New simulation model of multicomponent crystal growth and inhibition.

PubMed

Wathen, Brent; Kuiper, Michael; Walker, Virginia; Jia, Zongchao

2004-04-02

We review a novel computational model for the study of crystal structures both on their own and in conjunction with inhibitor molecules. The model advances existing Monte Carlo (MC) simulation techniques by extending them from modeling 3D crystal surface patches to modeling entire 3D crystals, and by including the use of "complex" multicomponent molecules within the simulations. These advances makes it possible to incorporate the 3D shape and non-uniform surface properties of inhibitors into simulations, and to study what effect these inhibitor properties have on the growth of whole crystals containing up to tens of millions of molecules. The application of this extended MC model to the study of antifreeze proteins (AFPs) and their effects on ice formation is reported, including the success of the technique in achieving AFP-induced ice-growth inhibition with concurrent changes to ice morphology that mimic experimental results. Simulations of ice-growth inhibition suggest that the degree of inhibition afforded by an AFP is a function of its ice-binding position relative to the underlying anisotropic growth pattern of ice. This extended MC technique is applicable to other crystal and crystal-inhibitor systems, including more complex crystal systems such as clathrates.

BUDEM: an urban growth simulation model using CA for Beijing metropolitan area

NASA Astrophysics Data System (ADS)

Long, Ying; Shen, Zhenjiang; Du, Liqun; Mao, Qizhi; Gao, Zhanping

2008-10-01

It is in great need of identifying the future urban form of Beijing, which faces challenges of rapid growth in urban development projects implemented in Beijing. We develop Beijing Urban Developing Model (BUDEM in short) to support urban planning and corresponding policies evaluation. BUDEM is the spatio-temporal dynamic model for simulating urban growth in Beijing metropolitan area, using cellular automata (CA) and Multi-agent system (MAS) approaches. In this phase, the computer simulation using CA in Beijing metropolitan area is conducted, which attempts to provide a premise of urban activities including different kinds of urban development projects for industrial plants, shopping facilities, houses. In the paper, concept model of BUDEM is introduced, which is established basing on prevalent urban growth theories. The method integrating logistic regression and MonoLoop is used to retrieve weights in the transition rule by MCE. After model sensibility analysis, we apply BUDEM into three aspects of urban planning practices: (1) Identifying urban growth mechanism in various historical phases since 1986; (2) Identifying urban growth policies needed to implement desired urban form (BEIJING2020), namely planned urban form; (3) Simulating urban growth scenarios of 2049 (BEIJING2049) basing on the urban form and parameter set of BEIJING2020.

Mistletoe-induced growth reductions at the forest stand scale.

PubMed

Kollas, Chris; Gutsch, Martin; Hommel, Robert; Lasch-Born, Petra; Suckow, Felicitas

2018-05-01

The hemiparasite European mistletoe (Viscum album L.) adversely affects growth and reproduction of the host Scots pine (Pinus sylvestris L.) and in consequence may lead to tree death. Here, we aimed to estimate mistletoe-induced losses in timber yield applying the process-based forest growth model 4C. The parasite was implemented into the eco-physiological forest growth model 4C using (literature-derived) established impacts of the parasite on the tree's water and carbon cycle. The amended model was validated simulating a sample forest stand in the Berlin area (Germany) comprising trees with and without mistletoe infection. At the same forest stand, tree core measurements were taken to evaluate simulated and observed growth. A subsample of trees were harvested to quantify biomass compartments of the tree canopy and to derive a growth function of the mistletoe population. The process-based simulations of the forest stand revealed 27% reduction in basal area increment (BAI) during the last 9 years of heavy infection, which was confirmed by the measurements (29% mean growth reduction). The long-term simulations of the forest stand before and during the parasite infection showed that the amended forest growth model 4C depicts well the BAI growth pattern during >100 years and also quantifies well the mistletoe-induced growth reductions in Scots pine stands.

Simulating the effects of climatic variation on stem carbon accumulation of a ponderosa pine stand: comparison with annual growth increment data.

PubMed

Hunt, E R; Martin, F C; Running, S W

1991-01-01

Simulation models of ecosystem processes may be necessary to separate the long-term effects of climate change on forest productivity from the effects of year-to-year variations in climate. The objective of this study was to compare simulated annual stem growth with measured annual stem growth from 1930 to 1982 for a uniform stand of ponderosa pine (Pinus ponderosa Dougl.) in Montana, USA. The model, FOREST-BGC, was used to simulate growth assuming leaf area index (LAI) was either constant or increasing. The measured stem annual growth increased exponentially over time; the differences between the simulated and measured stem carbon accumulations were not large. Growth trends were removed from both the measured and simulated annual increments of stem carbon to enhance the year-to-year variations in growth resulting from climate. The detrended increments from the increasing LAI simulation fit the detrended increments of the stand data over time with an R(2) of 0.47; the R(2) increased to 0.65 when the previous year's simulated detrended increment was included with the current year's simulated increment to account for autocorrelation. Stepwise multiple linear regression of the detrended increments of the stand data versus monthly meteorological variables had an R(2) of 0.37, and the R(2) increased to 0.47 when the previous year's meteorological data were included to account for autocorrelation. Thus, FOREST-BGC was more sensitive to the effects of year-to-year climate variation on annual stem growth than were multiple linear regression models.

Normal Brain-Skull Development with Hybrid Deformable VR Models Simulation.

PubMed

Jin, Jing; De Ribaupierre, Sandrine; Eagleson, Roy

2016-01-01

This paper describes a simulation framework for a clinical application involving skull-brain co-development in infants, leading to a platform for craniosynostosis modeling. Craniosynostosis occurs when one or more sutures are fused early in life, resulting in an abnormal skull shape. Surgery is required to reopen the suture and reduce intracranial pressure, but is difficult without any predictive model to assist surgical planning. We aim to study normal brain-skull growth by computer simulation, which requires a head model and appropriate mathematical methods for brain and skull growth respectively. On the basis of our previous model, we further specified suture model into fibrous and cartilaginous sutures and develop algorithm for skull extension. We evaluate the resulting simulation by comparison with datasets of cases and normal growth.

The review of dynamic monitoring technology for crop growth

NASA Astrophysics Data System (ADS)

Zhang, Hong-wei; Chen, Huai-liang; Zou, Chun-hui; Yu, Wei-dong

2010-10-01

In this paper, crop growth monitoring methods are described elaborately. The crop growth models, Netherlands-Wageningen model system, the United States-GOSSYM model and CERES models, Australia APSIM model and CCSODS model system in China, are introduced here more focus on the theories of mechanism, applications, etc. The methods and application of remote sensing monitoring methods, which based on leaf area index (LAI) and biomass were proposed by different scholars at home and abroad, are highly stressed in the paper. The monitoring methods of remote sensing coupling with crop growth models are talked out at large, including the method of "forced law" which using remote sensing retrieval state parameters as the crop growth model parameters input, and then to enhance the dynamic simulation accuracy of crop growth model and the method of "assimilation of Law" which by reducing the gap difference between the value of remote sensing retrieval and the simulated values of crop growth model and thus to estimate the initial value or parameter values to increasing the simulation accuracy. At last, the developing trend of monitoring methods are proposed based on the advantages and shortcomings in previous studies, it is assured that the combination of remote sensing with moderate resolution data of FY-3A, MODIS, etc., crop growth model, "3S" system and observation in situ are the main methods in refinement of dynamic monitoring and quantitative assessment techniques for crop growth in future.

Dry matter partitioning models for the simulation of individual fruit growth in greenhouse cucumber canopies

PubMed Central

Wiechers, Dirk; Kahlen, Katrin; Stützel, Hartmut

2011-01-01

Background and Aims Growth imbalances between individual fruits are common in indeterminate plants such as cucumber (Cucumis sativus). In this species, these imbalances can be related to differences in two growth characteristics, fruit growth duration until reaching a given size and fruit abortion. Both are related to distribution, and environmental factors as well as canopy architecture play a key role in their differentiation. Furthermore, events leading to a fruit reaching its harvestable size before or simultaneously with a prior fruit can be observed. Functional–structural plant models (FSPMs) allow for interactions between environmental factors, canopy architecture and physiological processes. Here, we tested hypotheses which account for these interactions by introducing dominance and abortion thresholds for the partitioning of assimilates between growing fruits. Methods Using the L-System formalism, an FSPM was developed which combined a model for architectural development, a biochemical model of photosynthesis and a model for assimilate partitioning, the last including a fruit growth model based on a size-related potential growth rate (RP). Starting from a distribution proportional to RP, the model was extended by including abortion and dominance. Abortion was related to source strength and dominance to sink strength. Both thresholds were varied to test their influence on fruit growth characteristics. Simulations were conducted for a dense row and a sparse isometric canopy. Key Results The simple partitioning models failed to simulate individual fruit growth realistically. The introduction of abortion and dominance thresholds gave the best results. Simulations of fruit growth durations and abortion rates were in line with measurements, and events in which a fruit was harvestable earlier than an older fruit were reproduced. Conclusions Dominance and abortion events need to be considered when simulating typical fruit growth traits. By integrating environmental factors, the FSPM can be a valuable tool to analyse and improve existing knowledge about the dynamics of assimilates partitioning. PMID:21715366

Dissipative-particle-dynamics model of biofilm growth

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

Xu, Zhijie; Meakin, Paul; Tartakovsky, Alexandre M.

2011-06-13

A dissipative particle dynamics (DPD) model for the quantitative simulation of biofilm growth controlled by substrate (nutrient) consumption, advective and diffusive substrate transport, and hydrodynamic interactions with fluid flow (including fragmentation and reattachment) is described. The model was used to simulate biomass growth, decay, and spreading. It predicts how the biofilm morphology depends on flow conditions, biofilm growth kinetics, the rheomechanical properties of the biofilm and adhesion to solid surfaces. The morphology of the model biofilm depends strongly on its rigidity and the magnitude of the body force that drives the fluid over the biofilm.

Cellular automata-based modelling and simulation of biofilm structure on multi-core computers.

PubMed

Skoneczny, Szymon

2015-01-01

The article presents a mathematical model of biofilm growth for aerobic biodegradation of a toxic carbonaceous substrate. Modelling of biofilm growth has fundamental significance in numerous processes of biotechnology and mathematical modelling of bioreactors. The process following double-substrate kinetics with substrate inhibition proceeding in a biofilm has not been modelled so far by means of cellular automata. Each process in the model proposed, i.e. diffusion of substrates, uptake of substrates, growth and decay of microorganisms and biofilm detachment, is simulated in a discrete manner. It was shown that for flat biofilm of constant thickness, the results of the presented model agree with those of a continuous model. The primary outcome of the study was to propose a mathematical model of biofilm growth; however a considerable amount of focus was also placed on the development of efficient algorithms for its solution. Two parallel algorithms were created, differing in the way computations are distributed. Computer programs were created using OpenMP Application Programming Interface for C++ programming language. Simulations of biofilm growth were performed on three high-performance computers. Speed-up coefficients of computer programs were compared. Both algorithms enabled a significant reduction of computation time. It is important, inter alia, in modelling and simulation of bioreactor dynamics.

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

PubMed

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

2017-06-01

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

A framework for multi-scale simulation of crystal growth in the presence of polymers.

PubMed

Mandal, Taraknath; Huang, Wenjun; Mecca, Jodi M; Getchell, Ashley; Porter, William W; Larson, Ronald G

2017-03-01

We present a multi-scale simulation method for modeling crystal growth in the presence of polymer excipients. The method includes a coarse-grained (CG) model for small molecules of known crystal structure whose force field is obtained using structural properties from atomistic simulations. This CG model is capable of stabilizing the molecular crystal structure and capturing the crystal growth from the melt for a wide range of small organic molecules, as demonstrated by application of our method to the molecules isoniazid, urea, sulfamethoxazole, prilocaine, oxcarbazepine, and phenytoin. This CG model can also be used to study the effect of additives, such as polymers, on the inhibition of crystal growth by polymers, as exemplified by our simulation of suppression of the rate of crystal growth of phenytoin, an active pharmaceutical ingredient (API), by a cellulose excipient, functionalized with acetate (Ac), hydroxy-propyl (Hp) and succinate (Su) groups. We show that the efficacy of the cellulosic polymers in slowing crystal growth of small molecules strongly depends on the functional group substitution on the cellulose backbone, with the acetate substituent group slowing crystal growth more than does the deprotonated succinate group, which we confirm by experimental drug supersaturation studies.

Application of enthalpy model for floating zone silicon crystal growth

NASA Astrophysics Data System (ADS)

Krauze, A.; Bergfelds, K.; Virbulis, J.

2017-09-01

A 2D simplified crystal growth model based on the enthalpy method and coupled with a low-frequency harmonic electromagnetic model is developed to simulate the silicon crystal growth near the external triple point (ETP) and crystal melting on the open melting front of a polycrystalline feed rod in FZ crystal growth systems. Simulations of the crystal growth near the ETP show significant influence of the inhomogeneities of the EM power distribution on the crystal growth rate for a 4 in floating zone (FZ) system. The generated growth rate fluctuations are shown to be larger in the system with higher crystal pull rate. Simulations of crystal melting on the open melting front of the polycrystalline rod show the development of melt-filled grooves at the open melting front surface. The distance between the grooves is shown to grow with the increase of the skin-layer depth in the solid material.

Cotton irrigation scheduling using a crop growth model and FAO-56 methods: Field and simulation studies

USDA-ARS?s Scientific Manuscript database

Crop growth simulation models can address a variety of agricultural problems, but their use to directly assist in-season irrigation management decisions is less common. Confidence in model reliability can be increased if models are shown to provide improved in-season management recommendations, whi...

Numerical simulation of dendrite growth in nickel-based superalloy and validated by in-situ observation using high temperature confocal laser scanning microscopy

NASA Astrophysics Data System (ADS)

Yan, Xuewei; Xu, Qingyan; Liu, Baicheng

2017-12-01

Dendritic structures are the predominant microstructural constituents of nickel-based superalloys, an understanding of the dendrite growth is required in order to obtain the desirable microstructure and improve the performance of castings. For this reason, numerical simulation method and an in-situ observation technology by employing high temperature confocal laser scanning microscopy (HT-CLSM) were used to investigate dendrite growth during solidification process. A combined cellular automaton-finite difference (CA-FD) model allowing for the prediction of dendrite growth of binary alloys was developed. The algorithm of cells capture was modified, and a deterministic cellular automaton (DCA) model was proposed to describe neighborhood tracking. The dendrite and detail morphology, especially hundreds of dendrites distribution at a large scale and three-dimensional (3-D) polycrystalline growth, were successfully simulated based on this model. The dendritic morphologies of samples before and after HT-CLSM were both observed by optical microscope (OM) and scanning electron microscope (SEM). The experimental observations presented a reasonable agreement with the simulation results. It was also found that primary or secondary dendrite arm spacing, and segregation pattern were significantly influenced by dendrite growth. Furthermore, the directional solidification (DS) dendritic evolution behavior and detail morphology were also simulated based on the proposed model, and the simulation results also agree well with experimental results.

A model of milk production in lactating dairy cows in relation to energy and nitrogen dynamics.

PubMed

Johnson, I R; France, J; Cullen, B R

2016-02-01

A generic daily time-step model of a dairy cow, designed to be included in whole-system pasture simulation models, is described that includes growth, milk production, and lactation in relation to energy and nitrogen dynamics. It is a development of a previously described animal growth and metabolism model that describes animal body composition in terms of protein, water, and fat, and energy dynamics in relation to growth requirements, resynthesis of degraded protein, and animal activity. This is further developed to include lactation and fetal growth. Intake is calculated in relation to stage of lactation, pasture availability, supplementary feed, and feed quality. Energy costs associated with urine N excretion and methane fermentation are accounted for. Milk production and fetal growth are then calculated in relation to the overall energy and nitrogen dynamics. The general behavior of the model is consistent with expected characteristics. Simulations using the model as part of a whole-system pasture simulation model (DairyMod) are compared with experimental data where good agreement between pasture, concentrate and forage intake, as well as milk production over 3 consecutive lactation cycles, is observed. The model is shown to be well suited for inclusion in large-scale system simulation models. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Accuracy and equivalence testing of crown ratio models and assessment of their impact on diameter growth and basal area increment predictions of two variants of the Forest Vegetation Simulator

Treesearch

Laura P. Leites; Andrew P. Robinson; Nicholas L. Crookston

2009-01-01

Diameter growth (DG) equations in many existing forest growth and yield models use tree crown ratio (CR) as a predictor variable. Where CR is not measured, it is estimated from other measured variables. We evaluated CR estimation accuracy for the models in two Forest Vegetation Simulator variants: the exponential and the logistic CR models used in the North...

3-PG simulations of young ponderosa pine plantations under varied management intensity: why do they grow so differently?

Treesearch

Liang Wei; Marshall John; Jianwei Zhang; Hang Zhou; Robert Powers

2014-01-01

Models can be powerful tools for estimating forest productivity and guiding forest management, but their credibility and complexity are often an issue for forest managers. We parameterized a process-based forest growth model, 3-PG (Physiological Principles Predicting Growth), to simulate growth of ponderosa pine (Pinus ponderosa) plantations in...

AN INDIVIDUAL-BASED SIMULATION MODEL FOR MOTTLED SCULPIN (COTTUS BAIRDI) IN A SOUTHERN APPALACHIAN STREAM

EPA Science Inventory

We describe and analyze a spatially explicit, individual-based model for the local population dynamics of mottled sculpin (Cottus bairdi). The model simulated daily growth, mortality, movement and spawning of individuals within a reach of stream. Juvenile and adult growth was bas...

Computer simulation studies of the growth of strained layers by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Faux, D. A.; Gaynor, G.; Carson, C. L.; Hall, C. K.; Bernholc, J.

1990-08-01

Two new types of discrete-space Monte Carlo computer simulation are presented for the modeling of the early stages of strained-layer growth by molecular-beam epitaxy. The simulations are more economical on computer resources than continuous-space Monte Carlo or molecular dynamics. Each model is applied to the study of growth onto a substrate in two dimensions with use of Lennard-Jones interatomic potentials. Up to seven layers are deposited for a variety of lattice mismatches, temperatures, and growth rates. Both simulations give similar results. At small lattice mismatches (<~4%) the growth is in registry with the substrate, while at high mismatches (>~6%) the growth is incommensurate with the substrate. At intermediate mismatches, a transition from registered to incommensurate growth is observed which commences at the top of the crystal and propagates down to the first layer. Faster growth rates are seen to inhibit this transition. The growth mode is van der Merwe (layer-by-layer) at 2% lattice mismatch, but at larger mismatches Volmer-Weber (island) growth is preferred. The Monte Carlo simulations are assessed in the light of these results and the ease at which they can be extended to three dimensions and to more sophisticated potentials is discussed.

The effect of crystallinity on cell growth in semi-crystalline microcellular foams by solid-state process: modeling and numerical simulation

NASA Astrophysics Data System (ADS)

Rezvanpanah, Elham; Ghaffarian Anbaran, S. Reza

2017-11-01

This study establishes a model and simulation scheme to describe the effect of crystallinity as one of the most effective parameters on cell growth phenomena in a solid batch foaming process. The governing model of cell growth dynamics, based on the well-known ‘Cell model’, is attained in details. To include the effect of crystallinity in the model, the properties of the polymer/gas mixtures (i.e. solubility, diffusivity, surface tension and viscosity) are estimated by modifying relations to consider the effect of crystallinity. A finite element-finite difference (FEFD) method is employed to solve the highly nonlinear and coupled equations of cell growth dynamics. The proposed simulation is able to evaluate all properties of the system at the given process condition and uses them to calculate the cell size, pressure and gas concentration gradient with time. A high-density polyethylene/nitrogen (HDPE/N2) system is used herein as a case study. Comparing the simulation results with the others works and experimental results verify the accuracy of the simulation scheme. The cell growth is a complicated combination of several phenomena. This study attempted to reach a better understanding of cell growth trend, driving and retarding forces and the effect of crystallinity on them.

