brazil. Four crop models were used to simulate yields: AQUACROP, MONICA, DSSAT, and APSIM, as well as their ensemble. The simulations were performed considering changes of air temperature (0, + 1.5, + 3.0, + 4.5, and + 6.0 °C), [CO2] (380, 480, 580, 680, and 780 ppm), rainfall (- 30, - 15, 0, + 15, and + 30%), and solar radiation (- 15, 0, + 15), applied to daily values. The baseline climate was from 1961 to 2014, totalizing 53 crop seasons. The crop models simulated a reduction of attainable yield with temperature increase, reaching 2000 kg ha-1 for the ensemble at + 6 °C, mainly due to shorter crop cycle. For rainfall, the yield had a higher rate of reduction when it was diminished than when rainfall was increased. The crop models increased yield variability when solar radiation was changed from - 15 to + 15%, whereas [CO2] rise resulted in yield gains, following an asymptotic response, with a mean increase of 31% from 380 to 680 ppm. The models used require further attention to improvements in optimal and maximum cardinal temperature for development rate; runoff, water infiltration, deep drainage, and dynamic of root growth; photosynthesis parameters related to soil water availability; and energy balance of soil-plant system to define leaf temperature under elevated CO2.

Optimized Sensor Network and Multi-Agent Decision Support for Smart Traffic Light Management.

PubMed

Cruz-Piris, Luis; Rivera, Diego; Fernandez, Susel; Marsa-Maestre, Ivan

2018-02-02

One of the biggest challenges in modern societies is to solve vehicular traffic problems. Sensor networks in traffic environments have contributed to improving the decision-making process of Intelligent Transportation Systems. However, one of the limiting factors for the effectiveness of these systems is in the deployment of sensors to provide accurate information about the traffic. Our proposal is using the centrality measurement of a graph as a base to locate the best locations for sensor installation in a traffic network. After integrating these sensors in a simulation scenario, we define a Multi-Agent Systems composed of three types of agents: traffic light management agents, traffic jam detection agents, and agents that control the traffic lights at an intersection. The ultimate goal of these Multi-Agent Systems is to improve the trip duration for vehicles in the network. To validate our solution, we have developed the needed elements for modelling the sensors and agents in the simulation environment. We have carried out experiments using the Simulation of Urban MObility (SUMO) traffic simulator and the Travel and Activity PAtterns Simulation (TAPAS) Cologne traffic scenario. The obtained results show that our proposal allows to reduce the sensor network while still obtaining relevant information to have a global view of the environment. Finally, regarding the Multi-Agent Systems, we have carried out experiments that show that our proposal is able to improve other existing solutions such as conventional traffic light management systems (static or dynamic) in terms of reduction of vehicle trip duration and reduction of the message exchange overhead in the sensor network.

Sensitivity and requirement of improvements of four soybean crop simulation models for climate change studies in Southern Brazil

NASA Astrophysics Data System (ADS)

Battisti, R.; Sentelhas, P. C.; Boote, K. J.

2018-05-01

Crop growth models have many uncertainties that affect the yield response to climate change. Based on that, the aim of this study was to evaluate the sensitivity of crop models to systematic changes in climate for simulating soybean attainable yield in Southern Brazil. Four crop models were used to simulate yields: AQUACROP, MONICA, DSSAT, and APSIM, as well as their ensemble. The simulations were performed considering changes of air temperature (0, + 1.5, + 3.0, + 4.5, and + 6.0 °C), [CO2] (380, 480, 580, 680, and 780 ppm), rainfall (- 30, - 15, 0, + 15, and + 30%), and solar radiation (- 15, 0, + 15), applied to daily values. The baseline climate was from 1961 to 2014, totalizing 53 crop seasons. The crop models simulated a reduction of attainable yield with temperature increase, reaching 2000 kg ha-1 for the ensemble at + 6 °C, mainly due to shorter crop cycle. For rainfall, the yield had a higher rate of reduction when it was diminished than when rainfall was increased. The crop models increased yield variability when solar radiation was changed from - 15 to + 15%, whereas [CO2] rise resulted in yield gains, following an asymptotic response, with a mean increase of 31% from 380 to 680 ppm. The models used require further attention to improvements in optimal and maximum cardinal temperature for development rate; runoff, water infiltration, deep drainage, and dynamic of root growth; photosynthesis parameters related to soil water availability; and energy balance of soil-plant system to define leaf temperature under elevated CO2.

Optimized Sensor Network and Multi-Agent Decision Support for Smart Traffic Light Management

PubMed Central

2018-01-01

One of the biggest challenges in modern societies is to solve vehicular traffic problems. Sensor networks in traffic environments have contributed to improving the decision-making process of Intelligent Transportation Systems. However, one of the limiting factors for the effectiveness of these systems is in the deployment of sensors to provide accurate information about the traffic. Our proposal is using the centrality measurement of a graph as a base to locate the best locations for sensor installation in a traffic network. After integrating these sensors in a simulation scenario, we define a Multi-Agent Systems composed of three types of agents: traffic light management agents, traffic jam detection agents, and agents that control the traffic lights at an intersection. The ultimate goal of these Multi-Agent Systems is to improve the trip duration for vehicles in the network. To validate our solution, we have developed the needed elements for modelling the sensors and agents in the simulation environment. We have carried out experiments using the Simulation of Urban MObility (SUMO) traffic simulator and the Travel and Activity PAtterns Simulation (TAPAS) Cologne traffic scenario. The obtained results show that our proposal allows to reduce the sensor network while still obtaining relevant information to have a global view of the environment. Finally, regarding the Multi-Agent Systems, we have carried out experiments that show that our proposal is able to improve other existing solutions such as conventional traffic light management systems (static or dynamic) in terms of reduction of vehicle trip duration and reduction of the message exchange overhead in the sensor network. PMID:29393884

Two Decades of WRF/CMAQ simulations over the continental ...

EPA Pesticide Factsheets

Confidence in the application of models for forecasting and regulatory assessments is furthered by conducting four types of model evaluation: operational, dynamic, diagnostic, and probabilistic. Operational model evaluation alone does not reveal the confidence limits that can be associated with modeled air quality concentrations. This paper presents novel approaches for performing dynamic model evaluation and for evaluating the confidence limits of ozone exceedances using the WRF/CMAQ model simulations over the continental United States for the period from 1990 to 2010. The methodology presented here entails spectral decomposition of ozone time series using the KZ filter to assess the variations in the strengths of the synoptic (i.e., weather-induced variation) and baseline (i.e., long-term variation attributable to emissions, policy, and trends) forcings embedded in the modeled and observed concentrations. A method is presented where the future year observations are estimated based on the changes in the concentrations predicted by the model applied to the current year observations. The proposed method can provide confidence limits for ozone exceedances for a given emission reduction scenario. We present and discuss these new approaches to identify the strengths of the model in representing the changes in simulated O3 air quality over the 21-year period. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates

Traction–separation relationships for hydrogen induced grain boundary embrittlement in nickel via molecular dynamics simulations

DOE PAGES

Barrows, Wesley; Dingreville, Rémi; Spearot, Douglas

2015-10-19

A statistical approach combined with molecular dynamics simulations is used to study the influence of hydrogen on intergranular decohesion. This methodology is applied to a Ni Σ3(112)[11¯0] symmetric tilt grain boundary. Hydrogenated grain boundaries with different H concentrations are constructed using an energy minimization technique with initial H atom positions guided by Monte Carlo simulation results. Decohesion behavior is assessed through extraction of a traction–separation relationship during steady-state crack propagation in a statistically meaningful approach, building upon prior work employing atomistic cohesive zone volume elements (CZVEs). A sensitivity analysis is performed on the numerical approach used to extract the traction–separationmore » relationships, clarifying the role of CZVE size, threshold parameters necessary to differentiate elastic and decohesion responses, and the numerical averaging technique. Results show that increasing H coverage at the Ni Σ3(112)[11¯0] grain boundary asymmetrically influences the crack tip velocity during propagation, leads to a general decrease in the work of separation required for crack propagation, and provides a reduction in the peak stress in the extracted traction–separation relationship. Furthermore the present framework offers a meaningful vehicle to pass atomistically derived interfacial behavior to higher length scale formulations for intergranular fracture.« less

Dispersal responses override density effects on genetic diversity during post-disturbance succession

PubMed Central

Landguth, Erin L.; Bull, C. Michael; Banks, Sam C.; Gardner, Michael G.; Driscoll, Don A.

2016-01-01

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus. We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus. Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics. PMID:27009225

Reduction of the allotropic transition temperature in nanocrystalline zirconium: Predicted by modified equation of state (MEOS) method and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Salati, Amin; Mokhtari, Esmail; Panjepour, Masoud; Aryanpour, Gholamreza

2013-04-01

The temperature at which polymorphic phase transformation occurs in nanocrystalline (NC) materials is different from that of coarse-grained specimens. This anomaly has been related to the role of grain boundary component in these materials and can be predicted by a dilated crystal model. In this study, based on this model, a modified equation of state (MEOS) method (instead of equation of state, EOS, method) is used to calculate the total Gibbs free energy of each phase (β-Zr or α-Zr) in NC Zr. Thereupon, the change in the total Gibbs free energy for β-Zr to α-Zr phase transformation (ΔGβ→α) via the grain size is calculated by this method. Similar to polymorphic transformation in other NC materials (Fe, Nb, Co, TiO2, Al2O3 and ZnS), it is found that the estimated transformation temperature in NC Zr (β→α) is reduced with decreasing grain size. Finally, a molecular dynamics (MD) simulation is employed to confirm the theoretical results.

Membrane-based actuation for high-speed single molecule force spectroscopy studies using AFM.

PubMed

Sarangapani, Krishna; Torun, Hamdi; Finkler, Ofer; Zhu, Cheng; Degertekin, Levent

2010-07-01

Atomic force microscopy (AFM)-based dynamic force spectroscopy of single molecular interactions involves characterizing unbinding/unfolding force distributions over a range of pulling speeds. Owing to their size and stiffness, AFM cantilevers are adversely affected by hydrodynamic forces, especially at pulling speeds >10 microm/s, when the viscous drag becomes comparable to the unbinding/unfolding forces. To circumvent these adverse effects, we have fabricated polymer-based membranes capable of actuating commercial AFM cantilevers at speeds >or=100 microm/s with minimal viscous drag effects. We have used FLUENT, a computational fluid dynamics (CFD) software, to simulate high-speed pulling and fast actuation of AFM cantilevers and membranes in different experimental configurations. The simulation results support the experimental findings on a variety of commercial AFM cantilevers and predict significant reduction in drag forces when membrane actuators are used. Unbinding force experiments involving human antibodies using these membranes demonstrate that it is possible to achieve bond loading rates >or=10(6) pN/s, an order of magnitude greater than that reported with commercial AFM cantilevers and systems.

A Langevin dynamics simulation study of the tribology of polymer loop brushes.

PubMed

Yin, Fang; Bedrov, Dmitry; Smith, Grant D; Kilbey, S Michael

2007-08-28

The tribology of surfaces modified with doubly bound polymer chains (loops) has been investigated in good solvent conditions using Langevin dynamics simulations. The density profiles, brush interpenetration, chain inclination, normal forces, and shear forces for two flat substrates modified by doubly bound bead-necklace polymers and equivalent singly bound polymers (twice as many polymer chains of 12 the molecular weight of the loop chains) were determined and compared as a function of surface separation, grafting density, and shear velocity. The doubly bound polymer layers showed less interpenetration with decreasing separation than the equivalent singly bound layers. Surprisingly, this difference in interpenetration between doubly bound polymer and singly bound polymer did not result in decreased friction at high shear velocity possibly due to the decreased ability of the doubly bound chains to deform in response to the applied shear. However, at lower shear velocity, where deformation of the chains in the flow direction is less pronounced and the difference in interpenetration is greater between the doubly bound and singly bound chains, some reduction in friction was observed.

Life cycle, techno-economic and dynamic simulation assessment of bioelectrochemical systems: A case of formic acid synthesis.

PubMed

Shemfe, Mobolaji; Gadkari, Siddharth; Yu, Eileen; Rasul, Shahid; Scott, Keith; Head, Ian M; Gu, Sai; Sadhukhan, Jhuma

2018-05-01

A novel framework, integrating dynamic simulation (DS), life cycle assessment (LCA) and techno-economic assessment (TEA) of a bioelectrochemical system (BES), has been developed to study for the first time wastewater treatment by removal of chemical oxygen demand (COD) by oxidation in anode and thereby harvesting electron and proton for carbon dioxide reduction reaction or reuse to produce products in cathode. Increases in initial COD and applied potential increase COD removal and production (in this case formic acid) rates. DS correlations are used in LCA and TEA for holistic performance analyses. The cost of production of HCOOH is €0.015-0.005 g -1 for its production rate of 0.094-0.26 kg yr -1 and a COD removal rate of 0.038-0.106 kg yr -1 . The life cycle (LC) benefits by avoiding fossil-based formic acid production (93%) and electricity for wastewater treatment (12%) outweigh LC costs of operation and assemblage of BES (-5%), giving a net 61MJkg -1 HCOOH saving. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Spacecraft Formation Flying Maneuvers Using Linear-Quadratic Regulation with No Radial Axis Inputs

NASA Technical Reports Server (NTRS)

Starin, Scott R.; Yedavalli, R. K.; Sparks, Andrew G.; Bauer, Frank H. (Technical Monitor)

2001-01-01

Regarding multiple spacecraft formation flying, the observation has been made that control thrust need only be applied coplanar to the local horizon to achieve complete controllability of a two-satellite (leader-follower) formation. A formulation of orbital dynamics using the state of one satellite relative to another is used. Without the need for thrust along the radial (zenith-nadir) axis of the relative reference frame ' propulsion system simplifications and weight reduction may be accomplished. Several linear-quadratic regulators (LQR) are explored and compared based on performance measures likely to be important to many missions, but not directly optimized in the LQR designs. Maneuver simulations are performed using commercial ODE solvers to propagate the Keplerian dynamics of a controlled satellite relative to an uncontrolled leader. These short maneuver simulations demonstrate the capacity of the controller to perform changes from one formation geometry to another. This work focusses on formations in which the controlled satellite has a relative trajectory which projects onto the local horizon of the uncontrolled satellite as a circle. This formation has potential uses for distributed remote sensing systems.

Bottom-up view of water network-mediated CO2 reduction using cryogenic cluster ion spectroscopy and direct dynamics simulations.

PubMed

Breen, Kristin J; DeBlase, Andrew F; Guasco, Timothy L; Voora, Vamsee K; Jordan, Kenneth D; Nagata, Takashi; Johnson, Mark A

2012-01-26

The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive "hydrated electron" onto a neutral CO(2) molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO(2) or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO(2)·(H(2)O)(6)(-) clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.

Spatio-temporal dynamics of security investments in an interdependent risk environment

NASA Astrophysics Data System (ADS)

Shafi, Kamran; Bender, Axel; Zhong, Weicai; Abbass, Hussein A.

2012-10-01

In a globalised world where risks spread through contagion, the decision of an entity to invest in securing its premises from stochastic risks no longer depends solely on its own actions but also on the actions of other interacting entities in the system. This phenomenon is commonly seen in many domains including airline, logistics and computer security and is referred to as Interdependent Security (IDS). An IDS game models this decision problem from a game-theoretic perspective and deals with the behavioural dynamics of risk-reduction investments in such settings. This paper enhances this model and investigates the spatio-temporal aspects of the IDS games. The spatio-temporal dynamics are studied using simple replicator dynamics on a variety of network structures and for various security cost tradeoffs that lead to different Nash equilibria in an IDS game. The simulation results show that the neighbourhood configuration has a greater effect on the IDS game dynamics than network structure. An in-depth empirical analysis of game dynamics is carried out on regular graphs, which leads to the articulation of necessary and sufficient conditions for dominance in IDS games under spatial constraints.

A data-driven dynamics simulation framework for railway vehicles

NASA Astrophysics Data System (ADS)

Nie, Yinyu; Tang, Zhao; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2018-03-01

The finite element (FE) method is essential for simulating vehicle dynamics with fine details, especially for train crash simulations. However, factors such as the complexity of meshes and the distortion involved in a large deformation would undermine its calculation efficiency. An alternative method, the multi-body (MB) dynamics simulation provides satisfying time efficiency but limited accuracy when highly nonlinear dynamic process is involved. To maintain the advantages of both methods, this paper proposes a data-driven simulation framework for dynamics simulation of railway vehicles. This framework uses machine learning techniques to extract nonlinear features from training data generated by FE simulations so that specific mesh structures can be formulated by a surrogate element (or surrogate elements) to replace the original mechanical elements, and the dynamics simulation can be implemented by co-simulation with the surrogate element(s) embedded into a MB model. This framework consists of a series of techniques including data collection, feature extraction, training data sampling, surrogate element building, and model evaluation and selection. To verify the feasibility of this framework, we present two case studies, a vertical dynamics simulation and a longitudinal dynamics simulation, based on co-simulation with MATLAB/Simulink and Simpack, and a further comparison with a popular data-driven model (the Kriging model) is provided. The simulation result shows that using the legendre polynomial regression model in building surrogate elements can largely cut down the simulation time without sacrifice in accuracy.

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

DTIC Science & Technology

2010-01-01

formulations of molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage...ad hoc force term in the SGLD model. Introduction Molecular dynamics (MD) simulations of small proteins provide insight into the mechanisms and... molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage mini-protein. All

Model Reduction in Biomechanics

NASA Astrophysics Data System (ADS)

Feng, Yan

The mechanical characteristic of the cell is primarily performed by the cytoskeleton. Microtubules, actin, and intermediate filaments are the three main cytoskeletal polymers. Of these, microtubules are the stiffest and have multiple functions within a cell that include: providing tracks for intracellular transport, transmitting the mechanical force necessary for cell division during mitosis, and providing sufficient stiffness for propulsion in flagella and cilia. Microtubule mechanics has been studied by a variety of methods: detailed molecular dynamics (MD), coarse-grained models, engineering type models, and elastic continuum models. In principle, atomistic MD simulations should be able to predict all desired mechanical properties of a single molecule, however, in practice the large computational resources are required to carry out a simulation of larger biomolecular system. Due to the limited accessibility using even the most ambitious all-atom models and the demand for the multiscale molecular modeling and simulation, the emergence of the reduced models is critically important to provide the capability for investigating the biomolecular dynamics that are critical to many biological processes. Then the coarse-grained models, such as elastic network models and anisotropic network models, have been shown to bequite accurate in predicting microtubule mechanical response, but still requires significant computational resources. On the other hand, the microtubule is treated as comprising materials with certain continuum material properties. Such continuum models, especially Euler-Bernoulli beam models, are often used to extract mechanical parameters from experimental results. The microtubule is treated as comprising materials with certain continuum material properties. Such continuum models, especially Euler-Bernoulli beam models in which the biomolecular system is assumed as homogeneous isotropic materials with solid cross-sections, are often used to extract mechanical parameters from experimental results. However, in real biological world, these homogeneous and isotropic assumptions are usually invalidate. Thus, instead of using hypothesized model, a specific continuum model at mesoscopic scale can be introduced based upon data reduction of the results from molecular simulations at atomistic level. Once a continuum model is established, it can provide details on the distribution of stresses and strains induced within the biomolecular system which is useful in determining the distribution and transmission of these forces to the cytoskeletal and sub-cellular components, and help us gain a better understanding in cell mechanics. A data-driven model reduction approach to the problem of microtubule mechanics as an application is present, a beam element is constructed for microtubules based upon data reduction of the results from molecular simulation of the carbon backbone chain of alphabeta-tubulin dimers. The data base of mechanical responses to various types of loads from molecular simulation is reduced to dominant modes. The dominant modes are subsequently used to construct the stiffness matrix of a beam element that captures the anisotropic behavior and deformation mode coupling that arises from a microtubule's spiral structure. In contrast to standard Euler-Bernoulli or Timoshenko beam elements, the link between forces and node displacements results not from hypothesized deformation behavior, but directly from the data obtained by molecular scale simulation. Differences between the resulting microtubule data-driven beam model (MTDDBM) and standard beam elements are presented, with a focus on coupling of bending, stretch, shear deformations. The MTDDBM is just as economical to use as a standard beam element, and allows accurate reconstruction of the mechanical behavior of structures within a cell as exemplified in a simple model of a component element of the mitotic spindle.