Random walk on lattices: Graph-theoretic approach to simulating long-range diffusion-attachment growth models

NASA Astrophysics Data System (ADS)

Limkumnerd, Surachate

2014-03-01

Interest in thin-film fabrication for industrial applications have driven both theoretical and computational aspects of modeling its growth. One of the earliest attempts toward understanding the morphological structure of a film's surface is through a class of solid-on-solid limited-mobility growth models such as the Family, Wolf-Villain, or Das Sarma-Tamborenea models, which have produced fascinating surface roughening behaviors. These models, however, restrict the motion of an incidence atom to be within the neighborhood of its landing site, which renders them inept for simulating long-distance surface diffusion such as that observed in thin-film growth using a molecular-beam epitaxy technique. Naive extension of these models by repeatedly applying the local diffusion rules for each hop to simulate large diffusion length can be computationally very costly when certain statistical aspects are demanded. We present a graph-theoretic approach to simulating a long-range diffusion-attachment growth model. Using the Markovian assumption and given a local diffusion bias, we derive the transition probabilities for a random walker to traverse from one lattice site to the others after a large, possibly infinite, number of steps. Only computation with linear-time complexity is required for the surface morphology calculation without other probabilistic measures. The formalism is applied, as illustrations, to simulate surface growth on a two-dimensional flat substrate and around a screw dislocation under the modified Wolf-Villain diffusion rule. A rectangular spiral ridge is observed in the latter case with a smooth front feature similar to that obtained from simulations using the well-known multiple registration technique. An algorithm for computing the inverse of a class of substochastic matrices is derived as a corollary.

Development of the vertical Bridgman technique for 6-inch diameter c-axis sapphire growth supported by numerical simulation

NASA Astrophysics Data System (ADS)

Miyagawa, Chihiro; Kobayashi, Takumi; Taishi, Toshinori; Hoshikawa, Keigo

2014-09-01

Based on the growth of 3-inch diameter c-axis sapphire using the vertical Bridgman (VB) technique, numerical simulations were made and used to guide the growth of a 6-inch diameter sapphire. A 2D model of the VB hot-zone was constructed, the seeding interface shape of the 3-inch diameter sapphire as revealed by green laser scattering was estimated numerically, and the temperature distributions of two VB hot-zone models designed for 6-inch diameter sapphire growth were numerically simulated to achieve the optimal growth of large crystals. The hot-zone model with one heater was selected and prepared, and 6-inch diameter c-axis sapphire boules were actually grown, as predicted by the numerical results.

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

NASA Astrophysics Data System (ADS)

van Walsum, P. E. V.; Supit, I.

2012-06-01

Hydrologic climate change modelling is hampered by climate-dependent model parameterizations. To reduce this dependency, we extended the regional hydrologic modelling framework SIMGRO to host a two-way coupling between the soil moisture model MetaSWAP and the crop growth simulation model WOFOST, accounting for ecohydrologic feedbacks in terms of radiation fraction that reaches the soil, crop coefficient, interception fraction of rainfall, interception storage capacity, and root zone depth. Except for the last, these feedbacks are dependent on the leaf area index (LAI). The influence of regional groundwater on crop growth is included via a coupling to MODFLOW. Two versions of the MetaSWAP-WOFOST coupling were set up: one with exogenous vegetation parameters, the "static" model, and one with endogenous crop growth simulation, the "dynamic" model. Parameterization of the static and dynamic models ensured that for the current climate the simulated long-term averages of actual evapotranspiration are the same for both models. Simulations were made for two climate scenarios and two crops: grass and potato. In the dynamic model, higher temperatures in a warm year under the current climate resulted in accelerated crop development, and in the case of potato a shorter growing season, thus partly avoiding the late summer heat. The static model has a higher potential transpiration; depending on the available soil moisture, this translates to a higher actual transpiration. This difference between static and dynamic models is enlarged by climate change in combination with higher CO2 concentrations. Including the dynamic crop simulation gives for potato (and other annual arable land crops) systematically higher effects on the predicted recharge change due to climate change. Crop yields from soils with poor water retention capacities strongly depend on capillary rise if moisture supply from other sources is limited. Thus, including a crop simulation model in an integrated hydrologic simulation provides a valuable addition for hydrologic modelling as well as for crop modelling.

Tissue-scale, personalized modeling and simulation of prostate cancer growth

NASA Astrophysics Data System (ADS)

Lorenzo, Guillermo; Scott, Michael A.; Tew, Kevin; Hughes, Thomas J. R.; Zhang, Yongjie Jessica; Liu, Lei; Vilanova, Guillermo; Gomez, Hector

2016-11-01

Recently, mathematical modeling and simulation of diseases and their treatments have enabled the prediction of clinical outcomes and the design of optimal therapies on a personalized (i.e., patient-specific) basis. This new trend in medical research has been termed “predictive medicine.” Prostate cancer (PCa) is a major health problem and an ideal candidate to explore tissue-scale, personalized modeling of cancer growth for two main reasons: First, it is a small organ, and, second, tumor growth can be estimated by measuring serum prostate-specific antigen (PSA, a PCa biomarker in blood), which may enable in vivo validation. In this paper, we present a simple continuous model that reproduces the growth patterns of PCa. We use the phase-field method to account for the transformation of healthy cells to cancer cells and use diffusion-reaction equations to compute nutrient consumption and PSA production. To accurately and efficiently compute tumor growth, our simulations leverage isogeometric analysis (IGA). Our model is shown to reproduce a known shape instability from a spheroidal pattern to fingered growth. Results of our computations indicate that such shift is a tumor response to escape starvation, hypoxia, and, eventually, necrosis. Thus, branching enables the tumor to minimize the distance from inner cells to external nutrients, contributing to cancer survival and further development. We have also used our model to perform tissue-scale, personalized simulation of a PCa patient, based on prostatic anatomy extracted from computed tomography images. This simulation shows tumor progression similar to that seen in clinical practice.

Improving the capability of an integrated CA-Markov model to simulate spatio-temporal urban growth trends using an Analytical Hierarchy Process and Frequency Ratio

NASA Astrophysics Data System (ADS)

Aburas, Maher Milad; Ho, Yuek Ming; Ramli, Mohammad Firuz; Ash'aari, Zulfa Hanan

2017-07-01

The creation of an accurate simulation of future urban growth is considered one of the most important challenges in urban studies that involve spatial modeling. The purpose of this study is to improve the simulation capability of an integrated CA-Markov Chain (CA-MC) model using CA-MC based on the Analytical Hierarchy Process (AHP) and CA-MC based on Frequency Ratio (FR), both applied in Seremban, Malaysia, as well as to compare the performance and accuracy between the traditional and hybrid models. Various physical, socio-economic, utilities, and environmental criteria were used as predictors, including elevation, slope, soil texture, population density, distance to commercial area, distance to educational area, distance to residential area, distance to industrial area, distance to roads, distance to highway, distance to railway, distance to power line, distance to stream, and land cover. For calibration, three models were applied to simulate urban growth trends in 2010; the actual data of 2010 were used for model validation utilizing the Relative Operating Characteristic (ROC) and Kappa coefficient methods Consequently, future urban growth maps of 2020 and 2030 were created. The validation findings confirm that the integration of the CA-MC model with the FR model and employing the significant driving force of urban growth in the simulation process have resulted in the improved simulation capability of the CA-MC model. This study has provided a novel approach for improving the CA-MC model based on FR, which will provide powerful support to planners and decision-makers in the development of future sustainable urban planning.

The pivotal role of angiogenesis in a multi-scale modeling of tumor growth exhibiting the avascular and vascular phases.

PubMed

Salavati, Hooman; Soltani, M; Amanpour, Saeid

2018-05-06

The mechanisms involved in tumor growth mainly occur at the microenvironment, where the interactions between the intracellular, intercellular and extracellular scales mediate the dynamics of tumor. In this work, we present a multi-scale model of solid tumor dynamics to simulate the avascular and vascular growth as well as tumor-induced angiogenesis. The extracellular and intercellular scales are modeled using partial differential equations and cellular Potts model, respectively. Also, few biochemical and biophysical rules control the dynamics of intracellular level. On the other hand, the growth of melanoma tumors is modeled in an animal in-vivo study to evaluate the simulation. The simulation shows that the model successfully reproduces a completed image of processes involved in tumor growth such as avascular and vascular growth as well as angiogenesis. The model incorporates the phenotypes of cancerous cells including proliferating, quiescent and necrotic cells, as well as endothelial cells during angiogenesis. The results clearly demonstrate the pivotal effect of angiogenesis on the progression of cancerous cells. Also, the model exhibits important events in tumor-induced angiogenesis like anastomosis. Moreover, the computational trend of tumor growth closely follows the observations in the experimental study. Copyright © 2018 Elsevier Inc. All rights reserved.

Brain tumor modeling: glioma growth and interaction with chemotherapy

NASA Astrophysics Data System (ADS)

Banaem, Hossein Y.; Ahmadian, Alireza; Saberi, Hooshangh; Daneshmehr, Alireza; Khodadad, Davood

2011-10-01

In last decade increasingly mathematical models of tumor growths have been studied, particularly on solid tumors which growth mainly caused by cellular proliferation. In this paper we propose a modified model to simulate the growth of gliomas in different stages. Glioma growth is modeled by a reaction-advection-diffusion. We begin with a model of untreated gliomas and continue with models of polyclonal glioma following chemotherapy. From relatively simple assumptions involving homogeneous brain tissue bounded by a few gross anatomical landmarks (ventricles and skull) the models have been expanded to include heterogeneous brain tissue with different motilities of glioma cells in grey and white matter. Tumor growth is characterized by a dangerous change in the control mechanisms, which normally maintain a balance between the rate of proliferation and the rate of apoptosis (controlled cell death). Result shows that this model closes to clinical finding and can simulate brain tumor behavior properly.

Simulation of growth of Adirondack conifers in relation to global climate change

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

Pan, Y.; Raynal, D.J.

1993-06-01

Several conifer species grown in plantations in the southeastern Adirondack mountains of New York were chosen to model tree growth. In the models, annual xylem growth was decomposed into several components that reflect various intrinsic or extrinsic factors. Growth signals indicative of climatic effects were used to construct response functions using both multivariate analysis and Kalman filter methods. Two models were used to simulate tree growth response to future CO[sub 2]-induced climate change projected by GCMs. The comparable results of both models indicate that different conifer species have individualistic growth responses to future climatic change. The response behaviors of treesmore » are affected greatly by local stand conditions. The results suggest possible changes in future growth and distributions of naturally occurring conifers in this region.« less

Simulation and modeling of whistler mode wave growth through cyclotron resonance with energetic electrons in the magnetosphere

NASA Astrophysics Data System (ADS)

Carlson, Curtis Ray

New models and simulations of wave growth experienced by electromagnetic waves propagating through the magnetosphere in the whistler mode are presented. The main emphasis is to simulate single frequency wave pulses, in the 2 to 6 kHz range, that have been injected into the magnetosphere, near L approximately 4. Simulations using a new transient model reproduce exponential wave growth and saturation coincident with a linearly increasing frequency versus time (up to 60 Hz/s). Unique methods for calculating the phased bunched currents, stimulated radiation, and radiation propagation are based upon test particle trajectories calculated by integrating nonlinear equations of motion generalized to allow the evolution of the frequency and wave number at each point in space. Results show the importance of the transient aspects in the wave growth process. The wave growth established as the wave propagates toward the equator is given a spatially advancing wave phase structure by the geomagnetic inhomogeneity. Through the feedback of this radiation upon other electrons, the conditions are set up which result in the linearly increasing output frequency with time. The transient simulations also show that features like growth rate and total growth are simply related to the various parameters, such as applied wave intensity, energetic electron flux, and energetic electron distribution.

A comparison of three approaches for simulating fine-scale surface winds in support of wildland fire management. Part II. An exploratory study of the effect of simulated winds on fire growth simulations

Treesearch

Jason M. Forthofer; Bret W. Butler; Charles W. McHugh; Mark A. Finney; Larry S. Bradshaw; Richard D. Stratton; Kyle S. Shannon; Natalie S. Wagenbrenner

2014-01-01

The effect of fine-resolution wind simulations on fire growth simulations is explored. The wind models are (1) a wind field consisting of constant speed and direction applied everywhere over the area of interest; (2) a tool based on the solution of the conservation of mass only (termed mass-conserving model) and (3) a tool based on a solution of conservation of mass...

How to use the Stand-Damage Model: Version 2.0. (Computer program)

Treesearch

J.J. Colbert; George Racin

2001-01-01

The Stand-Damage Model simulates the growth of a forest stand, a spatially homogeneous collection of trees growing on a site. The model simulates growth from an initial inventory, user-prescribed management practices, and the effects of gypsy moth defoliation. Here we provide installation and operating instructions for Version 2.0.

Numerical modeling of the traction process in the treatment for Pierre-Robin Sequence.

PubMed

Słowiński, Jakub J; Czarnecka, Aleksandra

2016-10-01

The goal of this numerical study was to identify the results of modulated growth simulation of the mandibular bone during traction in Pierre-Robin Sequence (PRS) treatment. Numerical simulation was conducted in the Ansys 16.2 environment. Two FEM (finite elements method) models of a newborn's mandible (a spatial and a flat model) were developed. The procedure simulated a 20-week traction period. The adopted growth measure was mandibular length increase, defined as the distance between the Co-Pog anatomic points used in cephalometric analysis. The simulation calculations conducted on the developed models showed that modulation had a significant influence on the pace of bone growth. In each of the analyzed cases, growth modulation resulted in an increase in pace. The largest value of increase was 6.91 mm. The modulated growth with the most beneficial load variant increased the basic value of the growth by as much as 24.6%, and growth with the least beneficial variant increased by 7.4%. Traction is a simple, minimally invasive and inexpensive procedure. The proposed algorithm may enable the development of a helpful forecasting tool, which could be of real use to doctors working on Pierre-Robin Sequence and other mandibular deformations in children. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Eye growth and myopia development: Unifying theory and Matlab model.

PubMed

Hung, George K; Mahadas, Kausalendra; Mohammad, Faisal

2016-03-01

The aim of this article is to present an updated unifying theory of the mechanisms underlying eye growth and myopia development. A series of model simulation programs were developed to illustrate the mechanism of eye growth regulation and myopia development. Two fundamental processes are presumed to govern the relationship between physiological optics and eye growth: genetically pre-programmed signaling and blur feedback. Cornea/lens is considered to have only a genetically pre-programmed component, whereas eye growth is considered to have both a genetically pre-programmed and a blur feedback component. Moreover, based on the Incremental Retinal-Defocus Theory (IRDT), the rate of change of blur size provides the direction for blur-driven regulation. The various factors affecting eye growth are shown in 5 simulations: (1 - unregulated eye growth): blur feedback is rendered ineffective, as in the case of form deprivation, so there is only genetically pre-programmed eye growth, generally resulting in myopia; (2 - regulated eye growth): blur feedback regulation demonstrates the emmetropization process, with abnormally excessive or reduced eye growth leading to myopia and hyperopia, respectively; (3 - repeated near-far viewing): simulation of large-to-small change in blur size as seen in the accommodative stimulus/response function, and via IRDT as well as nearwork-induced transient myopia (NITM), leading to the development of myopia; (4 - neurochemical bulk flow and diffusion): release of dopamine from the inner plexiform layer of the retina, and the subsequent diffusion and relay of neurochemical cascade show that a decrease in dopamine results in a reduction of proteoglycan synthesis rate, which leads to myopia; (5 - Simulink model): model of genetically pre-programmed signaling and blur feedback components that allows for different input functions to simulate experimental manipulations that result in hyperopia, emmetropia, and myopia. These model simulation programs (available upon request) can provide a useful tutorial for the general scientist and serve as a quantitative tool for researchers in eye growth and myopia. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dendritic growth shapes in kinetic Monte Carlo models

NASA Astrophysics Data System (ADS)

Krumwiede, Tim R.; Schulze, Tim P.

2017-02-01

For the most part, the study of dendritic crystal growth has focused on continuum models featuring surface energies that yield six pointed dendrites. In such models, the growth shape is a function of the surface energy anisotropy, and recent work has shown that considering a broader class of anisotropies yields a correspondingly richer set of growth morphologies. Motivated by this work, we generalize nanoscale models of dendritic growth based on kinetic Monte Carlo simulation. In particular, we examine the effects of extending the truncation radius for atomic interactions in a bond-counting model. This is done by calculating the model’s corresponding surface energy and equilibrium shape, as well as by running KMC simulations to obtain nanodendritic growth shapes. Additionally, we compare the effects of extending the interaction radius in bond-counting models to that of extending the number of terms retained in the cubic harmonic expansion of surface energy anisotropy in the context of continuum models.

A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

PubMed

Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

2017-06-07

Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.

Modelling volumetric growth in a thick walled fibre reinforced artery

NASA Astrophysics Data System (ADS)

Eriksson, T. S. E.; Watton, P. N.; Luo, X. Y.; Ventikos, Y.

2014-12-01

A novel framework for simulating growth and remodelling (G&R) of a fibre-reinforced artery, including volumetric adaption, is proposed. We show how to implement this model into a finite element framework and propose and examine two underlying assumptions for modelling growth, namely constant individual density (CID) or adaptive individual density (AID). Moreover, we formulate a novel approach which utilises a combination of both AID and CID to simulate volumetric G&R for a tissue composed of several different constituents. We consider a special case of the G&R of an artery subjected to prescribed elastin degradation and we theorise on the assumptions and suitability of CID, AID and the mixed approach for modelling arterial biology. For simulating the volumetric changes that occur during aneurysm enlargement, we observe that it is advantageous to describe the growth of collagen using CID whilst it is preferable to model the atrophy of elastin using AID.

Clinical study and numerical simulation of brain cancer dynamics under radiotherapy

NASA Astrophysics Data System (ADS)

Nawrocki, S.; Zubik-Kowal, B.

2015-05-01

We perform a clinical and numerical study of the progression of brain cancer tumor growth dynamics coupled with the effects of radiotherapy. We obtained clinical data from a sample of brain cancer patients undergoing radiotherapy and compare it to our numerical simulations to a mathematical model of brain tumor cell population growth influenced by radiation treatment. We model how the body biologically receives a physically delivered dose of radiation to the affected tumorous area in the form of a generalized LQ model, modified to account for the conversion process of sublethal lesions into lethal lesions at high radiation doses. We obtain good agreement between our clinical data and our numerical simulations of brain cancer progression given by the mathematical model, which couples tumor growth dynamics and the effect of irradiation. The correlation, spanning a wide dataset, demonstrates the potential of the mathematical model to describe the dynamics of brain tumor growth influenced by radiotherapy.

Phase-field simulations of GaN growth by selective area epitaxy on complex mask geometries

DOE PAGES

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung; ...

2015-05-15

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

Simulations of Quantum Dot Growth on Semiconductor Surfaces: Morphological Design of Sensor Concepts

DTIC Science & Technology

2008-12-01

size equalization can be clearly illustrated during the growth process. In this work we develop a fast multiscale 3D kinetic Monte Carlo ( KMC ) QD...model will provide an attractive means for producing predictably ordered nanostructures. MODEL DESCRIPTION The 3D layer-by-layer KMC growth model...Voter, 2001) and KMC simulation experience (Pan et al., 2004; Pan et al., 2006; Meixner et al, 2003) in 2D, we therefore propose the following simple

Kinetic Monte Carlo Simulation of the Growth of Various Nanostructures through Atomic and Cluster Deposition: Application to Gold Nanostructure Growth on Graphite

NASA Astrophysics Data System (ADS)

Claassens, C. H.; Hoffman, M. J. H.; Terblans, J. J.; Swart, H. C.

2006-01-01

A Kinetic Monte Carlo (KMC) method is presented to describe the growth of metallic nanostructures through atomic and cluster deposition in the mono -and multilayer regime. The model makes provision for homo- and heteroepitaxial systems with small lattice mismatch. The accuracy of the model is tested with simulations of the growth of gold nanostructures on HOPG and comparisons are made with existing experimental data.

Dynamic energy budget model: a monitoring tool for growth and reproduction performance of Mytilus galloprovincialis in Bizerte Lagoon (Southwestern Mediterranean Sea).

PubMed

Béjaoui-Omri, Amel; Béjaoui, Béchir; Harzallah, Ali; Aloui-Béjaoui, Nejla; El Bour, Monia; Aleya, Lotfi

2014-11-01

Mussel farming is the main economic activity in Bizerte Lagoon, with a production that fluctuates depending on environmental factors. In the present study, we apply a bioenergetic growth model to the mussel Mytilus galloprovincialis, based on dynamic energy budget (DEB) theory which describes energy flux variation through the different compartments of the mussel body. Thus, the present model simulates both mussel growth and sexual cycle steps according to food availability and water temperature and also the effect of climate change on mussel behavior and reproduction. The results point to good concordance between simulations and growth parameters (metric length and weight) for mussels in the lagoon. A heat wave scenario was also simulated using the DEB model, which highlighted mussel mortality periods during a period of high temperature.

Numerical simulation of biofilm growth in flow channels using a cellular automaton approach coupled with a macro flow computation.