Simulating land-atmosphere feedbacks and response to widespread forest disturbance: The role of lower boundary configuration and dynamic water table in meteorological modeling

NASA Astrophysics Data System (ADS)

Forrester, M.; Maxwell, R. M.; Bearup, L. A.; Gochis, D.

2017-12-01

Numerical meteorological models are frequently used to diagnose land-atmosphere interactions and predict large-scale response to extreme or hazardous events, including widespread land disturbance or perturbations to near-surface moisture. However, few atmospheric modeling platforms consider the impact that dynamic groundwater storage, specifically 3D subsurface flow, has on land-atmosphere interactions. In this study, we use the Weather Research and Forecasting (WRF) mesoscale meteorological model to identify ecohydrologic and land-atmosphere feedbacks to disturbance by the mountain pine beetle (MPB) over the Colorado Headwaters region. Disturbance simulations are applied to WRF with various lower boundary configurations: Including default Noah land surface model soil moisture representation; a version of WRF coupled to ParFlow (PF), an integrated groundwater-surface water model that resolves variably saturated flow in the subsurface; and WRF coupled to PF in a static water table version, simulating only vertical and no lateral subsurface flow. Our results agree with previous literature showing MPB-induced reductions in canopy transpiration in all lower boundary scenarios, as well as energy repartitioning, higher water tables, and higher planetary boundary layer over infested regions. Simulations show that expanding from local to watershed scale results in significant damping of MPB signal as unforested and unimpacted regions are added; and, while deforestation appears to have secondary feedbacks to planetary boundary layer and convection, these slight perturbations to cumulative summer precipitation are insignificant in the context of ensemble methodologies. Notably, the results suggest that groundwater representation in atmospheric modeling affects the response intensity of a land disturbance event. In the WRF-PF case, energy and atmospheric processes are more sensitive to disturbance in regions with higher water tables. Also, when dynamic subsurface hydrology is removed, WRF simulates a greater response to MPB at the land-atmosphere interface, including greater changes to daytime skin temperature, Bowen ratio and near-surface humidity. These findings highlight lower boundary representations in computational meteorology and numerical land-atmosphere modeling.

Dynamical modeling and analysis of large cellular regulatory networks

NASA Astrophysics Data System (ADS)

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

2013-06-01

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

Development of a precise controller for an electrohydraulic total artificial heart. Improvement of the motor's dynamic response.

PubMed

Ahn, J M; Masuzawa, T; Taenaka, Y; Tatsumi, E; Ohno, T; Choi, W W; Toda, K; Miyazaki, K; Baba, Y; Nakatani, T; Takano, H; Min, B G

1996-01-01

In an electrohydraulic total artificial heart developed at the National Cardiovascular Center (Osaka, Japan), two blood pumps are pushed alternatively by means of the bidirectional motion of a brushless DC motor for pump systole and diastole. Improvement in the dynamic response of the motor is very important to obtain better pump performance; this was accomplished by using power electronic simulation. For the motor to have the desired dynamic response, it must be commutated properly and the damping ratio (zeta), which represents transient characteristics of the motor, must lie between 0.4 and 0.8. Consequently, all satisfactory specifications with respect to power consumption must be obtained. Based on the simulated results, the design criteria were determined and the precise controller designed to reduce torque ripple and motor vibration, and determine motor stop time at every direction change. In in vitro tests, evaluation of the controller and dynamic response of the motor was justified in terms of zeta, power consumption, and motor stop time. The results indicated that the power consumption of the controller and the input power of the motor were decreased by 1.2 and 2.5 W at zeta = 0.6, respectively, compared to the previous system. An acceptable dynamic response of the motor, necessary for the reduction of torque ripple and motor vibration, was obtained between zeta = 0.5 and zeta = 0.7, with an increase in system efficiency from 10% to 12%. The motor stop time required for stable motor reoperation was determined to be over 10 msec, for a savings in power consumption of approximately 1.5 W. Therefore, the improved dynamic response of the motor can contribute to the stability and reliability of the pump.

Extreme learning machine for reduced order modeling of turbulent geophysical flows.

PubMed

San, Omer; Maulik, Romit

2018-04-01

We investigate the application of artificial neural networks to stabilize proper orthogonal decomposition-based reduced order models for quasistationary geophysical turbulent flows. An extreme learning machine concept is introduced for computing an eddy-viscosity closure dynamically to incorporate the effects of the truncated modes. We consider a four-gyre wind-driven ocean circulation problem as our prototype setting to assess the performance of the proposed data-driven approach. Our framework provides a significant reduction in computational time and effectively retains the dynamics of the full-order model during the forward simulation period beyond the training data set. Furthermore, we show that the method is robust for larger choices of time steps and can be used as an efficient and reliable tool for long time integration of general circulation models.

Influence of Non-Maxwellian Particles on Dust Acoustic Waves in a Dusty Magnetized Plasma

NASA Astrophysics Data System (ADS)

M. Nouri, Kadijani; Zareamoghaddam, H.

2013-11-01

In this paper an investigation into dust acoustic solitary waves (DASWs) in the presence of superthermal electrons and ions in a magnetized plasma with cold dust grains and trapped electrons is discussed. The dynamic of both electrons and ions is simulated by the generalized Lorentzian (κ) distribution function (DF). The dust grains are cold and their dynamics are studied by hydrodynamic equations. The basic set of fluid equations is reduced to modified Korteweg-de Vries (mKdV) equation using Reductive Perturbation Theory (RPT). Two types of solitary waves, fast and slow dust acoustic soliton (DAS) exist in this plasma. Calculations reveal that compressive solitary structures are possibly propagated in the plasma where dust grains are negatively (or positively) charged. The properties of DASs are also investigated numerically.

Volumetric visualization of 3D data

NASA Technical Reports Server (NTRS)

Russell, Gregory; Miles, Richard

1989-01-01

In recent years, there has been a rapid growth in the ability to obtain detailed data on large complex structures in three dimensions. This development occurred first in the medical field, with CAT (computer aided tomography) scans and now magnetic resonance imaging, and in seismological exploration. With the advances in supercomputing and computational fluid dynamics, and in experimental techniques in fluid dynamics, there is now the ability to produce similar large data fields representing 3D structures and phenomena in these disciplines. These developments have produced a situation in which currently there is access to data which is too complex to be understood using the tools available for data reduction and presentation. Researchers in these areas are becoming limited by their ability to visualize and comprehend the 3D systems they are measuring and simulating.

Extreme learning machine for reduced order modeling of turbulent geophysical flows

NASA Astrophysics Data System (ADS)

San, Omer; Maulik, Romit

2018-04-01

We investigate the application of artificial neural networks to stabilize proper orthogonal decomposition-based reduced order models for quasistationary geophysical turbulent flows. An extreme learning machine concept is introduced for computing an eddy-viscosity closure dynamically to incorporate the effects of the truncated modes. We consider a four-gyre wind-driven ocean circulation problem as our prototype setting to assess the performance of the proposed data-driven approach. Our framework provides a significant reduction in computational time and effectively retains the dynamics of the full-order model during the forward simulation period beyond the training data set. Furthermore, we show that the method is robust for larger choices of time steps and can be used as an efficient and reliable tool for long time integration of general circulation models.

Lithium concentration dependent structure and mechanics of amorphous silicon

NASA Astrophysics Data System (ADS)

Sitinamaluwa, H. S.; Wang, M. C.; Will, G.; Senadeera, W.; Zhang, S.; Yan, C.

2016-06-01

A better understanding of lithium-silicon alloying mechanisms and associated mechanical behavior is essential for the design of Si-based electrodes for Li-ion batteries. Unfortunately, the relationship between the dynamic mechanical response and microstructure evolution during lithiation and delithiation has not been well understood. We use molecular dynamic simulations to investigate lithiated amorphous silicon with a focus to the evolution of its microstructure, phase composition, and stress generation. The results show that the formation of LixSi alloy phase is via different mechanisms, depending on Li concentration. In these alloy phases, the increase in Li concentration results in reduction of modulus of elasticity and fracture strength but increase in ductility in tension. For a LixSi system with uniform Li distribution, volume change induced stress is well below the fracture strength in tension.

Upset Simulation and Training Initiatives for U.S. Navy Commercial Derived Aircraft

NASA Technical Reports Server (NTRS)

Donaldson, Steven; Priest, James; Cunningham, Kevin; Foster, John V.

2012-01-01

Militarized versions of commercial platforms are growing in popularity due to many logistical benefits in the form of commercial off-the-shelf (COTS) parts, established production methods, and commonality for different certifications. Commercial data and best practices are often leveraged to reduce procurement and engineering development costs. While the developmental and cost reduction benefits are clear, these militarized aircraft are routinely operated in flight at significantly different conditions and in significantly different manners than for routine commercial flight. Therefore they are at a higher risk of flight envelope exceedance. This risk may lead to departure from controlled flight and/or aircraft loss1. Historically, the risk of departure from controlled flight for military aircraft has been mitigated by piloted simulation training and engineering analysis of typical aircraft response. High-agility military aircraft simulation databases are typically developed to include high angles of attack (AoA) and sideslip due to the dynamic nature of their missions and have been developed for many tactical configurations over the previous decades. These aircraft simulations allow for a more thorough understanding of the vehicle flight dynamics characteristics at high AoA and sideslip. In recent years, government sponsored research on transport airplane aerodynamic characteristics at high angles of attack has produced a growing understanding of stall/post-stall behavior. This research along with recent commercial airline training initiatives has resulted in improved understanding of simulator-based training requirements and simulator model fidelity.2-5 In addition, inflight training research over the past decade has produced a database of pilot performance and recurrency metrics6. Innovative solutions to aerodynamically model large commercial aircraft for upset conditions such as high AoA, high sideslip, and ballistic damage, as well as capability to accurately account for scaling factors, is necessary to develop realistic engineering and training simulations. Such simulations should significantly reduce the risk of departure from controlled flight, loss of aircraft, and ease the airworthiness certification process. The characteristics of commercial derivative aircraft are exemplified by the P-8A Multi-mission Maritime Aircraft (MMA) aircraft, and the largest benefits of initial investigation are likely to be yielded from this platform. The database produced would also be utilized by flight dynamics engineers as a means to further develop and investigate vehicle flight characteristics as mission tactics evolve through the years ahead. This paper will describe ongoing efforts by the U.S. Navy to develop a methodology for simulation and training for large commercial-derived transport aircraft at unusual attitudes, typically experienced during an aircraft upset. This methodology will be applied to a representative Navy aircraft (P-8A) and utilized to develop a robust simulation that should accurately represent aircraft response in these extremes. Simulation capabilities would then extend to flight dynamics analysis and simulation, as well as potential training applications. Recent evaluations of integrated academic, ground-based simulation, and in-flight upset training will be described along with important lessons learned, specific to military requirements.

Flow diverter effect of LVIS stent on cerebral aneurysm hemodynamics: a comparison with Enterprise stents and the Pipeline device.

PubMed

Wang, Chao; Tian, Zhongbin; Liu, Jian; Jing, Linkai; Paliwal, Nikhil; Wang, Shengzhang; Zhang, Ying; Xiang, Jianping; Siddiqui, Adnan H; Meng, Hui; Yang, Xinjian

2016-07-02

The aim of this study was to quantify the effect of the new Low-profile Visualized Intraluminal Support (LVIS®D) device and the difference of fluid diverting effect compared with the Pipeline device and the Enterprise stent using computational fluid dynamics (CFD). In this research, we simulated three aneurysms constructed from 3D digital subtraction angiography (DSA). The Enterprise, LVIS and the Pipeline device were virtually conformed to fit into the vessel lumen and placed across the aneurysm orifice. Computational fluid dynamics analysis was performed to compare the hemodynamic differences such as WSS, Velocity and Pressure among these stents. Control referred to the unstented model, the percentage of hemodynamic changes were all compared to Control. A single LVIS stent caused more wall shear stress reduction than double Enterprise stents (39.96 vs. 30.51 %) and velocity (23.13 vs. 18.64 %). Significant reduction in wall shear stress (63.88 %) and velocity (46.05 %) was observed in the double-LVIS stents. A single Pipeline showed less reduction in WSS (51.08 %) and velocity (37.87 %) compared with double-LVIS stent. The double-Pipeline stents resulted in the most reduction in WSS (72.37 %) and velocity (54.26 %). Moreover, the pressure increased with minuscule extent after stenting, compared with the unstented model. This is the first study analyzing flow modifications associated with LVIS stents. We found that the LVIS stent has certain hemodynamic effects on cerebral aneurysms: a single LVIS stent caused more flow reductions than the double-Enterprise stent but less than a Pipeline device. Nevertheless, the double-LVIS stent resulted in a better flow diverting effect than a Pipeline device.

Simulating coupled carbon and nitrogen dynamics following mountain pine beetle outbreaks in the western United States

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

Edburg, Steven L.; Hicke, Jeffrey A.; Lawrence, David M.

2011-01-01

Insect outbreaks are major ecosystem disturbances, affecting a similar area as forest fires annually across North America. Tree mortality caused by epidemics of bark beetles alters carbon cycling in the first several years following the disturbance by reducing stand-level primary production and increasing decomposition rates. The few studies of biogeochemical cycling following outbreaks have shown a range of impacts from small responses of net carbon fluxes in the first several years after a severe outbreak to large forest areas that are sources of carbon to the atmosphere for decades. To gain more understanding about causes of this range of responses,more » we used an ecosystem model to assess impacts of different bark beetle outbreak conditions on coupled carbon and nitrogen cycling. We modified the Community Land Model with prognostic carbon and nitrogen to include prescribed bark beetle outbreaks. We then compared control simulations (without a bark beetle outbreak) to simulations with various mortality severity, durations of outbreak, and snagfall dynamics to quantify the range of carbon flux responses and recovery rates of net ecosystem exchange to a range of realistic outbreak conditions. Prescribed mortality by beetles reduced leaf area and thus productivity. Gross primary productivity decreased by as much as 80% for a severe outbreak (95% mortality) and by 10% for less severe outbreaks (25% mortality). Soil mineral nitrogen dynamics (immobilization and plant uptake) were important in governing post-outbreak productivity, and were strongly modulated by carbon inputs to the soil from killed trees. Initial increases in heterotrophic respiration caused by a pulse of labile carbon from roots were followed by a slight reduction (from pre-snagfall reduced inputs), then a secondary increase (from inputs due to snagfall). Secondary increases in heterotrophic respiration were largest for simulated windthrow of snags after a prescribed snagfall delay period. Net ecosystem productivity recovered within 40 years for all simulations, with the largest increases in the first 10 years. Our simulations illustrate that, given the large variability in bark beetle outbreak conditions, a wide range of responses in carbon and nitrogen dynamics can occur. The fraction of trees killed, timing of snagfall, snagfall rate, and management decisions as to whether or not to remove snags for harvesting or for fire prevention will have a major impact on post-outbreak carbon fluxes up to 100 years following an outbreak.« less

Optimal dimensionality reduction of complex dynamics: the chess game as diffusion on a free-energy landscape.

PubMed

Krivov, Sergei V

2011-07-01

Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game--the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.

Optimal dimensionality reduction of complex dynamics: The chess game as diffusion on a free-energy landscape

NASA Astrophysics Data System (ADS)

Krivov, Sergei V.

2011-07-01

Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game—the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.

Coupling of a distributed stakeholder-built system dynamics socio-economic model with SAHYSMOD for sustainable soil salinity management. Part 2: Model coupling and application

NASA Astrophysics Data System (ADS)

Inam, Azhar; Adamowski, Jan; Prasher, Shiv; Halbe, Johannes; Malard, Julien; Albano, Raffaele

2017-08-01

Many simulation models focus on simulating a single physical process and do not constitute balanced representations of the physical, social and economic components of a system. The present study addresses this challenge by integrating a physical (P) model (SAHYSMOD) with a group (stakeholder) built system dynamics model (GBSDM) through a component modeling approach based on widely applied tools such as MS Excel, Python and Visual Basic for Applications (VBA). The coupled model (P-GBSDM) was applied to test soil salinity management scenarios (proposed by stakeholders) for the Haveli region of the Rechna Doab Basin in Pakistan. Scenarios such as water banking, vertical drainage, canal lining, and irrigation water reallocation were simulated with the integrated model. Spatiotemporal maps and economic and environmental trade-off criteria were used to examine the effectiveness of the selected management scenarios. After 20 years of simulation, canal lining reduced soil salinity by 22% but caused an initial reduction of 18% in farm income, which requires an initial investment from the government. The government-sponsored Salinity Control and Reclamation Project (SCARP) is a short-term policy that resulted in a 37% increase in water availability with a 12% increase in farmer income. However, it showed detrimental effects on soil salinity in the long term, with a 21% increase in soil salinity due to secondary salinization. The new P-GBSDM was shown to be an effective platform for engaging stakeholders and simulating their proposed management policies while taking into account socioeconomic considerations. This was not possible using the physically based SAHYSMOD model alone.

Characterization of protein-folding pathways by reduced-space modeling.

PubMed

Kmiecik, Sebastian; Kolinski, Andrzej

2007-07-24

Ab initio simulations of the folding pathways are currently limited to very small proteins. For larger proteins, some approximations or simplifications in protein models need to be introduced. Protein folding and unfolding are among the basic processes in the cell and are very difficult to characterize in detail by experiment or simulation. Chymotrypsin inhibitor 2 (CI2) and barnase are probably the best characterized experimentally in this respect. For these model systems, initial folding stages were simulated by using CA-CB-side chain (CABS), a reduced-space protein-modeling tool. CABS employs knowledge-based potentials that proved to be very successful in protein structure prediction. With the use of isothermal Monte Carlo (MC) dynamics, initiation sites with a residual structure and weak tertiary interactions were identified. Such structures are essential for the initiation of the folding process through a sequential reduction of the protein conformational space, overcoming the Levinthal paradox in this manner. Furthermore, nucleation sites that initiate a tertiary interactions network were located. The MC simulations correspond perfectly to the results of experimental and theoretical research and bring insights into CI2 folding mechanism: unambiguous sequence of folding events was reported as well as cooperative substructures compatible with those obtained in recent molecular dynamics unfolding studies. The correspondence between the simulation and experiment shows that knowledge-based potentials are not only useful in protein structure predictions but are also capable of reproducing the folding pathways. Thus, the results of this work significantly extend the applicability range of reduced models in the theoretical study of proteins.