PubMed

Yamamoto, Takehiro; Ueda, Shuya

2013-01-01

Biofilm is a slime-like complex aggregate of microorganisms and their products, extracellular polymer substances, that grows on a solid surface. The growth phenomenon of biofilm is relevant to the corrosion and clogging of water pipes, the chemical processes in a bioreactor, and bioremediation. In these phenomena, the behavior of the biofilm under flow has an important role. Therefore, controlling the biofilm behavior in each process is important. To provide a computational tool for analyzing biofilm growth, the present study proposes a computational model for the simulation of biofilm growth in flows. This model accounts for the growth, decay, detachment and adhesion of biofilms. The proposed model couples the computation of the surrounding fluid flow, using the finite volume method, with the simulation of biofilm growth, using the cellular automaton approach, a relatively low-computational-cost method. Furthermore, a stochastic approach for considering the adhesion process is proposed. Numerical simulations for the biofilm growth on a planar wall and that in an L-shaped rectangular channel were carried out. A variety of biofilm structures were observed depending on the strength of the flow. Moreover, the importance of the detachment and adhesion processes was confirmed.

An individual-based simulation model for mottled sculpin (Cottus bairdi) in a southern Appalachian stream

Treesearch

Brenda Rashleigh; Gary D. Grossman

2005-01-01

We describe and analyze a spatially explicit, individual-based model for the local population dynamics of mottled sculpin (Cottus bairdi). The model simulated daily growth, mortality, movement and spawning of individuals within a reach of stream. Juvenile and adult growth was based on consumption bioenergetics of benthic macroinvertebrate prey;...

Forward modeling of tree-ring data: a case study with a global network

NASA Astrophysics Data System (ADS)

Breitenmoser, P. D.; Frank, D.; Brönnimann, S.

2012-04-01

Information derived from tree-rings is one of the most powerful tools presently available for studying past climatic variability as well as identifying fundamental relationships between tree-growth and climate. Climate reconstructions are typically performed by extending linear relationships, established during the overlapping period of instrumental and climate proxy archives into the past. Such analyses, however, are limited by methodological assumptions, including stationarity and linearity of the climate-proxy relationship. We investigate climate and tree-ring data using the Vaganov-Shashkin-Lite (VS-Lite) forward model of tree-ring width formation to examine the relations among actual tree growth and climate (as inferred from the simulated chronologies) to reconstruct past climate variability. The VS-lite model has been shown to produce skill comparable to that achieved using classical dendrochronological statistical modeling techniques when applied on simulations of a network of North American tree-ring chronologies. Although the detailed mechanistic processes such as photosynthesis, storage, or cell processes are not modeled directly, the net effect of the dominating nonlinear climatic controls on tree-growth are implemented into the model by the principle of limiting factors and threshold growth response functions. The VS-lite model requires as inputs only latitude, monthly mean temperature and monthly accumulated precipitation. Hence, this simple, process-based model enables ring-width simulation at any location where monthly climate records exist. In this study, we analyse the growth response of simulated tree-rings to monthly climate conditions obtained from the 20th century reanalysis project back to 1871. These simulated tree-ring chronologies are compared to the climate-driven variability in worldwide observed tree-ring chronologies from the International Tree Ring Database. Results point toward the suitability of the relationship among actual tree growth and climate (as inferred from the simulated chronologies) for use in global palaeoclimate reconstructions.

Role of meteorology in simulating methane seasonal cycle and growth rate

NASA Astrophysics Data System (ADS)

Ghosh, A.; Patra, P. K.; Ishijima, K.; Morimoto, S.; Aoki, S.; Nakazawa, T.

2012-12-01

Methane (CH4) is the second most important anthropogenically produced greenhouse gas whose radiative effect is comparable to that of carbon dioxide since the preindustrial time. Methane also contributes to formation of tropospheric ozone and water vapor in the stratosphere, further increasing its importance to the Earth's radiative balance. In the present study, model simulation of CH4 for three different emission scenarios has been conducted using the CCSR/NIES/FRCGC Atmospheric General Circulation Model (AGCM) based Chemistry Transport Model (ACTM) with and without nudging of meteorological parameters for the period of 1981-2011. The model simulations are compared with measurements at monthly timescale at surface monitoring stations. We show the overall trends in CH4 growth rate and seasonal cycle at most measurement sites can be fairly successfully modeled by using existing knowledge of CH4 flux trends and seasonality. Detailed analysis reveals the model simulation without nudging has greater seasonal cycle amplitude compared to observation as well as the model simulation with nudging. The growth rate is slightly overestimated for the model simulation without nudging. For better representation of regional/global flux distribution pattern and strength in the future, we are exploring various dynamical and chemical aspects in the forward model with and without nudging.

Development of the AFRL Aircrew Perfomance and Protection Data Bank

DTIC Science & Technology

2007-12-01

Growth model and statistical model of hypobaric chamber simulations. It offers a quick and readily accessible online DCS risk assessment tool for...are used for the DCS prediction instead of the original model. ADRAC is based on more than 20 years of hypobaric chamber studies using human...prediction based on the combined Bubble Growth model and statistical model of hypobaric chamber simulations was integrated into the Data Bank. It

Computational modelling of the scaffold-free chondrocyte regeneration: a two-way coupling between the cell growth and local fluid flow and nutrient concentration.

PubMed

Hossain, Md Shakhawath; Bergstrom, D J; Chen, X B

2015-11-01

The in vitro chondrocyte cell culture process in a perfusion bioreactor provides enhanced nutrient supply as well as the flow-induced shear stress that may have a positive influence on the cell growth. Mathematical and computational modelling of such a culture process, by solving the coupled flow, mass transfer and cell growth equations simultaneously, can provide important insight into the biomechanical environment of a bioreactor and the related cell growth process. To do this, a two-way coupling between the local flow field and cell growth is required. Notably, most of the computational and mathematical models to date have not taken into account the influence of the cell growth on the local flow field and nutrient concentration. The present research aimed at developing a mathematical model and performing a numerical simulation using the lattice Boltzmann method to predict the chondrocyte cell growth without a scaffold on a flat plate placed inside a perfusion bioreactor. The model considers the two-way coupling between the cell growth and local flow field, and the simulation has been performed for 174 culture days. To incorporate the cell growth into the model, a control-volume-based surface growth modelling approach has been adopted. The simulation results show the variation of local fluid velocity, shear stress and concentration distribution during the culture period due to the growth of the cell phase and also illustrate that the shear stress can increase the cell volume fraction to a certain extent.

The timing of bud burst and its effect on tree growth.

PubMed

Rötzer, T; Grote, R; Pretzsch, H

2004-02-01

A phenology model for estimating the timings of bud burst--one of the most influential phenological phases for the simulation of tree growth--is presented in this study. The model calculates the timings of the leafing of beech (Fagus sylvatica L.) and oak (Quercus robur L.) and the May shoot of Norway spruce (Picea abies L.) and Scots pine (Pinus sylvestris L.) on the basis of the daily maximum temperature. The data for parameterisation and validation of the model have been taken from 40 climate and 120 phenological stations in southern Germany with time series for temperature and bud burst of up to 30 years. The validation of the phenology module by means of an independent data set showed correlation coefficients for comparisons between observed and simulated values of 54% (beech), 55% (oak), 59% (spruce) and 56% (pine) with mean absolute errors varying from 4.4 days (spruce) to 5.0 days (pine). These results correspond well with the results of other--often more complex--phenology models. After the phenology module had been implemented in the tree-growth model BALANCE, the growth of a mixed forest stand with the former static and the new dynamic timings for the bud burst was simulated. The results of the two simulation runs showed that phenology has to be taken into account when simulating forest growth, particularly in mixed stands.

Joint modelling compared with two stage methods for analysing longitudinal data and prospective outcomes: A simulation study of childhood growth and BP.

PubMed

Sayers, A; Heron, J; Smith, Adac; Macdonald-Wallis, C; Gilthorpe, M S; Steele, F; Tilling, K

2017-02-01

There is a growing debate with regards to the appropriate methods of analysis of growth trajectories and their association with prospective dependent outcomes. Using the example of childhood growth and adult BP, we conducted an extensive simulation study to explore four two-stage and two joint modelling methods, and compared their bias and coverage in estimation of the (unconditional) association between birth length and later BP, and the association between growth rate and later BP (conditional on birth length). We show that the two-stage method of using multilevel models to estimate growth parameters and relating these to outcome gives unbiased estimates of the conditional associations between growth and outcome. Using simulations, we demonstrate that the simple methods resulted in bias in the presence of measurement error, as did the two-stage multilevel method when looking at the total (unconditional) association of birth length with outcome. The two joint modelling methods gave unbiased results, but using the re-inflated residuals led to undercoverage of the confidence intervals. We conclude that either joint modelling or the simpler two-stage multilevel approach can be used to estimate conditional associations between growth and later outcomes, but that only joint modelling is unbiased with nominal coverage for unconditional associations.

Monte Carlo simulation of ferroelectric domain growth

NASA Astrophysics Data System (ADS)

Li, B. L.; Liu, X. P.; Fang, F.; Zhu, J. L.; Liu, J.-M.

2006-01-01

The kinetics of two-dimensional isothermal domain growth in a quenched ferroelectric system is investigated using Monte Carlo simulation based on a realistic Ginzburg-Landau ferroelectric model with cubic-tetragonal (square-rectangle) phase transitions. The evolution of the domain pattern and domain size with annealing time is simulated, and the stability of trijunctions and tetrajunctions of domain walls is analyzed. It is found that in this much realistic model with strong dipole alignment anisotropy and long-range Coulomb interaction, the powerlaw for normal domain growth still stands applicable. Towards the late stage of domain growth, both the average domain area and reciprocal density of domain wall junctions increase linearly with time, and the one-parameter dynamic scaling of the domain growth is demonstrated.

Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

2015-03-01

We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

AmapSim: a structural whole-plant simulator based on botanical knowledge and designed to host external functional models.

PubMed

Barczi, Jean-François; Rey, Hervé; Caraglio, Yves; de Reffye, Philippe; Barthélémy, Daniel; Dong, Qiao Xue; Fourcaud, Thierry

2008-05-01

AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function. Simulations were performed on tomato plants to demonstrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model. The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment.

AmapSim: A Structural Whole-plant Simulator Based on Botanical Knowledge and Designed to Host External Functional Models

PubMed Central

Barczi, Jean-François; Rey, Hervé; Caraglio, Yves; de Reffye, Philippe; Barthélémy, Daniel; Dong, Qiao Xue; Fourcaud, Thierry

2008-01-01

Background and Aims AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. Methods The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function. Key Results Simulations were performed on tomato plants to demostrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model. Conclusions The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment. PMID:17766310

Estimating solar radiation for plant simulation models

NASA Technical Reports Server (NTRS)

Hodges, T.; French, V.; Leduc, S.

1985-01-01

Five algorithms producing daily solar radiation surrogates using daily temperatures and rainfall were evaluated using measured solar radiation data for seven U.S. locations. The algorithms were compared both in terms of accuracy of daily solar radiation estimates and terms of response when used in a plant growth simulation model (CERES-wheat). Requirements for accuracy of solar radiation for plant growth simulation models are discussed. One algorithm is recommended as being best suited for use in these models when neither measured nor satellite estimated solar radiation values are available.

Chaotic attractors in tumor growth and decay: a differential equation model.

PubMed

Harney, Michael; Yim, Wen-sau

2015-01-01

Tumorigenesis can be modeled as a system of chaotic nonlinear differential equations. A simulation of the system is realized by converting the differential equations to difference equations. The results of the simulation show that an increase in glucose in the presence of low oxygen levels decreases tumor growth.

A New Model for Root Growth in Soil with Macropores

NASA Astrophysics Data System (ADS)

Landl, M.; Huber, K.; Schnepf, A.; Vanderborght, J.; Javaux, M.; Bengough, G.; Vereecken, H.

2016-12-01

In order to study soil-root interaction processes, dynamic root architecture models which are linked to models that simulate water flow and nutrient transport in the soil-root system are needed. Such models can be used to predict the impact of soil structural features, e.g. the presence of macropores in dense subsoil, on water and nutrient uptake by plants. In dynamic root architecture models, root growth is represented by moving root tips whose growth trajectory results in the creation of linear root segments. Typically, the direction of each new root segment is calculated as the vector sum of various direction-affecting components. The use of these established methods to simulate root growth in soil containing macropores, however, failed to reproduce experimentally observed root growth patterns. We therefore developed an alternative modelling approach where we distinguish between, firstly, the driving force for root growth which is determined by the orientation of the previous root segment as well as the influence of gravitropism and, secondly, soil mechanical resistance to root growth. The latter is expressed by root conductance which represents the inverse of soil penetration resistance and is treated similarly to hydraulic conductivity in Darcy's law. At the presence of macropores, root conductance is anisotropic which leads to a difference between the direction of the driving force and the direction of the root tip movement. The model was tested using data from the literature, at pot scale, at macropore scale, and in a series of simulations where sensitivity to gravity and macropore orientation was evaluated. The model simulated root growth trajectories in structured soil at both single root and whole root-system scales, generating root systems that were similar to images from experiments. Its implementation in the three dimensional soil and root water uptake model R-SWMS enables the use of the model in the future to evaluate the effect of macropores on crop access to water and nutrients.

An improved SWAT vegetation growth module and its evaluation for four tropical ecosystems

NASA Astrophysics Data System (ADS)

Alemayehu, Tadesse; van Griensven, Ann; Taddesse Woldegiorgis, Befekadu; Bauwens, Willy

2017-09-01

The Soil and Water Assessment Tool (SWAT) is a globally applied river basin ecohydrological model used in a wide spectrum of studies, ranging from land use change and climate change impacts studies to research for the development of the best water management practices. However, SWAT has limitations in simulating the seasonal growth cycles for trees and perennial vegetation in the tropics, where rainfall rather than temperature is the dominant plant growth controlling factor. Our goal is to improve the vegetation growth module of SWAT for simulating the vegetation variables - such as the leaf area index (LAI) - for tropical ecosystems. Therefore, we present a modified SWAT version for the tropics (SWAT-T) that uses a straightforward but robust soil moisture index (SMI) - a quotient of rainfall (P) and reference evapotranspiration (ETr) - to dynamically initiate a new growth cycle within a predefined period. Our results for the Mara Basin (Kenya/Tanzania) show that the SWAT-T-simulated LAI corresponds well with the Moderate Resolution Imaging Spectroradiometer (MODIS) LAI for evergreen forest, savanna grassland and shrubland. This indicates that the SMI is reliable for triggering a new annual growth cycle. The water balance components (evapotranspiration and streamflow) simulated by the SWAT-T exhibit a good agreement with remote-sensing-based evapotranspiration (ET-RS) and observed streamflow. The SWAT-T model, with the proposed vegetation growth module for tropical ecosystems, can be a robust tool for simulating the vegetation growth dynamics in hydrologic models in tropical regions.

Using a GIS-based spot growth model and visual simulator to evaluate the effects of silvicultural treatments on southern pine beetle-infested stands

Treesearch

Chiao-Ying Chou; Roy L. Hedden; Bo Song; Thomas M. Williams

2013-01-01

Many models are available for simulating the probability of southern pine beetle (Dendroctonus frontalis Zimmermann) (SPB) infestation and outbreak dynamics. However, only a few models focused on the potential spatial SPB growth. Although the integrated pest management systems are currently adopted, SPB management is still challenging because of...

Large historical growth in global terrestrial gross primary production

DOE PAGES

Campbell, J. E.; Berry, J. A.; Seibt, U.; ...

2017-04-05

Growth in terrestrial gross primary production (GPP) may provide a negative feedback for climate change. It remains uncertain, however, to what extent biogeochemical processes can suppress global GPP growth. In consequence, model estimates of terrestrial carbon storage and carbon cycle –climate feedbacks remain poorly constrained. Here we present a global, measurement-based estimate of GPP growth during the twentieth century based on long-term atmospheric carbonyl sulphide (COS) records derived from ice core, firn, and ambient air samples. Here, we interpret these records using a model that simulates changes in COS concentration due to changes in its sources and sinks, including amore » large sink that is related to GPP. We find that the COS record is most consistent with climate-carbon cycle model simulations that assume large GPP growth during the twentieth century (31% ± 5%; mean ± 95% confidence interval). Finally, while this COS analysis does not directly constrain estimates of future GPP growth it provides a global-scale benchmark for historical carbon cycle simulations.« less

Large historical growth in global terrestrial gross primary production

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

Campbell, J. E.; Berry, J. A.; Seibt, U.

Growth in terrestrial gross primary production (GPP) may provide a negative feedback for climate change. It remains uncertain, however, to what extent biogeochemical processes can suppress global GPP growth. In consequence, model estimates of terrestrial carbon storage and carbon cycle –climate feedbacks remain poorly constrained. Here we present a global, measurement-based estimate of GPP growth during the twentieth century based on long-term atmospheric carbonyl sulphide (COS) records derived from ice core, firn, and ambient air samples. Here, we interpret these records using a model that simulates changes in COS concentration due to changes in its sources and sinks, including amore » large sink that is related to GPP. We find that the COS record is most consistent with climate-carbon cycle model simulations that assume large GPP growth during the twentieth century (31% ± 5%; mean ± 95% confidence interval). Finally, while this COS analysis does not directly constrain estimates of future GPP growth it provides a global-scale benchmark for historical carbon cycle simulations.« less

Comparing models for growth and management of forest tracts

Treesearch

J.J. Colbert; Michael Schuckers; Desta Fekedulegn

2003-01-01

The Stand Damage Model (SDM) is a PC-based model that is easily installed, calibrated and initialized for use in exploring the future growth and management of forest stands or small wood lots. We compare the basic individual tree growth model incorporated in this model with alternative models that predict the basal area growth of trees. The SDM is a gap-type simulator...

Storage and growth of denitrifiers in aerobic granules: part I. model development.

PubMed

Ni, Bing-Jie; Yu, Han-Qing

2008-02-01

A mathematical model, based on the Activated Sludge Model No.3 (ASM3), is developed to describe the storage and growth activities of denitrifiers in aerobic granules under anoxic conditions. In this model, mass transfer, hydrolysis, simultaneous anoxic storage and growth, anoxic maintenance, and endogenous decay are all taken into account. The model established is implemented in the well-established AQUASIM simulation software. A combination of completely mixed reactor and biofilm reactor compartments provided by AQUASIM is used to simulate the mass transport and conversion processes occurring in both bulk liquid and granules. The modeling results explicitly show that the external substrate is immediately utilized for storage and growth at feast phase. More external substrates are diverted to storage process than the primary biomass production process. The model simulation indicates that the nitrate utilization rate (NUR) of granules-based denitrification process includes four linear phases of nitrate reduction. Furthermore, the methodology for determining the most important parameter in this model, that is, anoxic reduction factor, is established. (c) 2007 Wiley Periodicals, Inc.

Simulating the onset of spring vegetation growth across the Northern Hemisphere.

PubMed

Liu, Qiang; Fu, Yongshuo H; Liu, Yongwen; Janssens, Ivan A; Piao, Shilong

2018-03-01

Changes in the spring onset of vegetation growth in response to climate change can profoundly impact climate-biosphere interactions. Thus, robust simulation of spring onset is essential to accurately predict ecosystem responses and feedback to ongoing climate change. To date, the ability of vegetation phenology models to reproduce spatiotemporal patterns of spring onset at larger scales has not been thoroughly investigated. In this study, we took advantage of phenology observations via remote sensing to calibrate and evaluated six models, including both one-phase (considering only forcing temperatures) and two-phase (involving forcing, chilling, and photoperiod) models across the Northern Hemisphere between 1982 and 2012. Overall, we found that the model that integrated the photoperiod effect performed best at capturing spatiotemporal patterns of spring phenology in boreal and temperate forests. By contrast, all of the models performed poorly in simulating the onset of growth in grasslands. These results suggest that the photoperiod plays a role in controlling the onset of growth in most Northern Hemisphere forests, whereas other environmental factors (e.g., precipitation) should be considered when simulating the onset of growth in grasslands. We also found that the one-phase model performed as well as the two-phase models in boreal forests, which implies that the chilling requirement is probably fulfilled across most of the boreal zone. Conversely, two-phase models performed better in temperate forests than the one-phase model, suggesting that photoperiod and chilling play important roles in these temperate forests. Our results highlight the significance of including chilling and photoperiod effects in models of the spring onset of forest growth at large scales, and indicate that the consideration of additional drivers may be required for grasslands. © 2017 John Wiley & Sons Ltd.

Growth modeling of Listeria monocytogenes in pasteurized liquid egg.

PubMed

Ohkochi, Miho; Koseki, Shigenobu; Kunou, Masaaki; Sugiura, Katsuaki; Tsubone, Hirokazu

2013-09-01

The growth kinetics of Listeria monocytogenes and natural flora in commercially produced pasteurized liquid egg was examined at 4.1 to 19.4°C, and a growth simulation model that can estimate the range of the number of L. monocytogenes bacteria was developed. The experimental kinetic data were fitted to the Baranyi model, and growth parameters, such as maximum specific growth rate (μ(max)), maximum population density (N(max)), and lag time (λ), were estimated. As a result of estimating these parameters, we found that L. monocytogenes can grow without spoilage below 12.2°C, and we then focused on storage temperatures below 12.2°C in developing our secondary models. The temperature dependency of the μ(max) was described by Ratkowsky's square root model. The N(max) of L. monocytogenes was modeled as a function of temperature, because the N(max) of L. monocytogenes decreased as storage temperature increased. A tertiary model of L. monocytogenes was developed using the Baranyi model and μ(max) and N(max) secondary models. The ranges of the numbers of L. monocytogenes bacteria were simulated using Monte Carlo simulations with an assumption that these parameters have variations that follow a normal distribution. Predictive simulations under both constant and fluctuating temperature conditions demonstrated a high accuracy, represented by root mean square errors of 0.44 and 0.34, respectively. The predicted ranges also seemed to show a reasonably good estimation, with 55.8 and 51.5% of observed values falling into the prediction range of the 25th to 75th percentile, respectively. These results suggest that the model developed here can be used to estimate the kinetics and range of L. monocytogenes growth in pasteurized liquid egg under refrigerated temperature.

FARSITE: Fire Area Simulator-model development and evaluation

Treesearch

Mark A. Finney

1998-01-01

A computer simulation model, FARSITE, includes existing fire behavior models for surface, crown, spotting, point-source fire acceleration, and fuel moisture. The model's components and assumptions are documented. Simulations were run for simple conditions that illustrate the effect of individual fire behavior models on two-dimensional fire growth.

Using a bioenergetic model to assess growth reduction from catch-and-release fishing and hooking injury in rainbow trout, Oncorhynchus mykiss

USGS Publications Warehouse

Meka, Julie M.; Margraf, F.J.

2007-01-01

A bioenergetic model was used to predict the potential effects of feeding cessation caused by catch-and-release capture and a reduction in feeding efficiency from hooking injuries on rainbow trout, Oncorhynchus mykiss (Walbaum), growth in southwest Alaska, USA. Simulations indicated that a 1-day feeding cessation for a rainbow trout captured one to two times during summer months resulted in deviations from expected growth of −3% to −15%. To represent debilitating hooking injuries, the proportion of the maximum feeding potential was decreased by 5–50% resulting in deviations from expected growth of −9% to −164%. Simulated growth effects were most prominent from captures during months when salmon eggs and flesh constituted the majority of the trout diet. Simulated growth effects from reduced foraging efficiency were most prominent when hooking injuries occurred early in the fishing season. These simulations suggest that rainbow trout are most vulnerable to decreases in growth when salmon are abundant and spawning and, coincidentally, during the months when most fishing occurs.

Evaluation of CSM-CROPGRO-Cotton for simulating effects of management and climate change on cotton growth and evapotranspiration in an arid environment

USDA-ARS?s Scientific Manuscript database

Originally developed for simulating soybean growth and development, the CROPGRO model was recently re-parameterized for cotton. However, further efforts are necessary to evaluate the model's performance against field measurements for new environments and management options. The objective of this stu...

Key algorithms used in GR02: A computer simulation model for predicting tree and stand growth

Treesearch

Garrett A. Hughes; Paul E. Sendak; Paul E. Sendak

1985-01-01

GR02 is an individual tree, distance-independent simulation model for predicting tree and stand growth over time. It performs five major functions during each run: (1) updates diameter at breast height, (2) updates total height, (3) estimates mortality, (4) determines regeneration, and (5) updates crown class.

Simulating the effects of fluctuating dissolved oxygen on growth, reproduction, and survival of fish and shrimp.

PubMed

Miller Neilan, Rachael; Rose, Kenneth

2014-02-21

Individuals are commonly exposed to fluctuating levels of stressors, while most laboratory experiments focus on constant exposures. We develop and test a mathematical model for predicting the effects of low dissolved oxygen (hypoxia) on growth, reproduction, and survival using laboratory experiments on fish and shrimp. The exposure-effects model simulates the hourly reductions in growth and survival, and the reduction in reproduction (fecundity) at times of spawning, of an individual as it is exposed to constant or hourly fluctuating dissolved oxygen (DO) concentrations. The model was applied to seven experiments involving fish and shrimp that included constant and fluctuating DO exposures, with constant exposures used for parameter estimation and the model then used to simulate the growth, reproduction, and survival in the fluctuating treatments. Cumulative effects on growth, reproduction, and survival were predicted well by the model, but the model did not replay the observed episodic low survival days. Further investigation should involve the role of acclimation, possible inclusion of repair effects in reproduction and survival, and the sensitivity of model predictions to the shape of the immediate effects function. Additional testing of the model with other taxa, different patterns of fluctuating exposures, and different stressors is needed to determine the model's generality and robustness. © 2013 Elsevier Ltd. All rights reserved.

Modelling spatio-temporal variability of Mytilus edulis (L.) growth by forcing a dynamic energy budget model with satellite-derived environmental data

NASA Astrophysics Data System (ADS)

Thomas, Yoann; Mazurié, Joseph; Alunno-Bruscia, Marianne; Bacher, Cédric; Bouget, Jean-François; Gohin, Francis; Pouvreau, Stéphane; Struski, Caroline

2011-11-01

In order to assess the potential of various marine ecosystems for shellfish aquaculture and to evaluate their carrying capacities, there is a need to clarify the response of exploited species to environmental variations using robust ecophysiological models and available environmental data. For a large range of applications and comparison purposes, a non-specific approach based on 'generic' individual growth models offers many advantages. In this context, we simulated the response of blue mussel ( Mytilus edulis L.) to the spatio-temporal fluctuations of the environment in Mont Saint-Michel Bay (North Brittany) by forcing a generic growth model based on Dynamic Energy Budgets with satellite-derived environmental data (i.e. temperature and food). After a calibration step based on data from mussel growth surveys, the model was applied over nine years on a large area covering the entire bay. These simulations provide an evaluation of the spatio-temporal variability in mussel growth and also show the ability of the DEB model to integrate satellite-derived data and to predict spatial and temporal growth variability of mussels. Observed seasonal, inter-annual and spatial growth variations are well simulated. The large-scale application highlights the strong link between food and mussel growth. The methodology described in this study may be considered as a suitable approach to account for environmental effects (food and temperature variations) on physiological responses (growth and reproduction) of filter feeders in varying environments. Such physiological responses may then be useful for evaluating the suitability of coastal ecosystems for shellfish aquaculture.

Modeling the effects of ozone on soybean growth and yield.

PubMed

Kobayashi, K; Miller, J E; Flagler, R B; Heck, W W

1990-01-01

A simple mechanistic model was developed based on an existing growth model in order to address the mechanisms of the effects of ozone on growth and yield of soybean [Glycine max. (L.) Merr. 'Davis'] and interacting effects of other environmental stresses. The model simulates daily growth of soybean plants using environmental data including shortwave radiation, temperature, precipitation, irrigation and ozone concentration. Leaf growth, dry matter accumulation, water budget, nitrogen input and seed growth linked to senescence and abscission of leaves are described in the model. The effects of ozone are modeled as reduced photosynthate production and accelerated senescence. The model was applied to the open-top chamber experiments in which soybean plants were exposed to ozone under two levels of soil moisture regimes. After calibrating the model to the growth data and seed yield, goodness-of-fit of the model was tested. The model fitted well for top dry weight in the vegetative growth phase and also at maturity. The effect of ozone on seen yield was also described satisfactorily by the model. The simulation showed apparent interaction between the effect of ozone and soil moisture stress on the seed yield. The model revealed that further work is needed concerning the effect of ozone on the senescence process and the consequences of alteration of canopy microclimate by the open-top chambers.

Visual simulation of fatigue crack growth

NASA Astrophysics Data System (ADS)

Wang, Shuanzhu; Margolin, Harold; Lin, Fengbao

1998-07-01

An attempt has been made to visually simulate fatigue crack propagation from a precrack. An integrated program was developed for this purpose. The crack-tip shape was determined at four load positions in the first load cycle. The final shape was a blunt front with an “ear” profile at the precrack tip. A more general model, schematically illustrating the mechanism of fatigue crack growth and striation formation in a ductile material, was proposed based on this simulation. According to the present model, fatigue crack growth is an intermittent process; cyclic plastic shear strain is the driving force applied to both state I and II crack growth. No fracture mode transition occurs between the two stages in the present study. The crack growth direction alternates, moving up and down successively, producing fatigue striations. A brief examination has been made of the crack growth path in a ductile two-phase material.

Integrated modeling and heat treatment simulation of austempered ductile iron

NASA Astrophysics Data System (ADS)

Hepp, E.; Hurevich, V.; Schäfer, W.

2012-07-01

The integrated modeling and simulation of the casting and heat treatment processes for producing austempered ductile iron (ADI) castings is presented. The focus is on describing different models to simulate the austenitization, quenching and austempering steps during ADI heat treatment. The starting point for the heat treatment simulation is the simulated microstructure after solidification and cooling. The austenitization model considers the transformation of the initial ferrite-pearlite matrix into austenite as well as the dissolution of graphite in austenite to attain a uniform carbon distribution. The quenching model is based on measured CCT diagrams. Measurements have been carried out to obtain these diagrams for different alloys with varying Cu, Ni and Mo contents. The austempering model includes nucleation and growth kinetics of the ADI matrix. The model of ADI nucleation is based on experimental measurements made for varied Cu, Ni, Mo contents and austempering temperatures. The ADI kinetic model uses a diffusion controlled approach to model the growth. The models have been integrated in a tool for casting process simulation. Results are shown for the optimization of the heat treatment process of a planetary carrier casting.

Simulating crop growth with Expert-N-GECROS under different site conditions in Southwest Germany

NASA Astrophysics Data System (ADS)

Poyda, Arne; Ingwersen, Joachim; Demyan, Scott; Gayler, Sebastian; Streck, Thilo

2016-04-01

When feedbacks between the land surface and the atmosphere are investigated by Atmosphere-Land surface-Crop-Models (ALCM) it is fundamental to accurately simulate crop growth dynamics as plants directly influence the energy partitioning at the plant-atmosphere interface. To study both the response and the effect of intensive agricultural crop production systems on regional climate change in Southwest Germany, the crop growth model GECROS (YIN & VAN LAAR, 2005) was calibrated based on multi-year field data from typical crop rotations in the Kraichgau and Swabian Alb regions. Additionally, the SOC (soil organic carbon) model DAISY (MÜLLER et al., 1998) was implemented in the Expert-N model tool (ENGEL & PRIESACK, 1993) and combined with GECROS. The model was calibrated based on a set of plant (BBCH, LAI, plant height, aboveground biomass, N content of biomass) and weather data for the years 2010 - 2013 and validated with the data of 2014. As GECROS adjusts the root-shoot partitioning in response to external conditions (water, nitrogen, CO2), it is suitable to simulate crop growth dynamics under changing climate conditions and potentially more frequent stress situations. As C and N pools and turnover rates in soil as well as preceding crop effects were expected to considerably influence crop growth, the model was run in a multi-year, dynamic way. Crop residues and soil mineral N (nitrate, ammonium) available for the subsequent crop were accounted for. The model simulates growth dynamics of winter wheat, winter rape, silage maize and summer barley at the Kraichgau and Swabian Alb sites well. The Expert-N-GECROS model is currently parameterized for crops with potentially increasing shares in future crop rotations. First results will be shown.

Modeling Vegetation Growth Impact on Groundwater Recharge

NASA Astrophysics Data System (ADS)

Anurag, H.; Ng, G. H. C.; Tipping, R.

2017-12-01

Vegetation growth is affected by variability in climate and land-cover / land-use over a range of temporal and spatial scales. Vegetation also modifies water budget through interception and evapotranspiration and thus has a significant impact on groundwater recharge. Most groundwater recharge assessments represent vegetation using specified, static parameter, such as for leaf-area-index, but this neglects the effect of vegetation dynamics on recharge estimates. Our study addresses this gap by including vegetation growth in model simulations of recharge. We use NCAR's Community Land Model v4.5 with its BGC module (BGC is the new CLM4.5 biogeochemistry). It integrates prognostic vegetation growth with land-surface and subsurface hydrological processes and can thus capture the effect of vegetation on groundwater. A challenge, however, is the need to resolve uncertainties in model inputs ranging from vegetation growth parameters all the way down to the water table. We have compiled diverse data spanning meteorological inputs to subsurface geology and use these to implement ensemble model simulations to evaluate the possible effects of dynamic vegetation growth (versus specified, static vegetation parameterizations) on estimating groundwater recharge. We present preliminary results for select data-intensive test locations throughout the state of Minnesota (USA), which has a sharp east-west precipitation gradient that makes it an apt testbed for examining ecohydrologic relationships across different temperate climatic settings and ecosystems. Using the ensemble simulations, we examine the effect of seasonal to interannual variability of vegetation growth on recharge and water table depths, which has implications for predicting the combined impact of climate, vegetation, and geology on groundwater resources. Future work will include distributed model simulations over the entire state, as well as conditioning uncertain vegetation and subsurface parameters on remote sensing data and statewide water table records using data assimilation.

Detecting Growth Shape Misspecifications in Latent Growth Models: An Evaluation of Fit Indexes

ERIC Educational Resources Information Center

Leite, Walter L.; Stapleton, Laura M.

2011-01-01

In this study, the authors compared the likelihood ratio test and fit indexes for detection of misspecifications of growth shape in latent growth models through a simulation study and a graphical analysis. They found that the likelihood ratio test, MFI, and root mean square error of approximation performed best for detecting model misspecification…

Using FIA data in the Forest Vegetation Simulator

Treesearch

John D. Shaw

2009-01-01

The Forest Vegetation Simulator (FVS) is a national system of forest growth models maintained by the USDA Forest Service. It is the official tool for stand growth projection on National Forest lands, but it is also used widely on other ownerships. Model extensions and post-processors permit FVS users to perform a broad range of functions, including silvicultural...

A mathematical framework for modelling cambial surface evolution using a level set method

PubMed Central

Sellier, Damien; Plank, Michael J.; Harrington, Jonathan J.

2011-01-01

Background and Aims During their lifetime, tree stems take a series of successive nested shapes. Individual tree growth models traditionally focus on apical growth and architecture. However, cambial growth, which is distributed over a surface layer wrapping the whole organism, equally contributes to plant form and function. This study aims at providing a framework to simulate how organism shape evolves as a result of a secondary growth process that occurs at the cellular scale. Methods The development of the vascular cambium is modelled as an expanding surface using the level set method. The surface consists of multiple compartments following distinct expansion rules. Growth behaviour can be formulated as a mathematical function of surface state variables and independent variables to describe biological processes. Key Results The model was coupled to an architectural model and to a forest stand model to simulate cambium dynamics and wood formation at the scale of the organism. The model is able to simulate competition between cambia, surface irregularities and local features. Predicting the shapes associated with arbitrarily complex growth functions does not add complexity to the numerical method itself. Conclusions Despite their slenderness, it is sometimes useful to conceive of trees as expanding surfaces. The proposed mathematical framework provides a way to integrate through time and space the biological and physical mechanisms underlying cambium activity. It can be used either to test growth hypotheses or to generate detailed maps of wood internal structure. PMID:21470972

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

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

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

Aagesen, Larry K.; Thornton, Katsuyo, E-mail: kthorn@umich.edu; Coltrin, Michael E.

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. The model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. The model provides a route to optimize masks and processing conditions during materialsmore » synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

Computational Modeling of 3D Tumor Growth and Angiogenesis for Chemotherapy Evaluation

PubMed Central

Tang, Lei; van de Ven, Anne L.; Guo, Dongmin; Andasari, Vivi; Cristini, Vittorio; Li, King C.; Zhou, Xiaobo

2014-01-01

Solid tumors develop abnormally at spatial and temporal scales, giving rise to biophysical barriers that impact anti-tumor chemotherapy. This may increase the expenditure and time for conventional drug pharmacokinetic and pharmacodynamic studies. In order to facilitate drug discovery, we propose a mathematical model that couples three-dimensional tumor growth and angiogenesis to simulate tumor progression for chemotherapy evaluation. This application-oriented model incorporates complex dynamical processes including cell- and vascular-mediated interstitial pressure, mass transport, angiogenesis, cell proliferation, and vessel maturation to model tumor progression through multiple stages including tumor initiation, avascular growth, and transition from avascular to vascular growth. Compared to pure mechanistic models, the proposed empirical methods are not only easy to conduct but can provide realistic predictions and calculations. A series of computational simulations were conducted to demonstrate the advantages of the proposed comprehensive model. The computational simulation results suggest that solid tumor geometry is related to the interstitial pressure, such that tumors with high interstitial pressure are more likely to develop dendritic structures than those with low interstitial pressure. PMID:24404145

A mathematical model and computational framework for three-dimensional chondrocyte cell growth in a porous tissue scaffold placed inside a bi-directional flow perfusion bioreactor.

PubMed

Shakhawath Hossain, Md; Bergstrom, D J; Chen, X B

2015-12-01

The in vitro chondrocyte cell culture for cartilage tissue regeneration in a perfusion bioreactor is a complex process. Mathematical modeling and computational simulation can provide important insights into the culture process, which would be helpful for selecting culture conditions to improve the quality of the developed tissue constructs. However, simulation of the cell culture process is a challenging task due to the complicated interaction between the cells and local fluid flow and nutrient transport inside the complex porous scaffolds. In this study, a mathematical model and computational framework has been developed to simulate the three-dimensional (3D) cell growth in a porous scaffold placed inside a bi-directional flow perfusion bioreactor. The model was developed by taking into account the two-way coupling between the cell growth and local flow field and associated glucose concentration, and then used to perform a resolved-scale simulation based on the lattice Boltzmann method (LBM). The simulation predicts the local shear stress, glucose concentration, and 3D cell growth inside the porous scaffold for a period of 30 days of cell culture. The predicted cell growth rate was in good overall agreement with the experimental results available in the literature. This study demonstrates that the bi-directional flow perfusion culture system can enhance the homogeneity of the cell growth inside the scaffold. The model and computational framework developed is capable of providing significant insight into the culture process, thus providing a powerful tool for the design and optimization of the cell culture process. © 2015 Wiley Periodicals, Inc.

Evaluation of a kinetic model for computer simulation of growth and fermentation by Scheffersomyces (Pichia) stipitis fed D-xylose.

PubMed

Slininger, P J; Dien, B S; Lomont, J M; Bothast, R J; Ladisch, M R; Okos, M R

2014-08-01

Scheffersomyces (formerly Pichia) stipitis is a potential biocatalyst for converting lignocelluloses to ethanol because the yeast natively ferments xylose. An unstructured kinetic model based upon a system of linear differential equations has been formulated that describes growth and ethanol production as functions of ethanol, oxygen, and xylose concentrations for both growth and fermentation stages. The model was validated for various growth conditions including batch, cell recycle, batch with in situ ethanol removal and fed-batch. The model provides a summary of basic physiological yeast properties and is an important tool for simulating and optimizing various culture conditions and evaluating various bioreactor designs for ethanol production. © 2014 Wiley Periodicals, Inc.

Simulating unstressed crop development and growth using the Unified Plant Growth Model (UPGM)

USDA-ARS?s Scientific Manuscript database

Since development of the EPIC model in 1989, many versions of the plant growth component have been incorporated into other erosion and crop management models and subsequently modified to meet model objectives (e.g., WEPS, WEPP, SWAT, ALMANAC, GPFARM). This has resulted in different versions of the ...

Specification Search for Identifying the Correct Mean Trajectory in Polynomial Latent Growth Models

ERIC Educational Resources Information Center

Kim, Minjung; Kwok, Oi-Man; Yoon, Myeongsun; Willson, Victor; Lai, Mark H. C.

2016-01-01

This study investigated the optimal strategy for model specification search under the latent growth modeling (LGM) framework, specifically on searching for the correct polynomial mean or average growth model when there is no a priori hypothesized model in the absence of theory. In this simulation study, the effectiveness of different starting…

Modeling and simulation of the deposition/relaxation processes of polycrystalline diatomic structures of metallic nitride films

NASA Astrophysics Data System (ADS)

García, M. F.; Restrepo-Parra, E.; Riaño-Rojas, J. C.