Changing Amazon biomass and the role of atmospheric CO2 concentration, climate, and land use

NASA Astrophysics Data System (ADS)

Almeida Castanho, Andrea D.; Galbraith, David; Zhang, Ke; Coe, Michael T.; Costa, Marcos H.; Moorcroft, Paul

2016-01-01

The Amazon tropical evergreen forest is an important component of the global carbon budget. Its forest floristic composition, structure, and function are sensitive to changes in climate, atmospheric composition, and land use. In this study biomass and productivity simulated by three dynamic global vegetation models (Integrated Biosphere Simulator, Ecosystem Demography Biosphere Model, and Joint UK Land Environment Simulator) for the period 1970-2008 are compared with observations from forest plots (Rede Amazónica de Inventarios Forestales). The spatial variability in biomass and productivity simulated by the DGVMs is low in comparison to the field observations in part because of poor representation of the heterogeneity of vegetation traits within the models. We find that over the last four decades the CO2 fertilization effect dominates a long-term increase in simulated biomass in undisturbed Amazonian forests, while land use change in the south and southeastern Amazonia dominates a reduction in Amazon aboveground biomass, of similar magnitude to the CO2 biomass gain. Climate extremes exert a strong effect on the observed biomass on short time scales, but the models are incapable of reproducing the observed impacts of extreme drought on forest biomass. We find that future improvements in the accuracy of DGVM predictions will require improved representation of four key elements: (1) spatially variable plant traits, (2) soil and nutrients mediated processes, (3) extreme event mortality, and (4) sensitivity to climatic variability. Finally, continued long-term observations and ecosystem-scale experiments (e.g. Free-Air CO2 Enrichment experiments) are essential for a better understanding of the changing dynamics of tropical forests.

Simulation of polyethylene glycol and calcium-mediated membrane fusion

NASA Astrophysics Data System (ADS)

Pannuzzo, Martina; De Jong, Djurre H.; Raudino, Antonio; Marrink, Siewert J.

2014-03-01

We report on the mechanism of membrane fusion mediated by polyethylene glycol (PEG) and Ca2+ by means of a coarse-grained molecular dynamics simulation approach. Our data provide a detailed view on the role of cations and polymer in modulating the interaction between negatively charged apposed membranes. The PEG chains cause a reduction of the inter-lamellar distance and cause an increase in concentration of divalent cations. When thermally driven fluctuations bring the membranes at close contact, a switch from cis to trans Ca2+-lipid complexes stabilizes a focal contact acting as a nucleation site for further expansion of the adhesion region. Flipping of lipid tails induces subsequent stalk formation. Together, our results provide a molecular explanation for the synergistic effect of Ca2+ and PEG on membrane fusion.

Monitoring morphology and hydrogen coverage of nanometric Pt/γ-Al2 O3 particles by in situ HERFD-XANES and quantum simulations.

PubMed

Gorczyca, Agnes; Moizan, Virginie; Chizallet, Celine; Proux, Olivier; Del Net, William; Lahera, Eric; Hazemann, Jean-Louis; Raybaud, Pascal; Joly, Yves

2014-11-10

Platinum nanoclusters highly dispersed on γ-alumina are widely used as heterogeneous catalysts. To understand the chemical interplay between the Pt nanoparticles, the support, and the reductive atmosphere, we performed X-ray absorption near edge structure (XANES) in situ experiments recorded in high energy resolution fluorescence detection (HERFD) mode. Spectra are assigned by comparison with simulated XANES spectra on models obtained by molecular dynamics (DFT-MD). We propose platinum cluster morphologies and quantify the hydrogen coverages compatible with XANES spectra recorded at variable hydrogen pressures and temperatures. Using cutting-edge methodologies to assign XANES spectra, this work gives unequalled atomic insights into the characterization of supported nanoclusters. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insights into molecular interactions between CaM and its inhibitors from molecular dynamics simulations and experimental data.

PubMed

González-Andrade, Martin; Rodríguez-Sotres, Rogelio; Madariaga-Mazón, Abraham; Rivera-Chávez, José; Mata, Rachel; Sosa-Peinado, Alejandro; Del Pozo-Yauner, Luis; Arias-Olguín, Imilla I

2016-01-01

In order to contribute to the structural basis for rational design of calmodulin (CaM) inhibitors, we analyzed the interaction of CaM with 14 classic antagonists and two compounds that do not affect CaM, using docking and molecular dynamics (MD) simulations, and the data were compared to available experimental data. The Ca(2+)-CaM-Ligands complexes were simulated 20 ns, with CaM starting in the "open" and "closed" conformations. The analysis of the MD simulations provided insight into the conformational changes undergone by CaM during its interaction with these ligands. These simulations were used to predict the binding free energies (ΔG) from contributions ΔH and ΔS, giving useful information about CaM ligand binding thermodynamics. The ΔG predicted for the CaM's inhibitors correlated well with available experimental data as the r(2) obtained was 0.76 and 0.82 for the group of xanthones. Additionally, valuable information is presented here: I) CaM has two preferred ligand binding sites in the open conformation known as site 1 and 4, II) CaM can bind ligands of diverse structural nature, III) the flexibility of CaM is reduced by the union of its ligands, leading to a reduction in the Ca(2+)-CaM entropy, IV) enthalpy dominates the molecular recognition process in the system Ca(2+)-CaM-Ligand, and V) the ligands making more extensive contact with the protein have higher affinity for Ca(2+)-CaM. Despite their limitations, docking and MD simulations in combination with experimental data continue to be excellent tools for research in pharmacology, toward a rational design of new drugs.

Molecular dynamics simulations of fluoropolymers in the solid state

NASA Astrophysics Data System (ADS)

Holt, David Bryan

1998-10-01

Molecular mechanics and dynamics simulations have been utilized to address the behavior of helix reversal defects in fluoropolymers. The results of the simulations confirm that helix reversals do form and migrate in PTFE crystals. The most important defect structure is a helix reversal band: two helix reversals which bracker a small chain segment (typically 6-7 backbone atoms) having the opposite helical sense from the parent molecule. Small reversal bands had velocities ranging between 100 m/s (low temperature)-250 m/s (high temperature). The size of this reversal band defect is dependent upon the helical conformation and is equal to approximately half of the helical repeat unit in the low and intermediate temperature phases. In the high temperature phase where intermolecular effects are diminished, a wider distribution of reversal band sizes was observed during the simulations. A mechanism is identified by which significant reorientation of a chain segment about the molecular axis can occur when it is bracketed by two helix reversal bands. Simulations with a model containing a perfluoromethyl (PFM) group at low temperature showed that the presence of the PFM group significantly restricts chain mobility locally. However, a significant reduction in the helix reversal defect density was observed on neighboring chains as well. During simulations in which a shear deformation was applied to the models with and without a PFM group, an increase in reversal defect density was observed. However, the helix reversal density in the sheared model containing the PFM branch was less than that in the model without a PFM branch under no shear. These data implicate helix reversal defects and associated chain segment motions in the mechanical behavior of fluoropolymer materials.

Non-perturbative measurement of cross-field thermal diffusivity reduction at the O-point of 2/1 neoclassical tearing mode islands in the DIII-D tokamak

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

Bardóczi, L.; Rhodes, T. L.; Carter, T. A.

2016-05-15

Neoclassical tearing modes (NTMs) often lead to the decrease of plasma performance and can lead to disruptions, which makes them a major impediment in the development of operating scenarios in present toroidal fusion devices. Recent gyrokinetic simulations predict a decrease of plasma turbulence and cross-field transport at the O-point of the islands, which in turn affects the NTM dynamics. In this paper, a heat transport model of magnetic islands employing spatially non-uniform cross-field thermal diffusivity (χ{sub ⊥}) is presented. This model is used to derive χ{sub ⊥} at the O-point from electron temperature data measured across 2/1 NTM islands inmore » DIII-D. It was found that χ{sub ⊥} at the O-point is 1 to 2 orders of magnitude smaller than the background plasma transport, in qualitative agreement with gyrokinetic predictions. As the anomalously large values of χ{sub ⊥} are often attributed to turbulence driven transport, the reduction of the O-point χ{sub ⊥} is consistent with turbulence reduction found in recent experiments. Finally, the implication of reduced χ{sub ⊥} at the O-point on NTM dynamics was investigated using the modified Rutherford equation that predicts a significant effect of reduced χ{sub ⊥} at the O-point on NTM saturation.« less

Non-perturbative measurement of cross-field thermal diffusivity reduction at the O-point of 2/1 neoclassical tearing mode islands in the DIII-D tokamak

DOE PAGES

Bardóczi, Laszlo; Rhodes, Terry L.; Carter, Troy A.; ...

2016-05-09

Neoclassical Tearing Modes (NTMs) often lead to the decrease of plasma performance and can lead to disruptions, which makes them a major impediment in the development of operating scenarios in present toroidal fusion devices. Recent gyrokinetic simulations predict a decrease of plasma turbulence and cross- eld transport at the O-point of the islands, which in turn affects the NTM dynamics. In this paper a heat transport model of magnetic islands employing spatially non-uniform cross-field thermal diffusivity (χ more » $$\\perp$$) is presented. This model is used to derive χ $$\\perp$$ at the O-point from electron temperature data measured across 2/1 NTM islands in DIII-D. It was found that χ $$\\perp$$ at the O-point is 1 to 2 orders of magnitude smaller than the background plasma transport, in qualitative agreement with gyrokinetic predictions. As the anomalously large values of χ $$\\perp$$ are often attributed to turbulence driven transport, the reduction of the O-point χ $$\\perp$$ is consistent with turbulence reduction found in recent experiments. Lastly, the implication of reduced χ $$\\perp$$ at the O-point on NTM dynamics was investigated using the modi ed Rutherford equation that predicts a significant effect of reduced χ $$\\perp$$ at the O-point on NTM saturation.« less

Resting state networks in empirical and simulated dynamic functional connectivity.