2015-05-01

This work develops a model that mimics the growth of diatomic, polycrystalline thin films by artificially splitting the growth into deposition and relaxation processes including two stages: (1) a grain-based stochastic method (grains orientation randomly chosen) is considered and by means of the Kinetic Monte Carlo method employing a non-standard version, known as Constant Time Stepping, the deposition is simulated. The adsorption of adatoms is accepted or rejected depending on the neighborhood conditions; furthermore, the desorption process is not included in the simulation and (2) the Monte Carlo method combined with the metropolis algorithm is used to simulate the diffusion. The model was developed by accounting for parameters that determine the morphology of the film, such as the growth temperature, the interacting atomic species, the binding energy and the material crystal structure. The modeled samples exhibited an FCC structure with grain formation with orientations in the family planes of < 111 >, < 200 > and < 220 >. The grain size and film roughness were analyzed. By construction, the grain size decreased, and the roughness increased, as the growth temperature increased. Although, during the growth process of real materials, the deposition and relaxation occurs simultaneously, this method may perhaps be valid to build realistic polycrystalline samples.

Optimize Flue Gas Settings to Promote Microalgae Growth in Photobioreactors via Computer Simulations

PubMed Central

He, Lian; Chen, Amelia B; Yu, Yi; Kucera, Leah; Tang, Yinjie

2013-01-01

Flue gas from power plants can promote algal cultivation and reduce greenhouse gas emissions1. Microalgae not only capture solar energy more efficiently than plants3, but also synthesize advanced biofuels2-4. Generally, atmospheric CO2 is not a sufficient source for supporting maximal algal growth5. On the other hand, the high concentrations of CO2 in industrial exhaust gases have adverse effects on algal physiology. Consequently, both cultivation conditions (such as nutrients and light) and the control of the flue gas flow into the photo-bioreactors are important to develop an efficient “flue gas to algae” system. Researchers have proposed different photobioreactor configurations4,6 and cultivation strategies7,8 with flue gas. Here, we present a protocol that demonstrates how to use models to predict the microalgal growth in response to flue gas settings. We perform both experimental illustration and model simulations to determine the favorable conditions for algal growth with flue gas. We develop a Monod-based model coupled with mass transfer and light intensity equations to simulate the microalgal growth in a homogenous photo-bioreactor. The model simulation compares algal growth and flue gas consumptions under different flue-gas settings. The model illustrates: 1) how algal growth is influenced by different volumetric mass transfer coefficients of CO2; 2) how we can find optimal CO2 concentration for algal growth via the dynamic optimization approach (DOA); 3) how we can design a rectangular on-off flue gas pulse to promote algal biomass growth and to reduce the usage of flue gas. On the experimental side, we present a protocol for growing Chlorella under the flue gas (generated by natural gas combustion). The experimental results qualitatively validate the model predictions that the high frequency flue gas pulses can significantly improve algal cultivation. PMID:24121788

Comparing the STEMS and AFIS growth models with respect to the uncertainty of predictions

Treesearch

Ronald E. McRoberts; Margaret R. Holdaway; Veronica C. Lessard

2000-01-01

The uncertainty in 5-, 10-, and 20-year diameter growth predictions is estimated using Monte Carlo simulations for four Lake States tree species. Two sets of diameter growth models are used: recalibrations of the STEMS models using forest inventory and analysis data, and new growth models developed as a component of an annual forest inventory system for the North...

Spiral Growth in Plants: Models and Simulations

ERIC Educational Resources Information Center

Allen, Bradford D.

2004-01-01

The analysis and simulation of spiral growth in plants integrates algebra and trigonometry in a botanical setting. When the ideas presented here are used in a mathematics classroom/computer lab, students can better understand how basic assumptions about plant growth lead to the golden ratio and how the use of circular functions leads to accurate…

Modeling and predicting urban growth pattern of the Tokyo metropolitan area based on cellular automata

NASA Astrophysics Data System (ADS)

Zhao, Yaolong; Zhao, Junsan; Murayama, Yuji

2008-10-01

The period of high economic growth in Japan which began in the latter half of the 1950s led to a massive migration of population from rural regions to the Tokyo metropolitan area. This phenomenon brought about rapid urban growth and urban structure changes in this area. Purpose of this study is to establish a constrained CA (Cellular Automata) model with GIS (Geographical Information Systems) to simulate urban growth pattern in the Tokyo metropolitan area towards predicting urban form and landscape for the near future. Urban land-use is classified into multi-categories for interpreting the effect of interaction among land-use categories in the spatial process of urban growth. Driving factors of urban growth pattern, such as land condition, railway network, land-use zoning, random perturbation, and neighborhood interaction and so forth, are explored and integrated into this model. These driving factors are calibrated based on exploratory spatial data analysis (ESDA), spatial statistics, logistic regression, and "trial and error" approach. The simulation is assessed at both macro and micro classification levels in three ways: visual approach; fractal dimension; and spatial metrics. Results indicate that this model provides an effective prototype to simulate and predict urban growth pattern of the Tokyo metropolitan area.

Using growth and arrest of Richtmyer-Meshkov instabilities and Lagrangian simulations to study high-rate material strength

NASA Astrophysics Data System (ADS)

Prime, M. B.; Vaughan, D. E.; Preston, D. L.; Buttler, W. T.; Chen, S. R.; Oró, D. M.; Pack, C.

2014-05-01

Experiments applying a supported shock through mating surfaces (Atwood number = 1) with geometrical perturbations have been proposed for studying strength at strain rates up to 107/s using Richtmyer-Meshkov (RM) instabilities. Buttler et al. recently reported experimental results for RM instability growth in copper but with an unsupported shock applied by high explosives and the geometrical perturbations on the opposite free surface (Atwood number = -1). This novel configuration allowed detailed experimental observation of the instability growth and arrest. We present results and interpretation from numerical simulations of the Buttler RM instability experiments. Highly-resolved, two-dimensional simulations were performed using a Lagrangian hydrocode and the Preston-Tonks-Wallace (PTW) strength model. The model predictions show good agreement with the data. The numerical simulations are used to examine various assumptions previously made in an analytical model and to estimate the sensitivity of such experiments to material strength.

Effects of microscale inertia on dynamic ductile crack growth

NASA Astrophysics Data System (ADS)

Jacques, N.; Mercier, S.; Molinari, A.

2012-04-01

The aim of this paper is to investigate the role of microscale inertia in dynamic ductile crack growth. A constitutive model for porous solids that accounts for dynamic effects due to void growth is proposed. The model has been implemented in a finite element code and simulations of crack growth in a notched bar and in an edge cracked specimen have been performed. Results are compared to predictions obtained via the Gurson-Tvergaard-Needleman (GTN) model where micro-inertia effects are not accounted for. It is found that microscale inertia has a significant influence on the crack growth. In particular, it is shown that micro-inertia plays an important role during the strain localisation process by impeding void growth. Therefore, the resulting damage accumulation occurs in a more progressive manner. For this reason, simulations based on the proposed modelling exhibit much less mesh sensitivity than those based on the viscoplastic GTN model. Microscale inertia is also found to lead to lower crack speeds. Effects of micro-inertia on fracture toughness are evaluated.

Phase field models for heterogeneous nucleation: Application to inoculation in alpha-solidifying Ti-Al-B alloys

NASA Astrophysics Data System (ADS)

Apel, M.; Eiken, J.; Hecht, U.

2014-02-01

This paper aims at briefly reviewing phase field models applied to the simulation of heterogeneous nucleation and subsequent growth, with special emphasis on grain refinement by inoculation. The spherical cap and free growth model (e.g. A.L. Greer, et al., Acta Mater. 48, 2823 (2000)) has proven its applicability for different metallic systems, e.g. Al or Mg based alloys, by computing the grain refinement effect achieved by inoculation of the melt with inert seeding particles. However, recent experiments with peritectic Ti-Al-B alloys revealed that the grain refinement by TiB2 is less effective than predicted by the model. Phase field simulations can be applied to validate the approximations of the spherical cap and free growth model, e.g. by computing explicitly the latent heat release associated with different nucleation and growth scenarios. Here, simulation results for point-shaped nucleation, as well as for partially and completely wetted plate-like seed particles will be discussed with respect to recalescence and impact on grain refinement. It will be shown that particularly for large seeding particles (up to 30 μm), the free growth morphology clearly deviates from the assumed spherical cap and the initial growth - until the free growth barrier is reached - significantly contributes to the latent heat release and determines the recalescence temperature.

Modeling water scarcity over south Asia: Incorporating crop growth and irrigation models into the Variable Infiltration Capacity (VIC) model

NASA Astrophysics Data System (ADS)

Troy, Tara J.; Ines, Amor V. M.; Lall, Upmanu; Robertson, Andrew W.

2013-04-01

Large-scale hydrologic models, such as the Variable Infiltration Capacity (VIC) model, are used for a variety of studies, from drought monitoring to projecting the potential impact of climate change on the hydrologic cycle decades in advance. The majority of these models simulates the natural hydrological cycle and neglects the effects of human activities such as irrigation, which can result in streamflow withdrawals and increased evapotranspiration. In some parts of the world, these activities do not significantly affect the hydrologic cycle, but this is not the case in south Asia where irrigated agriculture has a large water footprint. To address this gap, we incorporate a crop growth model and irrigation model into the VIC model in order to simulate the impacts of irrigated and rainfed agriculture on the hydrologic cycle over south Asia (Indus, Ganges, and Brahmaputra basin and peninsular India). The crop growth model responds to climate signals, including temperature and water stress, to simulate the growth of maize, wheat, rice, and millet. For the primarily rainfed maize crop, the crop growth model shows good correlation with observed All-India yields (0.7) with lower correlations for the irrigated wheat and rice crops (0.4). The difference in correlation is because irrigation provides a buffer against climate conditions, so that rainfed crop growth is more tied to climate than irrigated crop growth. The irrigation water demands induce hydrologic water stress in significant parts of the region, particularly in the Indus, with the streamflow unable to meet the irrigation demands. Although rainfall can vary significantly in south Asia, we find that water scarcity is largely chronic due to the irrigation demands rather than being intermittent due to climate variability.

Status of growth and yield information for northern forest types

Treesearch

Dale S. Solomon

1977-01-01

Existing regional growth-and-yield information for most of the northern forest types is summarized by species. Present research is concentrated on growth-simulation models, constructed by either aggregating available information or through individual tree growth studies. A uniformity of more refined measurements is needed so that future growth models can be tried for...

Simulating stand climate, phenology, and photosynthesis of a forest stand with a process-based growth model.

PubMed

Rötzer, Thomas; Leuchner, Michael; Nunn, Angela J

2010-07-01

In the face of climate change and accompanying risks, forest management in Europe is becoming increasingly important. Model simulations can help to understand the reactions and feedbacks of a changing environment on tree growth. In order to simulate forest growth based on future climate change scenarios, we tested the basic processes underlying the growth model BALANCE, simulating stand climate (air temperature, photosynthetically active radiation (PAR) and precipitation), tree phenology, and photosynthesis. A mixed stand of 53- to 60-year-old Norway spruce (Picea abies) and European beech (Fagus sylvatica) in Southern Germany was used as a reference. The results show that BALANCE is able to realistically simulate air temperature gradients in a forest stand using air temperature measurements above the canopy and PAR regimes at different heights for single trees inside the canopy. Interception as a central variable for water balance of a forest stand was also estimated. Tree phenology, i.e. bud burst and leaf coloring, could be reproduced convincingly. Simulated photosynthesis rates were in accordance with measured values for beech both in the sun and the shade crown. For spruce, however, some discrepancies in the rates were obvious, probably due to changed environmental conditions after bud break. Overall, BALANCE has shown to respond to scenario simulations of a changing environment (e.g., climate change, change of forest stand structure).

Testing for a CO2 fertilization effect on growth of Canadian boreal forests

NASA Astrophysics Data System (ADS)

Girardin, Martin P.; Bernier, Pierre Y.; Raulier, FréDéRic; Tardif, Jacques C.; Conciatori, France; Guo, Xiao Jing

2011-03-01

The CO2 fertilization hypothesis stipulates that rising atmospheric CO2 has a direct positive effect on net primary productivity (NPP), with experimental evidence suggesting a 23% growth enhancement with a doubling of CO2. Here, we test this hypothesis by comparing a bioclimatic model simulation of NPP over the twentieth century against tree growth increment (TGI) data of 192 Pinus banksiana trees from the Duck Mountain Provincial Forest in Manitoba, Canada. We postulate that, if a CO2 fertilization effect has occurred, climatically driven simulations of NPP and TGI will diverge with increasing CO2. We use a two-level scaling approach to simulate NPP. A leaf-level model is first used to simulate high-frequency responses to climate variability. A canopy-level model of NPP is then adjusted to the aggregated leaf-level results and used to simulate yearly plot-level NPP. Neither model accounts for CO2 fertilization. The climatically driven simulations of NPP for 1912-2000 are effective for tracking the measured year-to-year variations in TGI, with 47.2% of the variance in TGI reproduced by the simulation. In addition, the simulation reproduces without divergence the positive linear trend detected in TGI over the same period. Our results therefore do not support the attribution of a portion of the historical linear trend in TGI to CO2 fertilization at the level suggested by current experimental evidence. A sensitivity analysis done by adding an expected CO2 fertilization effect to simulations suggests that the detection limit of the study is for a 14% growth increment with a doubling of atmospheric CO2 concentration.

Partitioning the Uncertainty in Estimates of Mean Basal Area Obtained from 10-year Diameter Growth Model Predictions

Treesearch

Ronald E. McRoberts

2005-01-01

Uncertainty in model-based predictions of individual tree diameter growth is attributed to three sources: measurement error for predictor variables, residual variability around model predictions, and uncertainty in model parameter estimates. Monte Carlo simulations are used to propagate the uncertainty from the three sources through a set of diameter growth models to...

Numerical simulation of convection and heat transfer in Czochralski crystal growth by multiple-relaxation-time LBM

NASA Astrophysics Data System (ADS)

Liu, Ding; Huang, Weichao; Zhang, Ni

2017-07-01

A two-dimensional axisymmetric swirling model based on the lattice Boltzmann method (LBM) in a pseudo Cartesian coordinate system is posited to simulate Czochralski (Cz) crystal growth in this paper. Specifically, the multiple-relaxation-time LBM (MRT-LBM) combined with the finite difference method (FDM) is used to analyze the melt convection and heat transfer in the process of Cz crystal growth. An incompressible axisymmetric swirling MRT-LB D2Q9 model is applied to solve for the axial and radial velocities by inserting thermal buoyancy and rotational inertial force into the two-dimensional lattice Boltzmann equation. In addition, the melt temperature and the azimuthal velocity are solved by MRT-LB D2Q5 models, and the crystal temperature is solved by FDM. The comparison results of stream functions values of different methods demonstrate that our hybrid model can be used to simulate the fluid-thermal coupling in the axisymmetric swirling model correctly and effectively. Furthermore, numerical simulations of melt convection and heat transfer are conducted under the conditions of high Grashof (Gr) numbers, within the range of 105 ˜ 107, and different high Reynolds (Re) numbers. The experimental results show our hybrid model can obtain the exact solution of complex crystal-growth models and analyze the fluid-thermal coupling effectively under the combined action of natural convection and forced convection.

The Effects of Autocorrelation on the Curve-of-Factors Growth Model

ERIC Educational Resources Information Center

Murphy, Daniel L.; Beretvas, S. Natasha; Pituch, Keenan A.

2011-01-01

This simulation study examined the performance of the curve-of-factors model (COFM) when autocorrelation and growth processes were present in the first-level factor structure. In addition to the standard curve-of factors growth model, 2 new models were examined: one COFM that included a first-order autoregressive autocorrelation parameter, and a…

Simulation of Climate Change Impacts on Wheat-Fallow Cropping Systems

USDA-ARS?s Scientific Manuscript database

Agricultural system simulation models are predictive tools for assessing climate change impacts on crop production. In this study, RZWQM2 that contains the DSSAT 4.0-CERES model was evaluated for simulating climate change impacts on wheat growth. The model was calibrated and validated using data fro...

Cancer growth and metastasis as a metaphor of Go gaming: An Ising model approach.

PubMed

Barradas-Bautista, Didier; Alvarado-Mentado, Matias; Agostino, Mark; Cocho, Germinal

2018-01-01

This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones that play first could correspond to a metaphor of the birth, growth, and metastasis of cancer. Moreover, playing white stones on the second turn could correspond the inhibition of cancer invasion. Mathematical modeling and algorithmic simulation of Go may therefore benefit the efforts to deploy therapies to surpass cancer illness by providing insight into the cellular growth and expansion over a tissue area. We use the Ising Hamiltonian, that models the energy exchange in interacting particles, for modeling the cancer dynamics. Parameters in the energy function refer the biochemical elements that induce cancer birth, growth, and metastasis; as well as the biochemical immune system process of defense.

The role of density-dependent individual growth in the persistence of freshwater salmonid populations.

PubMed

Vincenzi, Simone; Crivelli, Alain J; Jesensek, Dusan; De Leo, Giulio A

2008-06-01

Theoretical and empirical models of populations dynamics have paid little attention to the implications of density-dependent individual growth on the persistence and regulation of small freshwater salmonid populations. We have therefore designed a study aimed at testing our hypothesis that density-dependent individual growth is a process that enhances population recovery and reduces extinction risk in salmonid populations in a variable environment subject to disturbance events. This hypothesis was tested in two newly introduced marble trout (Salmo marmoratus) populations living in Slovenian streams (Zakojska and Gorska) subject to severe autumn floods. We developed a discrete-time stochastic individual-based model of population dynamics for each population with demographic parameters and compensatory responses tightly calibrated on data from individually tagged marble trout. The occurrence of severe flood events causing population collapses was explicitly accounted for in the model. We used the model in a population viability analysis setting to estimate the quasi-extinction risk and demographic indexes of the two marble trout populations when individual growth was density-dependent. We ran a set of simulations in which the effect of floods on population abundance was explicitly accounted for and another set of simulations in which flood events were not included in the model. These simulation results were compared with those of scenarios in which individual growth was modelled with density-independent Von Bertalanffy growth curves. Our results show how density-dependent individual growth may confer remarkable resilience to marble trout populations in case of major flood events. The resilience to flood events shown by the simulation results can be explained by the increase in size-dependent fecundity as a consequence of the drop in population size after a severe flood, which allows the population to quickly recover to the pre-event conditions. Our results suggest that density-dependent individual growth plays a potentially powerful role in the persistence of freshwater salmonids living in streams subject to recurrent yet unpredictable flood events.

Simulating effects of fire on northern Rocky Mountain landscapes with the ecological process model FIRE-BGC.

PubMed

Keane, R E; Ryan, K C; Running, S W

1996-03-01

A mechanistic, biogeochemical succession model, FIRE-BGC, was used to investigate the role of fire on long-term landscape dynamics in northern Rocky Mountain coniferous forests of Glacier National Park, Montana, USA. FIRE-BGC is an individual-tree model-created by merging the gap-phase process-based model FIRESUM with the mechanistic ecosystem biogeochemical model FOREST-BGC-that has mixed spatial and temporal resolution in its simulation architecture. Ecological processes that act at a landscape level, such as fire and seed dispersal, are simulated annually from stand and topographic information. Stand-level processes, such as tree establishment, growth and mortality, organic matter accumulation and decomposition, and undergrowth plant dynamics are simulated both daily and annually. Tree growth is mechanistically modeled based on the ecosystem process approach of FOREST-BGC where carbon is fixed daily by forest canopy photosynthesis at the stand level. Carbon allocated to the tree stem at the end of the year generates the corresponding diameter and height growth. The model also explicitly simulates fire behavior and effects on landscape characteristics. We simulated the effects of fire on ecosystem characteristics of net primary productivity, evapotranspiration, standing crop biomass, nitrogen cycling and leaf area index over 200 years for the 50,000-ha McDonald Drainage in Glacier National Park. Results show increases in net primary productivity and available nitrogen when fires are included in the simulation. Standing crop biomass and evapotranspiration decrease under a fire regime. Shade-intolerant species dominate the landscape when fires are excluded. Model tree increment predictions compared well with field data.

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.

Convection Effects in Three-dimensional Dendritic Growth

NASA Technical Reports Server (NTRS)

Lu, Yili; Beckermann, C.; Karma, A.

2003-01-01

A phase-field model is developed to simulate free dendritic growth coupled with fluid flow for a pure material in three dimensions. The preliminary results presented here illustrate the strong influence of convection on the three-dimensional (3D) dendrite growth morphology. The detailed knowledge of the flow and temperature fields in the melt around the dendrite from the simulations allows for a detailed understanding of the convection effects on dendritic growth.

Numerical simulations of epitaxial growth process in MOVPE reactor as a tool for design of modern semiconductors for high power electronics

NASA Astrophysics Data System (ADS)

Skibinski, Jakub; Caban, Piotr; Wejrzanowski, Tomasz; Kurzydlowski, Krzysztof J.

2014-10-01

In the present study numerical simulations of epitaxial growth of gallium nitride in Metal Organic Vapor Phase Epitaxy reactor AIX-200/4RF-S is addressed. Epitaxial growth means crystal growth that progresses while inheriting the laminar structure and the orientation of substrate crystals. One of the technological problems is to obtain homogeneous growth rate over the main deposit area. Since there are many agents influencing reaction on crystal area such as temperature, pressure, gas flow or reactor geometry, it is difficult to design optimal process. According to the fact that it's impossible to determine experimentally the exact distribution of heat and mass transfer inside the reactor during crystal growth, modeling is the only solution to understand the process precisely. Numerical simulations allow to understand the epitaxial process by calculation of heat and mass transfer distribution during growth of gallium nitride. Including chemical reactions in numerical model allows to calculate the growth rate of the substrate and estimate the optimal process conditions for obtaining the most homogeneous product.

Towards an integrative computational model for simulating tumor growth and response to radiation therapy

NASA Astrophysics Data System (ADS)

Marrero, Carlos Sosa; Aubert, Vivien; Ciferri, Nicolas; Hernández, Alfredo; de Crevoisier, Renaud; Acosta, Oscar

2017-11-01

Understanding the response to irradiation in cancer radiotherapy (RT) may help devising new strategies with improved tumor local control. Computational models may allow to unravel the underlying radiosensitive mechanisms intervening in the dose-response relationship. By using extensive simulations a wide range of parameters may be evaluated providing insights on tumor response thus generating useful data to plan modified treatments. We propose in this paper a computational model of tumor growth and radiation response which allows to simulate a whole RT protocol. Proliferation of tumor cells, cell life-cycle, oxygen diffusion, radiosensitivity, RT response and resorption of killed cells were implemented in a multiscale framework. The model was developed in C++, using the Multi-formalism Modeling and Simulation Library (M2SL). Radiosensitivity parameters extracted from literature enabled us to simulate in a regular grid (voxel-wise) a prostate cell tissue. Histopathological specimens with different aggressiveness levels extracted from patients after prostatectomy were used to initialize in silico simulations. Results on tumor growth exhibit a good agreement with data from in vitro studies. Moreover, standard fractionation of 2 Gy/fraction, with a total dose of 80 Gy as a real RT treatment was applied with varying radiosensitivity and oxygen diffusion parameters. As expected, the high influence of these parameters was observed by measuring the percentage of survival tumor cell after RT. This work paves the way to further models allowing to simulate increased doses in modified hypofractionated schemes and to develop new patient-specific combined therapies.

A nonlinear competitive model of the prostate tumor growth under intermittent androgen suppression.

PubMed

Yang, Jing; Zhao, Tong-Jun; Yuan, Chang-Qing; Xie, Jing-Hui; Hao, Fang-Fang

2016-09-07

Hormone suppression has been the primary modality of treatment for prostate cancer. However long-term androgen deprivation may induce androgen-independent (AI) recurrence. Intermittent androgen suppression (IAS) is a potential way to delay or avoid the AI relapse. Mathematical models of tumor growth and treatment are simple while they are capable of capturing the essence of complicated interactions. Game theory models have analyzed that tumor cells can enhance their fitness by adopting genetically determined survival strategies. In this paper, we consider the survival strategies as the competitive advantage of tumor cells and propose a new model to mimic the prostate tumor growth in IAS therapy. Then we investigate the competition effect in tumor development by numerical simulations. The results indicate that successfully IAS-controlled states can be achieved even though the net growth rate of AI cells is positive for any androgen level. There is crucial difference between the previous models and the new one in the phase diagram of successful and unsuccessful tumor control by IAS administration, which means that the suggestions from the models for medication can be different. Furthermore we introduce quadratic logistic terms to the competition model to simulate the tumor growth in the environment with a finite carrying capacity considering the nutrients or inhibitors. The simulations show that the tumor growth can reach an equilibrium state or an oscillatory state with the net growth rate of AI cells being androgen independent. Our results suggest that the competition and the restraint of a limited environment can enhance the possibility of relapse prevention. Copyright © 2016 Elsevier Ltd. All rights reserved.

Micromechanical models of delamination in aluminum-lithium alloys

NASA Astrophysics Data System (ADS)

Messner, Mark Christian

Aluminum lithium (Al-Li) alloys are lighter, stiffer, and tougher than conventional aerospace aluminum alloys. Replacing conventional aluminums with Al-Li could substantially decrease the weight and cost of aerospace structures. However, Al-Li alloys often fracture intergranularly via a mechanism called delamination cracking. While secondary delamination cracks can improve the effective toughness of a component, no current model accurately predicts the initiation and growth of intergranular cracks. Since simulations cannot incorporate delamination into a structural model, designers cannot quantify the effect of delamination cracking on a particular component. This uncertainty limits the application of Al-Li alloys. Previous experiments identify microstructural features linked to delamination. Fractography of failed surfaces indicates plastic void growth triggers intergranular failure. Furthermore, certain types of soft/stiff grain boundaries tend to localize void growth and nucleate delamination cracks. This dissertation develops a mechanism for the initiation of delamination on the microscale that accounts for these experimental observations. Microscale simulations of grain boundaries near a long primary crack explore the delamination mechanism on the mesoscale. In these simulations, a physically-based crystal plasticity (CP) model represents the constitutive response of individual grains. This CP model incorporates plastic voriticity correction terms into a standard objective stress rate integration, to accurately account for the kinematics of lattice deformation. The CP model implements slip system hardening with a modular approach to facilitate quick testing and calibration of different theories of hardening. The microscale models reveal soft/stiff grain boundaries develop elevated mean stress and plastic strain as a consequence of the mechanics of the interface. These elevated stresses and strain drive plastic void growth. The results indicate plastic void growth localizes to the grain boundaries even without the presence of material defects, such as precipitate free zones. Microscale simulations also explain the strong T-stress effect often observed in experimental fracture tests on Al-Li alloys. Finally, this dissertation develops a multiscale model of intergranular damage that incorporates the results of the microscale CP simulations. The multiscale model represents the mechanics of microscale deformation near grain boundaries with a simplified compatibility/equilibrium method. The intergranular stresses and strains from the simplified interface model drive a microscale damage index based on the physics of plastic void growth. Finally, a mesh-size independent scheme homogenizes damage on many grain boundaries into a macroscale damage index and projects the damage index to fail a plane of a macroscale structural model. The multiscale damage model, applied to 2195 Al-Li, successfully predicts delamination crack growth in a variety of standard experimental test configurations. The model correctly represents the microscale physics of delamination initiation and growth; after calibration to experimental data it can reliably predict the growth of delamination cracks in a component with any material configuration and loading. Therefore, the multiscale damage model forms the basis of a simulation method that allows designers to predict the development and net effect of delamination cracking in a structural model -- facilitating the application of lightweight Al-Li alloys in high-performance aerospace structures.

Modeling and numerical simulations of growth and morphologies of three dimensional aggregated silver films

NASA Astrophysics Data System (ADS)

Davis, L. J.; Boggess, M.; Kodpuak, E.; Deutsch, M.

2012-11-01

We report on a model for the deposition of three dimensional, aggregated nanocrystalline silver films, and an efficient numerical simulation method developed for visualizing such structures. We compare our results to a model system comprising chemically deposited silver films with morphologies ranging from dilute, uniform distributions of nanoparticles to highly porous aggregated networks. Disordered silver films grown in solution on silica substrates are characterized using digital image analysis of high resolution scanning electron micrographs. While the latter technique provides little volume information, plane-projected (two dimensional) island structure and surface coverage may be reliably determined. Three parameters governing film growth are evaluated using these data and used as inputs for the deposition model, greatly reducing computing requirements while still providing direct access to the complete (bulk) structure of the films throughout the growth process. We also show how valuable three dimensional characteristics of the deposited materials can be extracted using the simulated structures.

A highly efficient 3D level-set grain growth algorithm tailored for ccNUMA architecture

NASA Astrophysics Data System (ADS)

Mießen, C.; Velinov, N.; Gottstein, G.; Barrales-Mora, L. A.

2017-12-01

A highly efficient simulation model for 2D and 3D grain growth was developed based on the level-set method. The model introduces modern computational concepts to achieve excellent performance on parallel computer architectures. Strong scalability was measured on cache-coherent non-uniform memory access (ccNUMA) architectures. To achieve this, the proposed approach considers the application of local level-set functions at the grain level. Ideal and non-ideal grain growth was simulated in 3D with the objective to study the evolution of statistical representative volume elements in polycrystals. In addition, microstructure evolution in an anisotropic magnetic material affected by an external magnetic field was simulated.

FIBER handbook: a growth model for spruce-fir and northern hardwood types

Treesearch

Dale S. Solomon; Richard A. Hosmer; Homer T., Jr. Hayslett; Homer T. Hayslett

1987-01-01

A matrix model, FIBER, has been developed to provide the forest manager with a means of simulating the management and growth of forest stands in the Northeast. Instructional material is presented for the management of even-aged and multi-aged spruce-fir, mixedwood, and northern hardwood stands. FIBER allows the user to simulate a range of silvicultural treatments for a...

Monte Carlo Studies of Phase Separation in Compressible 2-dim Ising Models

NASA Astrophysics Data System (ADS)

Mitchell, S. J.; Landau, D. P.

2006-03-01

Using high resolution Monte Carlo simulations, we study time-dependent domain growth in compressible 2-dim ferromagnetic (s=1/2) Ising models with continuous spin positions and spin-exchange moves [1]. Spins interact with slightly modified Lennard-Jones potentials, and we consider a model with no lattice mismatch and one with 4% mismatch. For comparison, we repeat calculations for the rigid Ising model [2]. For all models, large systems (512^2) and long times (10^ 6 MCS) are examined over multiple runs, and the growth exponent is measured in the asymptotic scaling regime. For the rigid model and the compressible model with no lattice mismatch, the growth exponent is consistent with the theoretically expected value of 1/3 [1] for Model B type growth. However, we find that non-zero lattice mismatch has a significant and unexpected effect on the growth behavior.Supported by the NSF.[1] D.P. Landau and K. Binder, A Guide to Monte Carlo Simulations in Statistical Physics, second ed. (Cambridge University Press, New York, 2005).[2] J. Amar, F. Sullivan, and R.D. Mountain, Phys. Rev. B 37, 196 (1988).

The effects of mixed layer dynamics on ice growth in the central Arctic

NASA Astrophysics Data System (ADS)

Kitchen, Bruce R.

1992-09-01

The thermodynamic model of Thorndike (1992) is coupled to a one dimensional, two layer ocean entrainment model to study the effect of mixed layer dynamics on ice growth and the variation in the ocean heat flux into the ice due to mixed layer entrainment. Model simulations show the existence of a negative feedback between the ice growth and the mixed layer entrainment, and that the underlying ocean salinity has a greater effect on the ocean beat flux than does variations in the underlying ocean temperature. Model simulations for a variety of surface forcings and initial conditions demonstrate the need to include mixed layer dynamics for realistic ice prediction in the arctic.

Accounting for Age Uncertainty in Growth Modeling, the Case Study of Yellowfin Tuna (Thunnus albacares) of the Indian Ocean

PubMed Central

Dortel, Emmanuelle; Massiot-Granier, Félix; Rivot, Etienne; Million, Julien; Hallier, Jean-Pierre; Morize, Eric; Munaron, Jean-Marie; Bousquet, Nicolas; Chassot, Emmanuel

2013-01-01

Age estimates, typically determined by counting periodic growth increments in calcified structures of vertebrates, are the basis of population dynamics models used for managing exploited or threatened species. In fisheries research, the use of otolith growth rings as an indicator of fish age has increased considerably in recent decades. However, otolith readings include various sources of uncertainty. Current ageing methods, which converts an average count of rings into age, only provide periodic age estimates in which the range of uncertainty is fully ignored. In this study, we describe a hierarchical model for estimating individual ages from repeated otolith readings. The model was developed within a Bayesian framework to explicitly represent the sources of uncertainty associated with age estimation, to allow for individual variations and to include knowledge on parameters from expertise. The performance of the proposed model was examined through simulations, and then it was coupled to a two-stanza somatic growth model to evaluate the impact of the age estimation method on the age composition of commercial fisheries catches. We illustrate our approach using the saggital otoliths of yellowfin tuna of the Indian Ocean collected through large-scale mark-recapture experiments. The simulation performance suggested that the ageing error model was able to estimate the ageing biases and provide accurate age estimates, regardless of the age of the fish. Coupled with the growth model, this approach appeared suitable for modeling the growth of Indian Ocean yellowfin and is consistent with findings of previous studies. The simulations showed that the choice of the ageing method can strongly affect growth estimates with subsequent implications for age-structured data used as inputs for population models. Finally, our modeling approach revealed particularly useful to reflect uncertainty around age estimates into the process of growth estimation and it can be applied to any study relying on age estimation. PMID:23637773

Short-term responses of leaf growth rate to water deficit scale up to whole-plant and crop levels: an integrated modelling approach in maize.

PubMed

Chenu, Karine; Chapman, Scott C; Hammer, Graeme L; McLean, Greg; Salah, Halim Ben Haj; Tardieu, François

2008-03-01

Physiological and genetic studies of leaf growth often focus on short-term responses, leaving a gap to whole-plant models that predict biomass accumulation, transpiration and yield at crop scale. To bridge this gap, we developed a model that combines an existing model of leaf 6 expansion in response to short-term environmental variations with a model coordinating the development of all leaves of a plant. The latter was based on: (1) rates of leaf initiation, appearance and end of elongation measured in field experiments; and (2) the hypothesis of an independence of the growth between leaves. The resulting whole-plant leaf model was integrated into the generic crop model APSIM which provided dynamic feedback of environmental conditions to the leaf model and allowed simulation of crop growth at canopy level. The model was tested in 12 field situations with contrasting temperature, evaporative demand and soil water status. In observed and simulated data, high evaporative demand reduced leaf area at the whole-plant level, and short water deficits affected only leaves developing during the stress, either visible or still hidden in the whorl. The model adequately simulated whole-plant profiles of leaf area with a single set of parameters that applied to the same hybrid in all experiments. It was also suitable to predict biomass accumulation and yield of a similar hybrid grown in different conditions. This model extends to field conditions existing knowledge of the environmental controls of leaf elongation, and can be used to simulate how their genetic controls flow through to yield.

DRAINMOD-FOREST: Integrated modeling of hydrology, soil carbon and nitrogen dynamics, and plant growth for drained forests

Treesearch

Shiying Tian; Mohamed A. Youssef; R. Wayne Skaggs; Devendra M. Amatya; G.M. Chescheir

2012-01-01

We present a hybrid and stand-level forest ecosystem model, DRAINMOD-FOREST, for simulating the hydrology, carbon (C) and nitrogen (N) dynamics, and tree growth for drained forest lands under common silvicultural practices. The model was developed by linking DRAINMOD, the hydrological model, and DRAINMOD-N II, the soil C and N dynamics model, to a forest growth model,...

Modeling the atomistic growth behavior of gold nanoparticles in solution

NASA Astrophysics Data System (ADS)

Turner, C. Heath; Lei, Yu; Bao, Yuping

2016-04-01

The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

Phase-field simulations of velocity selection in rapidly solidified binary alloys

NASA Astrophysics Data System (ADS)

Fan, Jun; Greenwood, Michael; Haataja, Mikko; Provatas, Nikolas

2006-09-01

Time-dependent simulations of two-dimensional isothermal Ni-Cu dendrites are simulated using a phase-field model solved with a finite-difference adaptive mesh refinement technique. Dendrite tip velocity selection is examined and found to exhibit a transition between two markedly different regimes as undercooling is increased. At low undercooling, the dendrite tip growth rate is consistent with the kinetics of the classical Stefan problem, where the interface is assume to be in local equilibrium. At high undercooling, the growth velocity selected approaches a linear dependence on melt undercooling, consistent with the continuous growth kinetics of Aziz and with a one-dimensional steady-state phase-field asymptotic analysis of Ahmad [Phys. Rev. E 58, 3436 (1998)]. Our simulations are also consistent with other previously observed behaviors of dendritic growth as undercooling is increased. These include the transition of dendritic morphology to absolute stability and nonequilibrium solute partitioning. Our results show that phase-field models of solidification, which inherently contain a nonzero interface width, can be used to study the dynamics of complex solidification phenomena involving both equilibrium and nonequilibrium interface growth kinetics.

Simulation of Gravity Effects on Bulk Crystal Growth with Effects on undercooling

NASA Astrophysics Data System (ADS)

Chuang, S.-H.; Lu, M.-F.

For the production of a perfect single crystal by Bridgman, it is important to acquire the correct information about the heat transfer mechanism and to control the heat transfer in the Bridgman furnace. Because the quality of the crystal is closely related to its thermal history and the transport phenomena in the furnace. Ma et al. (2004) presented that faceting simulation of bulk crystal growth with undercooling method. Lan et al. (2003) developed a new model to study heat flow and facet formation in Bridgman growth with the undercooling satisfied the given growth mechanism. Considering the gravity effects added kinetic undercooling is thus developed. Heat conduction, convection and radiation are considered and coupled with the two-dimensional transient undercooling simulation. The solidification interface temperature is related to the undercooling along the interface and the melting temperature. In this investigation, we are going to apply the developed model to simulate interface in vertical Bridgman crystal growth process for yttrium aluminum garnet subjected to the normal gravity to microgravity. Also, it discusses the effect upon the shape and the propagation of the solidification crystal front.

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

NASA Astrophysics Data System (ADS)

Reinhardt, Aleks; Doye, Jonathan P. K.; Noya, Eva G.; Vega, Carlos

2012-11-01

We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

Alexandrium minutum growth controlled by phosphorus . An applied model

NASA Astrophysics Data System (ADS)

Chapelle, A.; Labry, C.; Sourisseau, M.; Lebreton, C.; Youenou, A.; Crassous, M. P.

2010-11-01

Toxic algae are a worldwide problem threatening aquaculture, public health and tourism. Alexandrium, a toxic dinoflagellate proliferates in Northwest France estuaries (i.e. the Penzé estuary) causing Paralytic Shellfish Poisoning events. Vegetative growth, and in particular the role of nutrient uptake and growth rate, are crucial parameters to understand toxic blooms. With the goal of modelling in situ Alexandrium blooms related to environmental parameters, we first try to calibrate a zero-dimensional box model of Alexandrium growth. This work focuses on phosphorus nutrition. Our objective is to calibrate Alexandrium minutum as well as Heterocapsa triquetra (a non-toxic dinoflagellate) growth under different rates of phosphorus supply, other factors being optimal and constant. Laboratory experiments are used to calibrate two growth models and three uptake models for each species. Models are then used to simulate monospecific batch and semi-continuous experiments as well as competition between the two algae (mixed cultures). Results show that the Droop growth model together with linear uptake versus quota can represent most of our observations, although a power law uptake function can more accurately simulate our phosphorus uptake data. We note that such models have limitations in non steady-state situations and cell quotas can depend on a variety of factors, so care must be taken in extrapolating these results beyond the specific conditions studied.

An immersed boundary-lattice Boltzmann model for biofilm growth and its impact on the NAPL dissolution in porous media

NASA Astrophysics Data System (ADS)

Benioug, M.; Yang, X.