PubMed

Glomb, Katharina; Ponce-Alvarez, Adrián; Gilson, Matthieu; Ritter, Petra; Deco, Gustavo

2017-10-01

It is well-established that patterns of functional connectivity (FC) - measures of correlated activity between pairs of voxels or regions observed in the human brain using neuroimaging - are robustly expressed in spontaneous activity during rest. These patterns are not static, but exhibit complex spatio-temporal dynamics. Over the last years, a multitude of methods have been proposed to reveal these dynamics on the level of the whole brain. One finding is that the brain transitions through different FC configurations over time, and substantial effort has been put into characterizing these configurations. However, the dynamics governing these transitions are more elusive, specifically, the contribution of stationary vs. non-stationary dynamics is an active field of inquiry. In this study, we use a whole-brain approach, considering FC dynamics between 66 ROIs covering the entire cortex. We combine an innovative dimensionality reduction technique, tensor decomposition, with a mean field model which possesses stationary dynamics. It has been shown to explain resting state FC averaged over time and multiple subjects, however, this average FC summarizes the spatial distribution of correlations while hiding their temporal dynamics. First, we apply tensor decomposition to resting state scans from 24 healthy controls in order to characterize spatio-temporal dynamics present in the data. We simultaneously utilize temporal and spatial information by creating tensors that are subsequently decomposed into sets of brain regions ("communities") that share similar temporal dynamics, and their associated time courses. The tensors contain pairwise FC computed inside of overlapping sliding windows. Communities are discovered by clustering features pooled from all subjects, thereby ensuring that they generalize. We find that, on the group level, the data give rise to four distinct communities that resemble known resting state networks (RSNs): default mode network, visual network, control networks, and somatomotor network. Second, we simulate data with our stationary mean field model whose nodes are connected according to results from DTI and fiber tracking. In this model, all spatio-temporal structure is due to noisy fluctuations around the average FC. We analyze the simulated data in the same way as the empirical data in order to determine whether stationary dynamics can explain the emergence of distinct FC patterns (RSNs) which have their own time courses. We find that this is the case for all four networks using the spatio-temporal information revealed by tensor decomposition if nodes in the simulation are connected according to model-based effective connectivity. Furthermore, we find that these results require only a small part of the FC values, namely the highest values that occur across time and ROI pair. Our findings show that stationary dynamics can account for the emergence of RSNs. We provide an innovative method that does not make strong assumptions about the underlying data and is generally applicable to resting state or task data from different subject populations. Copyright © 2017 Elsevier Inc. All rights reserved.

Reduced order modeling and active flow control of an inlet duct

NASA Astrophysics Data System (ADS)

Ge, Xiaoqing

Many aerodynamic applications require the modeling of compressible flows in or around a body, e.g., the design of aircraft, inlet or exhaust duct, wind turbines, or tall buildings. Traditional methods use wind tunnel experiments and computational fluid dynamics (CFD) to investigate the spatial and temporal distribution of the flows. Although they provide a great deal of insight into the essential characteristics of the flow field, they are not suitable for control analysis and design due to the high physical/computational cost. Many model reduction methods have been studied to reduce the complexity of the flow model. There are two main approaches: linearization based input/output modeling and proper orthogonal decomposition (POD) based model reduction. The former captures mostly the local behavior near a steady state, which is suitable to model laminar flow dynamics. The latter obtains a reduced order model by projecting the governing equation onto an "optimal" subspace and is able to model complex nonlinear flow phenomena. In this research we investigate various model reduction approaches and compare them in flow modeling and control design. We propose an integrated model-based control methodology and apply it to the reduced order modeling and active flow control of compressible flows within a very aggressive (length to exit diameter ratio, L/D, of 1.5) inlet duct and its upstream contraction section. The approach systematically applies reduced order modeling, estimator design, sensor placement and control design to improve the aerodynamic performance. The main contribution of this work is the development of a hybrid model reduction approach that attempts to combine the best features of input/output model identification and POD method. We first identify a linear input/output model by using a subspace algorithm. We next project the difference between CFD response and the identified model response onto a set of POD basis. This trajectory is fit to a nonlinear dynamical model to augment the linear input/output model. Thus, the full system is decomposed into a dominant linear subsystem and a low order nonlinear subsystem. The hybrid model is then used for control design and compared with other modeling methods in CFD simulations. Numerical results indicate that the hybrid model accurately predicts the nonlinear behavior of the flow for a 2D diffuser contraction section model. It also performs best in terms of feedback control design and learning control. Since some outputs of interest (e.g., the AIP pressure recovery) are not observable during normal operations, static and dynamic estimators are designed to recreate the information from available sensor measurements. The latter also provides a state estimation for feedback controller. Based on the reduced order models and estimators, different controllers are designed to improve the aerodynamic performance of the contraction section and inlet duct. The integrated control methodology is evaluated with CFD simulations. Numerical results demonstrate the feasibility and efficacy of the active flow control based on reduced order models. Our reduced order models not only generate a good approximation of the nonlinear flow dynamics over a wide input range, but also help to design controllers that significantly improve the flow response. The tools developed for model reduction, estimator and control design can also be applied to wind tunnel experiment.

Model and controller reduction of large-scale structures based on projection methods

NASA Astrophysics Data System (ADS)

Gildin, Eduardo

The design of low-order controllers for high-order plants is a challenging problem theoretically as well as from a computational point of view. Frequently, robust controller design techniques result in high-order controllers. It is then interesting to achieve reduced-order models and controllers while maintaining robustness properties. Controller designed for large structures based on models obtained by finite element techniques yield large state-space dimensions. In this case, problems related to storage, accuracy and computational speed may arise. Thus, model reduction methods capable of addressing controller reduction problems are of primary importance to allow the practical applicability of advanced controller design methods for high-order systems. A challenging large-scale control problem that has emerged recently is the protection of civil structures, such as high-rise buildings and long-span bridges, from dynamic loadings such as earthquakes, high wind, heavy traffic, and deliberate attacks. Even though significant effort has been spent in the application of control theory to the design of civil structures in order increase their safety and reliability, several challenging issues are open problems for real-time implementation. This dissertation addresses with the development of methodologies for controller reduction for real-time implementation in seismic protection of civil structures using projection methods. Three classes of schemes are analyzed for model and controller reduction: nodal truncation, singular value decomposition methods and Krylov-based methods. A family of benchmark problems for structural control are used as a framework for a comparative study of model and controller reduction techniques. It is shown that classical model and controller reduction techniques, such as balanced truncation, modal truncation and moment matching by Krylov techniques, yield reduced-order controllers that do not guarantee stability of the closed-loop system, that is, the reduced-order controller implemented with the full-order plant. A controller reduction approach is proposed such that to guarantee closed-loop stability. It is based on the concept of dissipativity (or positivity) of linear dynamical systems. Utilizing passivity preserving model reduction together with dissipative-LQG controllers, effective low-order optimal controllers are obtained. Results are shown through simulations.

Rhythmic crowd bobbing on a grandstand simulator

NASA Astrophysics Data System (ADS)

Comer, A. J.; Blakeborough, A.; Williams, M. S.

2013-01-01

It is widely accepted that concerted human activity such as bouncing or bobbing can excite cantilever grandstands. Crowd coordination can be unwitting and may be exacerbated by structural motion caused by resonant structural response. This is an area of uncertainty in the design and analysis of modern grandstands. This paper presents experimental measurement and analysis of rhythmic crowd bobbing loads obtained from tests on a grandstand simulator with two distinct support conditions; (a) rigid, and; (b) flexible. It was found that significant structural vibration at the bobbing frequency did not increase the effective bobbing load. Structural motion at the bobbing frequency caused a reduction in the dynamic load factor (DLF) at the frequency of the second harmonic while those at the first and third harmonics were unaffected. Two plausible reasons for this are: (a) the bobbing group were unable to supply significant energy to the system at the frequency of the second harmonic; (b) the bobbing group altered their bobbing style to reduce the response of the grandstand simulator. It was deduced that the bobbing group did not absorb energy from the dynamic system. Furthermore, dynamic load factors for groups of test subjects bobbing on a rigid structure were typically greater than those of synthesised groups derived from individuals bobbing alone, possibly due to group effects such as audio and visual stimuli from neighbouring test subjects. Last, the vibration levels experienced by the test subjects appear to be below levels likely to cause discomfort. This is to be expected as the test subjects were themselves controlling the magnitude and duration of vibration for the bobbing tests considered.

Denitrification nitrogen gas formation and gene expression in alpine grassland soil as affected by climate change conditions

NASA Astrophysics Data System (ADS)

Chen, Zhe; Wang, Changhui; Gschwendtner, Silvia; Schloter, Michael; Butterbach-Bahl, Klaus; Dannenmann, Michael

2013-04-01

Due to methodological problems, reliable data on soil dinitrogen (N2) emission by denitrification are extremely scarce, and the impacts of climate change on nitrogen (N) gas formation by denitrification and N gas product ratios as well as the underlying microbial drivers remain unclear. We combined the helium-gas-flow-soil-core technique for simultaneously quantification of nitrous oxide (N2O) and N2 emission with the reverse transcript qPCR technology. Our goals were to characterize denitrification dynamics and N gas product ratios in alpine grassland soil as affected by climate change conditions and to evaluate relationships between denitrification gene expression and N gas emission. We used soils from the pre-alpine grassland Terrestrial Environmental Observatory (TERENO), exposed to ambient temperature and precipitation (control treatment), or three years of simulated climate change conditions (increased temperature, reduction of summer precipitation and reduced snow cover). Soils were amended with glucose and nitrate and incubated subsequently at 1) 5°C and 20% oxygen; 2) 5°C and 0% oxygen; 3) 20°C and 0% oxygen until stabilization of N gas emissions in each incubation step. After switching incubation conditions to 0% oxygen and 20°C, N2O emission peaked immediately and declined again, followed by a delayed peak in N2 emission. The dynamics of cnorB gene expression, encoding the reduction of nitric oxide (NO) to N2O, followed the N2O emission pattern, while nosZ gene expression, encoding N2O reduction to N2 followed the course of N2 emission. The mean N2O:N2 ratios were 1.31 + 0.10 and 1.56 + 0.16 for control and climate change treatment respectively, but the denitrification potential was overall lower in climate change treatment. Hence, simulated climate change promoted N2O but lessened N2 emission. This stimulation of N2O was in accordance with increased cnorB gene expression in soil of the climate change treatment. N mass balance calculations revealed that denitrification N gas formation accounted for 21%, dissimilatory nitrate reduction to ammonium for 8%, and microbial immobilization for 73% of nitrate consumption. Overall, our study shows that changes in climate exert feedback on denitrification N gas formation and N gas product ratios via changes in microbial activity at the level of single denitrification steps. The close relationships found between denitrification N gas formation, N gas product ratios and denitrification gene expression suggests a large potential of molecular methods to predict denitrification dynamics in soil.

Modeling and simulation of RF photoinjectors for coherent light sources

NASA Astrophysics Data System (ADS)

Chen, Y.; Krasilnikov, M.; Stephan, F.; Gjonaj, E.; Weiland, T.; Dohlus, M.

2018-05-01

We propose a three-dimensional fully electromagnetic numerical approach for the simulation of RF photoinjectors for coherent light sources. The basic idea consists in incorporating a self-consistent photoemission model within a particle tracking code. The generation of electron beams in the injector is determined by the quantum efficiency (QE) of the cathode, the intensity profile of the driving laser as well as by the accelerating field and magnetic focusing conditions in the gun. The total charge emitted during an emission cycle can be limited by the space charge field at the cathode. Furthermore, the time and space dependent electromagnetic field at the cathode may induce a transient modulation of the QE due to surface barrier reduction of the emitting layer. In our modeling approach, all these effects are taken into account. The beam particles are generated dynamically according to the local QE of the cathode and the time dependent laser intensity profile. For the beam dynamics, a tracking code based on the Lienard-Wiechert retarded field formalism is employed. This code provides the single particle trajectories as well as the transient space charge field distribution at the cathode. As an application, the PITZ injector is considered. Extensive electron bunch emission simulations are carried out for different operation conditions of the injector, in the source limited as well as in the space charge limited emission regime. In both cases, fairly good agreement between measurements and simulations is obtained.

San Francisco Bay nutrients and plankton dynamics as simulated by a coupled hydrodynamic-ecosystem model

NASA Astrophysics Data System (ADS)

Liu, Qianqian; Chai, Fei; Dugdale, Richard; Chao, Yi; Xue, Huijie; Rao, Shivanesh; Wilkerson, Frances; Farrara, John; Zhang, Hongchun; Wang, Zhengui; Zhang, Yinglong

2018-06-01

An open source coupled physical-biogeochemical model is developed for San Francisco Bay (SFB) to study nutrient cycling and plankton dynamics as well as to assist ecosystem based management and risk assessment. The biogeochemical model in this study is based on the Carbon, Silicate and Nitrogen Ecosystem (CoSiNE) model, and coupled to the unstructured grid, Semi-Implicit Cross-scale Hydroscience Integrated System Model (SCHISM). The SCHISM-CoSiNE model reproduces the spatial and temporal variability in nutrients and plankton biomass, and its physical and biogeochemical performance is successfully tested using comparisons with shipboard and fixed station observations. The biogeochemical characteristics of the SFB during wet and dry years are investigated by changing the input of the major rivers. River discharges from the Sacramento and San Joaquin Rivers affect the phytoplankton biomass in North SFB through both advection and dilution of nutrient (including ammonium, NH4) concentrations in the river. The reduction in residence time caused by increased inflows can result in decreased biomass accumulation, while the corresponding reduction in NH4 concentration favors the growth of biomass. In addition, the model is used to make a series of sensitivity experiments to examine the response of SFB to changes in 1) nutrient loading from rivers and wastewater treatment plants (WWTPs), 2) a parameter (ψ) defining NH4 inhibition of nitrate (NO3) uptake by phytoplankton, 3) bottom grazing and 4) suspended sediment concentration. The model results show that changes in NH4 input from rivers or WWTPs affect the likelihood of phytoplankton blooms via NH4 inhibition and that the choice of ψ is critical. Bottom grazing simulated here as increased plankton mortality demonstrates the potential for bivalve reduction of chlorophyll biomass and the need to include bivalve grazing in future models. Furthermore, the model demonstrates the need to include sediments and their contribution to turbidity and availability of light. This biogeochemical model is suitable for other estuaries with similar ecological issues and anthropogenic stressors.

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Look-ahead Dynamic Simulation

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

2015-10-20

Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.

Methods, Computational Platform, Verification, and Application of Earthquake-Soil-Structure-Interaction Modeling and Simulation

NASA Astrophysics Data System (ADS)

Tafazzoli, Nima

Seismic response of soil-structure systems has attracted significant attention for a long time. This is quite understandable with the size and the complexity of soil-structure systems. The focus of three important aspects of ESSI modeling could be on consistent following of input seismic energy and a number of energy dissipation mechanisms within the system, numerical techniques used to simulate dynamics of ESSI, and influence of uncertainty of ESSI simulations. This dissertation is a contribution to development of one such tool called ESSI Simulator. The work is being done on extensive verified and validated suite for ESSI Simulator. Verification and validation are important for high fidelity numerical predictions of behavior of complex systems. This simulator uses finite element method as a numerical tool to obtain solutions for large class of engineering problems such as liquefaction, earthquake-soil-structure-interaction, site effect, piles, pile group, probabilistic plasticity, stochastic elastic-plastic FEM, and detailed large scale parallel models. Response of full three-dimensional soil-structure-interaction simulation of complex structures is evaluated under the 3D wave propagation. Domain-Reduction-Method is used for applying the forces as a two-step procedure for dynamic analysis with the goal of reducing the large size computational domain. The issue of damping of the waves at the boundary of the finite element models is studied using different damping patterns. This is used at the layer of elements outside of the Domain-Reduction-Method zone in order to absorb the residual waves coming out of the boundary layer due to structural excitation. Extensive parametric study is done on dynamic soil-structure-interaction of a complex system and results of different cases in terms of soil strength and foundation embedment are compared. High efficiency set of constitutive models in terms of computational time are developed and implemented in ESSI Simulator. Efficiency is done based on simplifying the elastic-plastic stiffness tensor of the constitutive models. Almost in all the soil-structure systems, there are interface zones in contact with each other. These zones can get detached during the loading or can slip on each other. In this dissertation the frictional contact element is implemented in ESSI Simulator. Extended verification has been done on the implemented element. The interest here is the effect of slipping and gap opening at the interface of soil and concrete foundation on the soil-structure system behavior. In fact transferring the loads to structure is defined based on the contact areas which will affect the response of the system. The effect of gap openings and sliding at the interfaces are shown through application examples. In addition, dissipation of the seismic energy due to frictional sliding of the interface zones are studied. Application Programming Interface (API) and Domain Specific Language (DSL) are being developed to increase developer's and user's modeling and simulation capabilities. API describes software services developed by developers that are used by users. A domain-specific language (DSL) is a small language which usually focuses on a particular problem domain in software. In general DSL programs are translated to a common function or library which can be viewed as a tool to hide the details of the programming, and make it easier for the user to deal with the commands.

Radiobiological foundation of crew radiation risk for mars mission

NASA Astrophysics Data System (ADS)

Shafirkin, A.

The results of a comprehensive clinico-physiological study of 250 dogs after 22 hours per day chronic exposure to gamma -radiation throughout their life are presented. The exposure duration was 3 and 6 years. The dose rate varied between 25 and 150 cSv/year to simulate galactic cosmic ray dose of crew members during mars mission. Several groups of the dogs received an additional acute dose of 10 and 50 cSv during a day three times per year to simulate stochastic irradiation caused by solar cosmic rays. Data on the status of regulatory systems of organism, exchange processes dynamics, organism reaction on additional functional loads are also presented. Organism reaction and dynamics of kinetic relations are considered in detail for most radiosensitive and regenerating tissue systems of the organism, namely, bloodforming system and spermatogenic epithelium. The results on life span reduction of the dogs and dog race characteristics after the radiation exposure are discussed. Based on the results obtained in this study and in model experiments realized with big amount of small laboratory animals that were exposed to a wide dose range, using other published data, mathematical models were developed, e. g. a model of radiation damage forming as dependent on time with taking into account recovery processes, and a model of radiation mortality rate of mammals. Based on these models and analysis of radiation environment behind various shielding on the route to Mars, crew radiation risk was calculated for space missions of various durations. Total radiation risk values for cosmonaut lifetime after the missions were also estimated together with expected life span reduction.

Radiobiological foundation of crew radiation risk for Mars mission

NASA Astrophysics Data System (ADS)

Aleksandr, Shafirkin; Grigoriev, Yurj

The results of a comprehensive clinico-physiological study of 250 dogs after 22 hours per day chronic exposure to gamma-radiation throughout their life are presented. The exposure duration was 3 and 6 years. The dose rate varied between 25 and 150 cSv/year to simulate galactic cosmic ray dose of crew members during mars mission. Several groups of the dogs received an additional acute dose of 10 and 50 cSv during a day three times per year to simulate stochastic irradiation caused by solar cosmic rays. Data on the status of regulatory systems of organism, exchange processes dynamics, organism reaction on additional functional loads are also presented. Organism reaction and dynamics of kinetic relations are considered in detail for most radiosensitive and regenerating tissue systems of the organism, namely, bloodforming system and spermatogenic epithelium. The results on life span reduction of the dogs and dog race characteristics after the radiation exposure are discussed. Based on the results obtained in this study and in model experiments realized with big amount of small laboratory animals that were exposed to a wide dose range, using other published data, mathematical models were developed, e. g. a model of radiation damage forming as dependent on time with taking into account recovery processes, and a model of radiation mortality rate of mammals. Based on these models and analysis of radiation environment behind various shielding on the route to Mars, crew radiation risk was calculated for space missions of various durations. Total radiation risk values for cosmonaut lifetime after the missions were also estimated together with expected life span reduction.