2017-12-01

The evolution of microbial phase within porous medium is a complex process that involves growth, mortality, and detachment of the biofilm or attachment of moving cells. A better understanding of the interactions among biofilm growth, flow and solute transport and a rigorous modeling of such processes are essential for a more accurate prediction of the fate of pollutants (e.g. NAPLs) in soils. However, very few works are focused on the study of such processes in multiphase conditions (oil/water/biofilm systems). Our proposed numerical model takes into account the mechanisms that control bacterial growth and its impact on the dissolution of NAPL. An Immersed Boundary - Lattice Boltzmann Model (IB-LBM) is developed for flow simulations along with non-boundary conforming finite volume methods (volume of fluid and reconstruction methods) used for reactive solute transport. A sophisticated cellular automaton model is also developed to describe the spatial distribution of bacteria. A series of numerical simulations have been performed on complex porous media. A quantitative diagram representing the transitions between the different biofilm growth patterns is proposed. The bioenhanced dissolution of NAPL in the presence of biofilms is simulated at the pore scale. A uniform dissolution approach has been adopted to describe the temporal evolution of trapped blobs. Our simulations focus on the dissolution of NAPL in abiotic and biotic conditions. In abiotic conditions, we analyze the effect of the spatial distribution of NAPL blobs on the dissolution rate under different assumptions (blobs size, Péclet number). In biotic conditions, different conditions are also considered (spatial distribution, reaction kinetics, toxicity) and analyzed. The simulated results are consistent with those obtained from the literature.

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

PubMed

Klier, Christine

2012-03-06

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

Cancer growth and metastasis as a metaphor of Go gaming: An Ising model approach

PubMed Central

Barradas-Bautista, Didier; Agostino, Mark; Cocho, Germinal

2018-01-01

This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones that play first could correspond to a metaphor of the birth, growth, and metastasis of cancer. Moreover, playing white stones on the second turn could correspond the inhibition of cancer invasion. Mathematical modeling and algorithmic simulation of Go may therefore benefit the efforts to deploy therapies to surpass cancer illness by providing insight into the cellular growth and expansion over a tissue area. We use the Ising Hamiltonian, that models the energy exchange in interacting particles, for modeling the cancer dynamics. Parameters in the energy function refer the biochemical elements that induce cancer birth, growth, and metastasis; as well as the biochemical immune system process of defense. PMID:29718932

Evaluating growth models: A case study using PrognosisBC

Treesearch

Peter Marshall; Pablo Parysow; Shadrach Akindele

2008-01-01

The ability of the PrognosisBC (Version 3.0) growth model to predict tree and stand growth was assessed against a series of remeasured permanent sample plots, including some which had been precommercially thinned. In addition, the model was evaluated for logical consistency across a variety of stand structures using simulation. By the end of the...

Formulating a stand-growth model for mathematical programming problems in Appalachian forests

Treesearch

Gary W. Miller; Jay Sullivan

1993-01-01

Some growth and yield simulators applicable to central hardwood forests can be formulated for use in mathematical programming models that are designed to optimize multi-stand, multi-resource management problems. Once in the required format, growth equations serve as model constraints, defining the dynamics of stand development brought about by harvesting decisions. In...

The Effect of Data Quality on Short-term Growth Model Projections

Treesearch

David Gartner

2005-01-01

This study was designed to determine the effect of FIA's data quality on short-term growth model projections. The data from Georgia's 1996 statewide survey were used for the Southern variant of the Forest Vegetation Simulator to predict Georgia's first annual panel. The effect of several data error sources on growth modeling prediction errors...

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Linking a modified EPIC-based growth model (UPGM) with a component-based watershed model (AGES-W)

USDA-ARS?s Scientific Manuscript database

Agricultural models and decision support systems (DSS) for assessing water use and management are increasingly being applied to diverse geographic regions at different scales. This requires models that can simulate different crops, however, very few plant growth models are available that “easily” ...

Simulating Spatial Growth Patterns in Developing Countries: A Case of Shama in the Western Region of Ghana.

NASA Astrophysics Data System (ADS)

Inkoom, J. N.; Nyarko, B. K.

2014-12-01

The integration of geographic information systems (GIS) and agent-based modelling (ABM) can be an efficient tool to improve spatial planning practices. This paper utilizes GIS and ABM approaches to simulate spatial growth patterns of settlement structures in Shama. A preliminary household survey on residential location decision-making choice served as the behavioural rule for household agents in the model. Physical environment properties of the model were extracted from a 2005 image implemented in NetLogo. The resulting growth pattern model was compared with empirical growth patterns to ascertain the model's accuracy. The paper establishes that the development of unplanned structures and its evolving structural pattern are a function of land price, proximity to economic centres, household economic status and location decision-making patterns. The application of the proposed model underlines its potential for integration into urban planning policies and practices, and for understanding residential decision-making processes in emerging cities in developing countries. Key Words: GIS; Agent-based modelling; Growth patterns; NetLogo; Location decision making; Computational Intelligence.

Proof test and fatigue crack growth modeling on 2024-T3 aluminum alloy

NASA Technical Reports Server (NTRS)

Newman, J. C., Jr.; Poe, C. C., Jr.; Dawicke, D. S.

1990-01-01

Pressure proof testing of aircraft fuselage structures has been suggested as a means of screening critical crack sizes and of extending their useful life. The objective of this paper is to study the proof-test concept and to model the crack-growth process on a ductile material. Simulated proof and operational fatigue life tests have been conducted on cracked panels made of 2024-T3 aluminum alloy sheet material. A fatigue crack-closure model was modified to simulate the proof test and operational fatigue cycling. Using crack-growth rate and resistance-curve data, the model was able to predict crack growth during and after the proof load. These tests and analyses indicate that the proof test increases fatigue life; but the beneficial life, after a 1.33 or 1.5 proof, was less than a few hundred cycles.

Modeling and simulating two cut-to-length harvesting systems in central Appalachian hardwoods

Treesearch

Jingxin Wang; Chris B. LeDoux; Yaoxiang Li

2003-01-01

The production rates and costs of two cut-to-length harvesting systems was simulated using a modular ground-based simulation model and stand yield data from fully stocked, second growth even aged central Appalachian hardwood forests. The two harvesters simulated were a modified John Deere 988 tracked excavator with a model RP 1600 single grip sawhead and an excavator...

The simulation model of growth and cell divisions for the root apex with an apical cell in application to Azolla pinnata.

PubMed

Piekarska-Stachowiak, Anna; Nakielski, Jerzy

2013-12-01

In contrast to seed plants, the roots of most ferns have a single apical cell which is the ultimate source of all cells in the root. The apical cell has a tetrahedral shape and divides asymmetrically. The root cap derives from the distal division face, while merophytes derived from three proximal division faces contribute to the root proper. The merophytes are produced sequentially forming three sectors along a helix around the root axis. During development, they divide and differentiate in a predictable pattern. Such growth causes cell pattern of the root apex to be remarkably regular and self-perpetuating. The nature of this regularity remains unknown. This paper shows the 2D simulation model for growth of the root apex with the apical cell in application to Azolla pinnata. The field of growth rates of the organ, prescribed by the model, is of a tensor type (symplastic growth) and cells divide taking principal growth directions into account. The simulations show how the cell pattern in a longitudinal section of the apex develops in time. The virtual root apex grows realistically and its cell pattern is similar to that observed in anatomical sections. The simulations indicate that the cell pattern regularity results from cell divisions which are oriented with respect to principal growth directions. Such divisions are essential for maintenance of peri-anticlinal arrangement of cell walls and coordinated growth of merophytes during the development. The highly specific division program that takes place in merophytes prior to differentiation seems to be regulated at the cellular level.

Diffusion, Viscosity and Crystal Growth in Microgravity

NASA Technical Reports Server (NTRS)

Myerson, Allan S.

1996-01-01

The diffusivity of TriGlycine Sulfate (TGS), Potassium Dihydrogen Phosphate (KDP), Ammonium Dihydrogen Phosphate (ADF) and other compounds of interest to microgravity crystal growth, in supersaturated solutions as a function of solution concentration, 'age' and 'history was studied experimentally. The factors that affect the growth of crystals from water solutions in microgravity have been examined. Three non-linear optical materials have been studied, potassium dihydrogen phosphate (KDP), ammonium dihydrogen phosphate (ADP) and triglycine sulfate (TGC). The diffusion coefficient and viscosity of supersaturated water solutions were measured. Also theoretical model of diffusivity and viscosity in a metastable state, model of crystal growth from solution including non-linear time dependent diffusivity and viscosity effect and computer simulation of the crystal growth process which allows simulation of the microgravity crystal growth were developed.

Saw-tooth instability in storage rings: simulations and dynamical model

NASA Astrophysics Data System (ADS)

Migliorati, M.; Palumbo, L.; Dattoli, G.; Mezi, L.

1999-11-01

The saw-tooth instability in storage rings is studied by means of a time-domain simulation code which takes into account the self-induced wake fields. The results are compared with those from a dynamical heuristic model exploiting two coupled non-linear differential equations, accounting for the time behavior of the instability growth rate and for the anomalous growth of the energy spread. This model is shown to reproduce the characteristic features of the instability in a fairly satisfactory way.

Appropriate Arrangement of Nori Aquafarming Grounds in the Ariake Sea on the Basis of Convective Dispersion Simulation Model

NASA Astrophysics Data System (ADS)

Tabata, Toshinori; Hiramatsu, Kazuaki; Harada, Masayoshi; Shiraishi, Hideto; Shuto, Toshio

This study investigated appropriate arrangement of nori aquafarming grounds from the view point of nori growth in the Ariake Sea coastal waters. Databases of the sea-bed topography and nori aquafarming grounds were constructed using GIS. Then the tidal currents and salinity in the Ariake Sea were simulated using a two-dimensional depth-integrated model, which was developed by integrating the three-dimensional continuity, momentum, and diffusion equations. The wetting and drying scheme was also introduced to account for the appearance and disappearance of tidal flats. The velocities and directions of the simulated tidal currents, salinity, and tidal land appearance were in good agreement with observed data. Five scenarios considered by the Fukuoka Prefectural Government were introduced in the simulation model to identify the most appropriate arrangement. An experimental formula for nitrogen assimilation kinetics in the nori body was introduced to evaluate the simulation results for the five scenarios. The scenarios with a reduced density of aquafarming grounds had increased nori growth, suggesting that the arrangement of the aquafarming grounds affected the nori growth. The simulation results were used to identify the most appropriate arrangement of aquafarming grounds.

Experimental simulation and morphological quantification of volcano growth

NASA Astrophysics Data System (ADS)

Grosse, Pablo; Kervyn, Matthieu; Gallland, Olivier; Delcamp, Audray; Poppe, Sam

2016-04-01

Volcanoes display very diverse morphologies as a result of a complex interplay of several constructive and destructive processes. Here the role played by the spatial distribution of eruption centre and by an underlying strike-slip fault in controlling the long term growth of volcanoes is investigated with analogue models. Volcano growth was simulated by depositing loads of granular material (sand-kaolin mixtures) from a point source. An individual load deposited at a fixed location produces a simple symmetrical cone with flank slopes at the angle of repose of the granular material (~33°) that can be considered as the building-block for the experiments. Two sets of experiments were undertaken: (1) the location of deposition of the granular material (i.e. the volcano growth location) was shifted with time following specific probability density functions simulating shifts or migrations in vent location; (2) the location of deposition was kept fixed, but the deposition rate (i.e. the volcano growth rate) was varied coupled with the movement of a basal plate attached to a step-motor simulating a strike-slip displacement under the growing cone (and hence deformation of the cone). During the progression of the experiments, the models were photographed at regular time intervals using four digital cameras positioned at slightly different angles over the models. The photographs were used to generate synthetic digital elevation models (DEMs) with 0.2 mm spatial resolution of each step of the models by applying the MICMAC digital stereo-photogrammetry software. Morphometric data were extracted from the DEMs by applying two IDL-language algorithms: NETVOLC, used to automatically calculate the volcano edifice basal outline, and MORVOLC, used to extract a set of morphometric parameters that characterize the volcano edifice in terms of size, plan shape, profile shape and slopes. Analysis of the DEM-derived morphometric parameters allows to quantitatively characterize the growth evolution of the volcano models in terms of vent distribution and growth rate-deformation rate ratios.

Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics

PubMed Central

Chindapol, Nol; Kaandorp, Jaap A.; Cronemberger, Carolina; Mass, Tali; Genin, Amatzia

2013-01-01

The growth of scleractinian corals is strongly influenced by the effect of water motion. Corals are known to have a high level of phenotypic variation and exhibit a diverse range of growth forms, which often contain a high level of geometric complexity. Due to their complex shape, simulation models represent an important option to complement experimental studies of growth and flow. In this work, we analyzed the impact of flow on coral's morphology by an accretive growth model coupled with advection-diffusion equations. We performed simulations under no-flow and uni-directional flow setup with the Reynolds number constant. The relevant importance of diffusion to advection was investigated by varying the diffusion coefficient, rather than the flow speed in Péclet number. The flow and transport equations were coupled and solved using COMSOL Multiphysics. We then compared the simulated morphologies with a series of Computed Tomography (CT) scans of scleractinian corals Pocillopora verrucosa exposed to various flow conditions in the in situ controlled flume setup. As a result, we found a similar trend associated with the increasing Péclet for both simulated forms and in situ corals; that is uni-directional current tends to facilitate asymmetrical growth response resulting in colonies with branches predominantly developed in the upstream direction. A closer look at the morphological traits yielded an interesting property about colony symmetry and plasticity induced by uni-directional flow. Both simulated and in situ corals exhibit a tendency where the degree of symmetry decreases and compactification increases in conjunction with the augmented Péclet thus indicates the significant importance of hydrodynamics. PMID:23326222

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

PubMed

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

2016-12-14

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

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

PubMed Central

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

2016-01-01

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

Analytical model of flame spread in full-scale room/corner tests (ISO9705)

Treesearch

Mark Dietenberger; Ondrej Grexa

1999-01-01

A physical, yet analytical, model of fire growth has predicted flame spread and rate of heat release (RHR) for an ISO9705 test scenario using bench-scale data from the cone calorimeter. The test scenario simulated was the propane ignition burner at the comer with a 100/300 kW program and the specimen lined on the walls only. Four phases of fire growth were simulated....

Simulated response of conterminous United States ecosystems to climate change at different levels of fire suppression, CO2 emission rate, and growth response to CO2

Treesearch

James M. Lenihan; Dominique Bachelet; Ronald P. Neilson; Raymond Drapek

2008-01-01

A modeling experiment was designed to investigate the impact of fire management, CO2 emission rate, and the growth response to CO2 on the response of ecosystems in the conterminous United States to climate scenarios produced by three different general circulation models (GCMs) as simulated by the MCl Dynamic General...

Simulation of an integrated system for the production of methane and single cell protein from biomass

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

Thomas, M.V.

1989-01-01

A numerical model was developed to simulate the operation of an integrated system for the production of methane and single-cell algal protein from a variety of biomass energy crops or waste streams. Economic analysis was performed at the end of each simulation. The model was capable of assisting in the determination of design parameters by providing relative economic information for various strategies. Three configurations of anaerobic reactors were simulated. These included fed-bed reactors, conventional stirred tank reactors, and continuously expanding reactors. A generic anaerobic digestion process model, using lumped substrate parameters, was developed for use by type-specific reactor models. Themore » generic anaerobic digestion model provided a tool for the testing of conversion efficiencies and kinetic parameters for a wide range of substrate types and reactor designs. Dynamic growth models were used to model the growth of algae and Eichornia crassipes was modeled as a function of daily incident radiation and temperature. The growth of Eichornia crassipes was modeled for the production of biomass as a substrate for digestion. Computer simulations with the system model indicated that tropical or subtropical locations offered the most promise for a viable system. The availability of large quantities of digestible waste and low land prices were found to be desirable in order to take advantage of the economies of scale. Other simulations indicated that poultry and swine manure produced larger biogas yields than cattle manure. The model was created in a modular fashion to allow for testing of a wide variety of unit operations. Coding was performed in the Pascal language for use on personal computers.« less

Coupling biomechanics to a cellular level model: an approach to patient-specific image driven multi-scale and multi-physics tumor simulation.

PubMed

May, Christian P; Kolokotroni, Eleni; Stamatakos, Georgios S; Büchler, Philippe

2011-10-01

Modeling of tumor growth has been performed according to various approaches addressing different biocomplexity levels and spatiotemporal scales. Mathematical treatments range from partial differential equation based diffusion models to rule-based cellular level simulators, aiming at both improving our quantitative understanding of the underlying biological processes and, in the mid- and long term, constructing reliable multi-scale predictive platforms to support patient-individualized treatment planning and optimization. The aim of this paper is to establish a multi-scale and multi-physics approach to tumor modeling taking into account both the cellular and the macroscopic mechanical level. Therefore, an already developed biomodel of clinical tumor growth and response to treatment is self-consistently coupled with a biomechanical model. Results are presented for the free growth case of the imageable component of an initially point-like glioblastoma multiforme tumor. The composite model leads to significant tumor shape corrections that are achieved through the utilization of environmental pressure information and the application of biomechanical principles. Using the ratio of smallest to largest moment of inertia of the tumor material to quantify the effect of our coupled approach, we have found a tumor shape correction of 20% by coupling biomechanics to the cellular simulator as compared to a cellular simulation without preferred growth directions. We conclude that the integration of the two models provides additional morphological insight into realistic tumor growth behavior. Therefore, it might be used for the development of an advanced oncosimulator focusing on tumor types for which morphology plays an important role in surgical and/or radio-therapeutic treatment planning. Copyright © 2011 Elsevier Ltd. All rights reserved.

Coupling individual kernel-filling processes with source-sink interactions into GREENLAB-Maize.

PubMed

Ma, Yuntao; Chen, Youjia; Zhu, Jinyu; Meng, Lei; Guo, Yan; Li, Baoguo; Hoogenboom, Gerrit

2018-02-13

Failure to account for the variation of kernel growth in a cereal crop simulation model may cause serious deviations in the estimates of crop yield. The goal of this research was to revise the GREENLAB-Maize model to incorporate source- and sink-limited allocation approaches to simulate the dry matter accumulation of individual kernels of an ear (GREENLAB-Maize-Kernel). The model used potential individual kernel growth rates to characterize the individual potential sink demand. The remobilization of non-structural carbohydrates from reserve organs to kernels was also incorporated. Two years of field experiments were conducted to determine the model parameter values and to evaluate the model using two maize hybrids with different plant densities and pollination treatments. Detailed observations were made on the dimensions and dry weights of individual kernels and other above-ground plant organs throughout the seasons. Three basic traits characterizing an individual kernel were compared on simulated and measured individual kernels: (1) final kernel size; (2) kernel growth rate; and (3) duration of kernel filling. Simulations of individual kernel growth closely corresponded to experimental data. The model was able to reproduce the observed dry weight of plant organs well. Then, the source-sink dynamics and the remobilization of carbohydrates for kernel growth were quantified to show that remobilization processes accompanied source-sink dynamics during the kernel-filling process. We conclude that the model may be used to explore options for optimizing plant kernel yield by matching maize management to the environment, taking into account responses at the level of individual kernels. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Development of an in silico stochastic 4D model of tumor growth with angiogenesis.

PubMed

Forster, Jake C; Douglass, Michael J J; Harriss-Phillips, Wendy M; Bezak, Eva

2017-04-01

A stochastic computer model of tumour growth with spatial and temporal components that includes tumour angiogenesis was developed. In the current work it was used to simulate head and neck tumour growth. The model also provides the foundation for a 4D cellular radiotherapy simulation tool. The model, developed in Matlab, contains cell positions randomised in 3D space without overlap. Blood vessels are represented by strings of blood vessel units which branch outwards to achieve the desired tumour relative vascular volume. Hypoxic cells have an increased cell cycle time and become quiescent at oxygen tensions less than 1 mmHg. Necrotic cells are resorbed. A hierarchy of stem cells, transit cells and differentiated cells is considered along with differentiated cell loss. Model parameters include the relative vascular volume (2-10%), blood oxygenation (20-100 mmHg), distance from vessels to the onset of necrosis (80-300 μm) and probability for stem cells to undergo symmetric division (2%). Simulations were performed to observe the effects of hypoxia on tumour growth rate for head and neck cancers. Simulations were run on a supercomputer with eligible parts running in parallel on 12 cores. Using biologically plausible model parameters for head and neck cancers, the tumour volume doubling time varied from 45 ± 5 days (n = 3) for well oxygenated tumours to 87 ± 5 days (n = 3) for severely hypoxic tumours. The main achievements of the current model were randomised cell positions and the connected vasculature structure between the cells. These developments will also be beneficial when irradiating the simulated tumours using Monte Carlo track structure methods. © 2017 American Association of Physicists in Medicine.

SIMULATION OF OZONE EFFECTS ON EIGHT TREE SPECIES AT SHENANDOAH NATIONAL PARK

EPA Science Inventory

As part of an assessment of potential effects of air pollutants on the vegetation of Shenandoah National Park (SHEN), we simulated the growth of eight important tree species using TREGRO, a mechanistic model of individual tree growth. Published TREGRO parameters for black cherry...