Analysis of Dynamic Avalanche Phenomenon in SOI Lateral High-speed Diode during Reverse Recovery and Development of a Novel Device Structure for Suppressing Dynamic Avalanche

NASA Astrophysics Data System (ADS)

Tokura, Norihito; Yamamoto, Takao; Kato, Hisato; Nakagawa, Akio

We have studied the dynamic avalanche phenomenon in an SOI lateral diode during reverse recovery by using a mixed-mode device simulation. In the study, it has been found that local impact ionization occurs near an anode-side field oxide edge, where a high-density hole current flows and a high electric field appears simultaneously. We propose that a p-type anode extension region (AER) along a trench side wall effectively sweeps out stored carriers beneath an anode p-diffusion layer during reverse recovery, resulting in reduction of the electric field and remarkable suppression of the dynamic avalanche. The AER reduces the total recovery charge and does not cause any increase in the total stored charge under a forward bias operation. This effect is verified experimentally by the fabricated device with AER. Thus, the developed SOI lateral diode is promising as a high-speed and highly rugged free-wheeling diode, which can be integrated into next-generation SOI microinverters.

A Model Structure for the Heterodimer apoA-IMilano–apoA-II Supports Its Peculiar Susceptibility to Proteolysis

PubMed Central

Rocco, Alessandro Guerini; Mollica, Luca; Gianazza, Elisabetta; Calabresi, Laura; Franceschini, Guido; Sirtori, Cesare R.; Eberini, Ivano

2006-01-01

In this study, we propose a structure for the heterodimer between apolipoprotein A-IMilano and apolipoprotein A-II (apoA-IM–apoA-II) in a synthetic high-density lipoprotein (HDL) containing L-α-palmitoyloleoyl phosphatidylcholine. We applied bioinformatics/computational tools and procedures, such as molecular docking, molecular and essential dynamics, starting from published crystal structures for apolipoprotein A-I and apolipoprotein A-II. Structural and energetic analyses onto the simulated system showed that the molecular dynamics produced a stabilized synthetic HDL. The essential dynamic analysis showed a deviation from the starting belt structure. Our structural results were validated by limited proteolysis experiments on HDL from apoA-IM carriers in comparison with control HDL. The high sensitivity of apoA-IM–apoA-II to proteases was in agreement with the high root mean-square fluctuation values and the reduction in secondary structure content from molecular dynamics data. Circular dichroism on synthetic HDL containing apoA-IM–apoA-II was consistent with the α-helix content computed on the proposed model. PMID:16891368

On Chaotic and Hyperchaotic Complex Nonlinear Dynamical Systems

NASA Astrophysics Data System (ADS)

Mahmoud, Gamal M.

Dynamical systems described by real and complex variables are currently one of the most popular areas of scientific research. These systems play an important role in several fields of physics, engineering, and computer sciences, for example, laser systems, control (or chaos suppression), secure communications, and information science. Dynamical basic properties, chaos (hyperchaos) synchronization, chaos control, and generating hyperchaotic behavior of these systems are briefly summarized. The main advantage of introducing complex variables is the reduction of phase space dimensions by a half. They are also used to describe and simulate the physics of detuned laser and thermal convection of liquid flows, where the electric field and the atomic polarization amplitudes are both complex. Clearly, if the variables of the system are complex the equations involve twice as many variables and control parameters, thus making it that much harder for a hostile agent to intercept and decipher the coded message. Chaotic and hyperchaotic complex systems are stated as examples. Finally there are many open problems in the study of chaotic and hyperchaotic complex nonlinear dynamical systems, which need further investigations. Some of these open problems are given.

Boundary Control of Linear Uncertain 1-D Parabolic PDE Using Approximate Dynamic Programming.

PubMed

Talaei, Behzad; Jagannathan, Sarangapani; Singler, John

2018-04-01

This paper develops a near optimal boundary control method for distributed parameter systems governed by uncertain linear 1-D parabolic partial differential equations (PDE) by using approximate dynamic programming. A quadratic surface integral is proposed to express the optimal cost functional for the infinite-dimensional state space. Accordingly, the Hamilton-Jacobi-Bellman (HJB) equation is formulated in the infinite-dimensional domain without using any model reduction. Subsequently, a neural network identifier is developed to estimate the unknown spatially varying coefficient in PDE dynamics. Novel tuning law is proposed to guarantee the boundedness of identifier approximation error in the PDE domain. A radial basis network (RBN) is subsequently proposed to generate an approximate solution for the optimal surface kernel function online. The tuning law for near optimal RBN weights is created, such that the HJB equation error is minimized while the dynamics are identified and closed-loop system remains stable. Ultimate boundedness (UB) of the closed-loop system is verified by using the Lyapunov theory. The performance of the proposed controller is successfully confirmed by simulation on an unstable diffusion-reaction process.

Control and dynamics of a flexible spacecraft during stationkeeping maneuvers

NASA Technical Reports Server (NTRS)

Liu, D.; Yocum, J.; Kang, D. S.

1991-01-01

A case study of a spacecraft having flexible solar arrays is presented. A stationkeeping attitude control mode using both earth and rate gyro reference signals and a flexible vehicle dynamics modeling and implementation is discussed. The control system is designed to achieve both pointing accuracy and structural mode stability during stationkeeping maneuvers. Reduction of structural mode interactions over the entire mode duration is presented. The control mode using a discrete time observer structure is described to show the convergence of the spacecraft attitude transients during Delta-V thrusting maneuvers without preloading thrusting bias to the onboard control processor. The simulation performance using the three axis, body stabilized nonlinear dynamics is provided. The details of a five body dynamics model are discussed. The spacecraft is modeled as a central rigid body having cantilevered flexible antennas, a pair of flexible articulated solar arrays, and to gimballed momentum wheels. The vehicle is free to undergo unrestricted rotations and translations relative to inertial space. A direct implementation of the equations of motion is compared to an indirect implementation that uses a symbolic manipulation software to generate rigid body equations.

Modeling recovery of Swedish ecosystems from acidification.

PubMed

Sverdrup, Harald; Martinson, Liisa; Alveteg, Mattias; Moldan, Filip; Kronnäs, Veronika; Munthe, John

2005-02-01

Dynamic models complement existing time series of observations and static critical load calculations by simulating past and future development of chemistry in forest and lake ecosystems. They are used for dynamic assessment of the acidification and to produce target load functions, that describe what combinations of nitrogen and sulfur emission reductions are needed to achieve a chemical or biological criterion in a given target year. The Swedish approach has been to apply the dynamic acidification models MAGIC, to 133 lakes unaffected by agriculture and SAFE, to 645 productive forest sites. While the long-term goal is to protect 95% of the area, implementation of the Gothenburg protocol will protect approximately 75% of forest soils in the long term. After 2030, recovery will be very slow and involve only a limited geographical area. If there had been no emission reductions after 1980, 87% of the forest area would have unwanted soil status in the long term. In 1990, approximately 17% of all Swedish lakes unaffected by agriculture received an acidifying deposition above critical load. This fraction will decrease to 10% in 2010 after implementation of the Gothenburg protocol. The acidified lakes of Sweden will recover faster than the soils. According to the MAGIC model the median pre-industrial ANC of 107 microeq L(-1) in acid sensitive lakes decreased to about 60 microeq L(-1) at the peak of the acidification (1975-1990) and increases to 80 microeq L(-1) by 2010. Further increases were small, only 2 microeq L(-1) between 2010 and 2040. Protecting 95% of the lakes will require further emission reductions below the Gothenburg protocol levels. More than 7000 lakes are limed regularly in Sweden and it is unlikely that this practice can be discontinued in the near future without adverse effects on lake chemistry and biology.

Mixing, Noise and Thrust Benefits Using Corrugated Designs

NASA Technical Reports Server (NTRS)

Morgan, Morris H., III; Gilinsky, Mikhail M.

2000-01-01

These projects are directed toward the analysis of several concepts for nozzle and inlet performance improvement and noise reduction from jet exhausts. Currently. The FM&AL also initiates new joint research between the HU/FM&AL, the Hyper-X Program Team at the LaRC, and the Central Institute of Aviation Motors (CIAM), Moscow, Russia in the field of optimization of fuel injection and mixing in air-breathing propulsion systems. The main results of theoretical, numerical simulation and experimental tests obtained in the previous research are in the papers and patents. The goals of the 14U/FM&AL programs are twofold: 1) to improve the working efficiency of the HU/FM&AL team in generating new innovative ideas and in conducting research in the field of fluid dynamics and acoustics, basically for improvement of supersonic and subsonic aircraft engines, and 2) to attract promising minority students to this research and training and, in cooperation with other HU departments, to teach them basic knowledge in Aerodynamics, Gas Dynamics, and Theoretical and Experimental Methods in Aeroacoustics and Computational Fluid Dynamics (CFD). The research at the HU/FM&AL supports reduction schemes associated with the emission of en 'ne pollutants for commercial aircraft and concepts for reduction of 91 observables for military aircraft. These research endeavors relate to the goals of the NASA Strategic Enterprise in Aeronautics concerning the development of environmentally acceptable aircraft. It is in this precise area, where the US aircraft industry, academia, and Government are in great need of trained professionals and which is a high priority goal of the Minority University Research and Education (MLTREP) Program, that the HU/FM&AL can make its most important contribution.

Computational Analyses of Offset Stream Nozzles for Noise Reduction

NASA Technical Reports Server (NTRS)

Dippold, Vance, III; Foster, Lancert; Wiese,Michael

2007-01-01

The Wind computational fluid dynamics code was used to perform a series of simulations on two offset stream nozzle concepts for jet noise reduction. The first concept used an S-duct to direct the secondary stream to the lower side of the nozzle. The second concept used vanes to turn the secondary flow downward. The analyses were completed in preparation of tests conducted in the NASA Glenn Research Center Aeroacoustic Propulsion Laboratory. The offset stream nozzles demonstrated good performance and reduced the amount of turbulence on the lower side of the jet plume. The computer analyses proved instrumental in guiding the development of the final test configurations and giving insight into the flow mechanics of offset stream nozzles. The computational predictions were compared with flowfield results from the jet rig testing and showed excellent agreement.