Population viability of Pediocactus bradyi (Cactaceae) in a changing climate.

PubMed

Shryock, Daniel F; Esque, Todd C; Hughes, Lee

2014-11-01

A key question concerns the vulnerability of desert species adapted to harsh, variable climates to future climate change. Evaluating this requires coupling long-term demographic models with information on past and projected future climates. We investigated climatic drivers of population growth using a 22-yr demographic model for Pediocactus bradyi, an endangered cactus in northern Arizona. We used a matrix model to calculate stochastic population growth rates (λs) and the relative influences of life-cycle transitions on population growth. Regression models linked population growth with climatic variability, while stochastic simulations were used to (1) understand how predicted increases in drought frequency and extreme precipitation would affect λs, and (2) quantify variability in λs based on temporal replication of data. Overall λs was below unity (0.961). Population growth was equally influenced by fecundity and survival and significantly correlated with increased annual precipitation and higher winter temperatures. Stochastic simulations increasing the probability of drought and extreme precipitation reduced λs, but less than simulations increasing the probability of drought alone. Simulations varying the temporal replication of data suggested 14 yr were required for accurate λs estimates. Pediocactus bradyi may be vulnerable to increases in the frequency and intensity of extreme climatic events, particularly drought. Biotic interactions resulting in low survival during drought years outweighed increased seedling establishment following heavy precipitation. Climatic extremes beyond historical ranges of variability may threaten rare desert species with low population growth rates and therefore high susceptibility to stochastic events. © 2014 Botanical Society of America, Inc.

Modeling and simulation of a low-grade urinary bladder carcinoma.

PubMed

Bunimovich-Mendrazitsky, Svetlana; Pisarev, Vladimir; Kashdan, Eugene

2015-03-01

In this work, we present a mathematical model of the initiation and progression of a low-grade urinary bladder carcinoma. We simulate the crucial processes affecting tumor growth, such as oxygen diffusion, carcinogen penetration, and angiogenesis, within the framework of the urothelial cell dynamics. The cell dynamics are modeled using the discrete technique of cellular automata, while the continuous processes of carcinogen penetration and oxygen diffusion are described by nonlinear diffusion-absorption equations. As the availability of oxygen is necessary for tumor progression, processes of oxygen transport to the tumor growth site seem most important. Our model yields a theoretical insight into the main stages of development and growth of urinary bladder carcinoma with emphasis on the two most common types: bladder polyps and carcinoma in situ. Analysis of histological structure of bladder tumor is important to avoid misdiagnosis and wrong treatment. We expect our model to be a valuable tool in the study of bladder cancer progression due to the exposure to carcinogens and the oxygen dependent expression of genes promoting tumor growth. Our numerical simulations have good qualitative agreement with in vivo results reported in the corresponding medical literature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phase-field modeling of void anisotropic growth behavior in irradiated zirconium

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

Han, G. M.; Wang, H.; Lin, De-Ye

2017-06-01

A three-dimensional (3D) phase field model was developed to study the effects of surface energy and diffusivity anisotropy on void growth behavior in irradiated Zr. The gamma surface energy function, which is used in the phase field model, was developed with the surface energy anisotropy calculated from the molecular dynamics (MD) simulations. It is assumed that vacancies have much larger mobility in c-axis than a- and b- axes while interstitials have much larger mobility in basal plane then that in c-axis. With the model, the equilibrium void morphology and the effect of defect concentrations and defect mobility anisotropy on voidmore » growth behavior were simulated. The simulations demonstrated that 1) The developed phase-field model can correctly reproduce the faceted void morphology predicted by the Wullf construction. 2) With isotropic diffusivity the void prefers to grow on the basal plane. 3) When the vacancy has large mobility along c-axis and interstitial has a large mobility on the basal plane of hexagonal closed packed (hcp) Zr alloys a platelet void grows in c-direction and shrinks on the basal plane, which is in agreement with the experimental observation of void growth behavior in irradiated Zr.« less

A 3-dimensional DTI MRI-based model of GBM growth and response to radiation therapy.

PubMed

Hathout, Leith; Patel, Vishal; Wen, Patrick

2016-09-01

Glioblastoma (GBM) is both the most common and the most aggressive intra-axial brain tumor, with a notoriously poor prognosis. To improve this prognosis, it is necessary to understand the dynamics of GBM growth, response to treatment and recurrence. The present study presents a mathematical diffusion-proliferation model of GBM growth and response to radiation therapy based on diffusion tensor (DTI) MRI imaging. This represents an important advance because it allows 3-dimensional tumor modeling in the anatomical context of the brain. Specifically, tumor infiltration is guided by the direction of the white matter tracts along which glioma cells infiltrate. This provides the potential to model different tumor growth patterns based on location within the brain, and to simulate the tumor's response to different radiation therapy regimens. Tumor infiltration across the corpus callosum is simulated in biologically accurate time frames. The response to radiation therapy, including changes in cell density gradients and how these compare across different radiation fractionation protocols, can be rendered. Also, the model can estimate the amount of subthreshold tumor which has extended beyond the visible MR imaging margins. When combined with the ability of being able to estimate the biological parameters of invasiveness and proliferation of a particular GBM from serial MRI scans, it is shown that the model has potential to simulate realistic tumor growth, response and recurrence patterns in individual patients. To the best of our knowledge, this is the first presentation of a DTI-based GBM growth and radiation therapy treatment model.

Modeling the Gas Nitriding Process of Low Alloy Steels

NASA Astrophysics Data System (ADS)

Yang, M.; Zimmerman, C.; Donahue, D.; Sisson, R. D.

2013-07-01

The effort to simulate the nitriding process has been ongoing for the last 20 years. Most of the work has been done to simulate the nitriding process of pure iron. In the present work a series of experiments have been done to understand the effects of the nitriding process parameters such as the nitriding potential, temperature, and time as well as surface condition on the gas nitriding process for the steels. The compound layer growth model has been developed to simulate the nitriding process of AISI 4140 steel. In this paper the fundamentals of the model are presented and discussed including the kinetics of compound layer growth and the determination of the nitrogen diffusivity in the diffusion zone. The excellent agreements have been achieved for both as-washed and pre-oxided nitrided AISI 4140 between the experimental data and simulation results. The nitrogen diffusivity in the diffusion zone is determined to be constant and only depends on the nitriding temperature, which is ~5 × 10-9 cm2/s at 548 °C. It proves the concept of utilizing the compound layer growth model in other steels. The nitriding process of various steels can thus be modeled and predicted in the future.

Modeling Nitrogen Dynamics in a Waste Stabilization Pond System Using Flexible Modeling Environment with MCMC.

PubMed

Mukhtar, Hussnain; Lin, Yu-Pin; Shipin, Oleg V; Petway, Joy R

2017-07-12

This study presents an approach for obtaining realization sets of parameters for nitrogen removal in a pilot-scale waste stabilization pond (WSP) system. The proposed approach was designed for optimal parameterization, local sensitivity analysis, and global uncertainty analysis of a dynamic simulation model for the WSP by using the R software package Flexible Modeling Environment (R-FME) with the Markov chain Monte Carlo (MCMC) method. Additionally, generalized likelihood uncertainty estimation (GLUE) was integrated into the FME to evaluate the major parameters that affect the simulation outputs in the study WSP. Comprehensive modeling analysis was used to simulate and assess nine parameters and concentrations of ON-N, NH₃-N and NO₃-N. Results indicate that the integrated FME-GLUE-based model, with good Nash-Sutcliffe coefficients (0.53-0.69) and correlation coefficients (0.76-0.83), successfully simulates the concentrations of ON-N, NH₃-N and NO₃-N. Moreover, the Arrhenius constant was the only parameter sensitive to model performances of ON-N and NH₃-N simulations. However, Nitrosomonas growth rate, the denitrification constant, and the maximum growth rate at 20 °C were sensitive to ON-N and NO₃-N simulation, which was measured using global sensitivity.

Module-based multiscale simulation of angiogenesis in skeletal muscle

PubMed Central

2011-01-01

Background Mathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem. Results We present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis. Conclusions This systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions. PMID:21463529

Phase-Field Modeling of Polycrystalline Solidification: From Needle Crystals to Spherulites—A Review

NASA Astrophysics Data System (ADS)

Gránásy, László; Rátkai, László; Szállás, Attila; Korbuly, Bálint; Tóth, Gyula I.; Környei, László; Pusztai, Tamás

2014-04-01

Advances in the orientation-field-based phase-field (PF) models made in the past are reviewed. The models applied incorporate homogeneous and heterogeneous nucleation of growth centers and several mechanisms to form new grains at the perimeter of growing crystals, a phenomenon termed growth front nucleation. Examples for PF modeling of such complex polycrystalline structures are shown as impinging symmetric dendrites, polycrystalline growth forms (ranging from disordered dendrites to spherulitic patterns), and various eutectic structures, including spiraling two-phase dendrites. Simulations exploring possible control of solidification patterns in thin films via external fields, confined geometry, particle additives, scratching/piercing the films, etc. are also displayed. Advantages, problems, and possible solutions associated with quantitative PF simulations are discussed briefly.

Multimodel ensembles of wheat growth: many models are better than one

USDA-ARS?s Scientific Manuscript database

Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but suc...

Analyzing The Uncertainty Of Diameter Growth Model Predictions

Treesearch

Ronald E. McRoberts; Veronica C. Lessard; Margaret R. Holdaway

1999-01-01

The North Central Research Station of the USDA Forest Service is developing a new set of individual tree, diameter growth models to be used as a component of an annual forest inventory system. The criterion for selection of predictor variables for these models is the uncertainty in 5-, 10-, and 20-year diameter growth predictions estimated using Monte Carlo simulations...

Plant growth modelling and applications: the increasing importance of plant architecture in growth models.

PubMed

Fourcaud, Thierry; Zhang, Xiaopeng; Stokes, Alexia; Lambers, Hans; Körner, Christian

2008-05-01

Modelling plant growth allows us to test hypotheses and carry out virtual experiments concerning plant growth processes that could otherwise take years in field conditions. The visualization of growth simulations allows us to see directly and vividly the outcome of a given model and provides us with an instructive tool useful for agronomists and foresters, as well as for teaching. Functional-structural (FS) plant growth models are nowadays particularly important for integrating biological processes with environmental conditions in 3-D virtual plants, and provide the basis for more advanced research in plant sciences. In this viewpoint paper, we ask the following questions. Are we modelling the correct processes that drive plant growth, and is growth driven mostly by sink or source activity? In current models, is the importance of soil resources (nutrients, water, temperature and their interaction with meristematic activity) considered adequately? Do classic models account for architectural adjustment as well as integrating the fundamental principles of development? Whilst answering these questions with the available data in the literature, we put forward the opinion that plant architecture and sink activity must be pushed to the centre of plant growth models. In natural conditions, sinks will more often drive growth than source activity, because sink activity is often controlled by finite soil resources or developmental constraints. PMA06: This viewpoint paper also serves as an introduction to this Special Issue devoted to plant growth modelling, which includes new research covering areas stretching from cell growth to biomechanics. All papers were presented at the Second International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA06), held in Beijing, China, from 13-17 November, 2006. Although a large number of papers are devoted to FS models of agricultural and forest crop species, physiological and genetic processes have recently been included and point the way to a new direction in plant modelling research.

A DYNAMIC MODEL OF AN ESTUARINE INVASION BY A NON-NATIVE SEAGRASS

EPA Science Inventory

Mathematical and simulation models provide an excellent tool for examining and predicting biological invasions in time and space; however, traditional models do not incorporate dynamic rates of population growth, which limits their realism. We developed a spatially explicit simul...

Estimating plant available water for general crop simulations in ALMANAC/APEX/EPIC/SWAT

USDA-ARS?s Scientific Manuscript database

Process-based simulation models ALMANAC/APEX/EPIC/SWAT contain generalized plant growth subroutines to predict biomass and crop yield. Environmental constraints typically restrict plant growth and yield. Water stress is often an important limiting factor; it is calculated as the sum of water use f...

Simulated Tree Growth across the Northern Hemisphere and the Seasonality of Climate Signals Encoded within Tree-ring Widths

NASA Astrophysics Data System (ADS)

Li, X.; St George, S.

2013-12-01

Both dendrochronological theory and regional and global networks of tree-ring width measurements indicate that trees can respond to climate variations quite differently from one location to another. To explain these geographical differences at hemispheric scale, we used a process-based model of tree-ring formation (the Vaganov-Shashkin model) to simulate tree growth at over 6000 locations across the Northern Hemisphere. We compared the seasonality and strength of climate signals in the simulated tree-ring records against parallel analysis conducted on a hemispheric network of real tree-ring observations, tested the ability of the model to reproduce behaviors that emerge from large networks of tree-ring widths and used the model outputs to explain why the network exhibits these behaviors. The simulated tree-ring records are consistent with observations with respect to the seasonality and relative strength of the encoded climate signals, and time-related changes in these climate signals can be predicted using the modeled relative growth rate due to temperature or soil moisture. The positive imprint of winter (DJF) precipitation is strongest in simulations from the American Southwest and northern Mexico as well as selected locations in the Mediterranean and central Asia. Summer (JJA) precipitation has higher positive correlations with simulations in the mid-latitudes, but some high-latitude coastal sites exhibit a negative association. The influence of summer temperature is mainly positive at high-latitude or high-altitude sites and negative in the mid-latitudes. The absolute magnitude of climate correlations are generally higher in simulations than in observations, but the pattern and geographical differences remain the same, demonstrating that the model has skill in reproducing tree-ring growth response to climate variability in the Northern Hemisphere. Because the model uses only temperature, precipitation and latitude as input and is not adjusted for species or other biological factors, the fact that the climate response of the simulations largely agrees with the observations may imply that climate, rather than biology, is the main factor that influences large-scale patterns of the climate information recorded by tree rings. Our results also suggest that the Vaganov-Shashkin model could be used to estimate the likely climate response of trees in ';frontier' areas that have not been sampled extensively. Seasonal Climate Correlations of Simulated Tree-ring Records

Geographic variation in Pacific herring growth in response to regime shifts in the North Pacific Ocean

NASA Astrophysics Data System (ADS)

Ito, Shin-ichi; Rose, Kenneth A.; Megrey, Bernard A.; Schweigert, Jake; Hay, Douglas; Werner, Francisco E.; Aita, Maki Noguchi

2015-11-01

Pacific herring populations at eight North Pacific Rim locations were simulated to compare basin-wide geographic variations in age-specific growth due to environmental influences on marine productivity and population-specific responses to regime shifts. Temperature and zooplankton abundance from a three-dimensional lower-trophic ecosystem model (NEMURO: North Pacific Ecosystem Model for Understanding Regional Oceanography) simulation from 1948 to 2002 were used as inputs to a herring bioenergetics growth model. Herring populations from California, the west coast of Vancouver Island (WCVI), Prince William Sound (PWS), Togiak Alaska, the western Bering Sea (WBS), the Sea of Okhotsk (SO), Sakhalin, and Peter the Great Bay (PGB) were examined. The half-saturation coefficients of herring feeding were calibrated to climatological conditions at each of the eight locations to reproduce averaged size-at-age data. The depth of averaging used for water temperature and zooplankton, and the maximum consumption rate parameter, were made specific to each location. Using the calibrated half-saturation coefficients, the 1948-2002 period was then simulated using daily values of water temperature and zooplankton densities interpolated from monthly model output. To detect regime shifts in simulated temperatures, zooplankton and herring growth rates, we applied sequential t-test analyses on the 54 years of hindcast simulation values. The detected shifts of herring age-5 growth showed closest match (69%) to the regime shift years (1957/58, 1970/71, 1976/77, 1988/89, 1998/99). We explored relationships among locations using cluster and principal component analyses. The first principal component of water temperature showed good correspondence to the Pacific Decadal Oscillation and all zooplankton groups showed a pan-Pacific decrease after the 1976/77 regime shift. However, the first principal component of herring growth rate showed decreased growth at the SO, PWS, WCVI and California locations and increased growth at the Sakhalin, WBS and Togiak locations after 1977. The SO location belonged to the same cluster as the location in with the eastern North Pacific. The calibrated half-saturation coefficients affected the degree to which growth was sensitive to interannual variation in water temperature versus zooplankton. For example, the half-saturation values for the SO location resulted in very efficient feeding that shifted the sensitivity of herring growth from food to temperature. The model results demonstrate how geographic specificity of bioenergetics parameters, coupled with location-specific variation in temperature and food, can combine to determine local and regional responses of fish growth to climate forcing.

Asymmetric Eyewall Vertical Motion in a High-Resolution Simulation of Hurricane Bonnie (1998)

NASA Technical Reports Server (NTRS)

Braun, Scott A.; Montgomery, Michael T.; Pu, Zhao-Xia

2003-01-01

This study examines a high-resolution simulation of Hurricane Bonnie. Results from the simulation will be compared to the conceptual model of Heymsfield et al. (2001) to determine the extent to which this conceptual model explains vertical motions and precipitation growth in the eyewall.

Improving plot- and regional-scale crop models for simulating impacts of climate variability and extremes

NASA Astrophysics Data System (ADS)

Tao, F.; Rötter, R.

2013-12-01

Many studies on global climate report that climate variability is increasing with more frequent and intense extreme events1. There are quite large uncertainties from both the plot- and regional-scale models in simulating impacts of climate variability and extremes on crop development, growth and productivity2,3. One key to reducing the uncertainties is better exploitation of experimental data to eliminate crop model deficiencies and develop better algorithms that more adequately capture the impacts of extreme events, such as high temperature and drought, on crop performance4,5. In the present study, in a first step, the inter-annual variability in wheat yield and climate from 1971 to 2012 in Finland was investigated. Using statistical approaches the impacts of climate variability and extremes on wheat growth and productivity were quantified. In a second step, a plot-scale model, WOFOST6, and a regional-scale crop model, MCWLA7, were calibrated and validated, and applied to simulate wheat growth and yield variability from 1971-2012. Next, the estimated impacts of high temperature stress, cold damage, and drought stress on crop growth and productivity based on the statistical approaches, and on crop simulation models WOFOST and MCWLA were compared. Then, the impact mechanisms of climate extremes on crop growth and productivity in the WOFOST model and MCWLA model were identified, and subsequently, the various algorithm and impact functions were fitted against the long-term crop trial data. Finally, the impact mechanisms, algorithms and functions in WOFOST model and MCWLA model were improved to better simulate the impacts of climate variability and extremes, particularly high temperature stress, cold damage and drought stress for location-specific and large area climate impact assessments. Our studies provide a good example of how to improve, in parallel, the plot- and regional-scale models for simulating impacts of climate variability and extremes, as needed for better informed decision-making on adaptation strategies. References 1. Coumou, D. & Rahmstorf, S. A decade of extremes. Nature Clim. Change, 2, 491-496 (2012). 2. Rötter, R. P., Carter, T. R., Olesen, J. E. & Porter, J. R. Crop-climate models need an overhaul. Nature Clim. Change, 1, 175-177 (2011). 3. Asseng, S. et al., Uncertainty in simulating wheat yields under climate change. Nature Clim. Change. 10.1038/nclimate1916. (2013). 4. Porter, J.R., & Semenov, M., Crop responses to climatic variation . Trans. R. Soc. B., 360, 2021-2035 (2005). 5. Porter, J.R. & Christensen, S. Deconstructing crop processes and models via identities. Plant, Cell and Environment . doi: 10.1111/pce.12107 (2013). 6. Boogaard, H.L., van Diepen C.A., Rötter R.P., Cabrera J.M. & van Laar H.H. User's guide for the WOFOST 7.1 crop growth simulation model and Control Center 1.5, Alterra, Wageningen, The Netherlands. (1998) 7. Tao, F. & Zhang, Z. Climate change, wheat productivity and water use in the North China Plain: a new super-ensemble-based probabilistic projection. Agric. Forest Meteorol., 170, 146-165. (2013).

Contribution of different generations of the brown shrimp Crangon crangon (L.) in the Dutch Wadden Sea to commercial fisheries: A dynamic energy budget approach

NASA Astrophysics Data System (ADS)

Campos, Joana; Van der Veer, Henk W.; Freitas, Vânia; Kooijman, Sebastiaan A. L. M.

2009-08-01

In this paper a contribution is made to the ongoing debate on which brown shrimp generation mostly sustains the autumn peak in coastal North Sea commercial fisheries: the generation born in summer, or the winter one. Since the two perspectives are based on different considerations on the growth timeframe from settlement till commercial size, the Dynamic Energy Budget (DEB) theory was applied to predict maximum possible growth under natural conditions. First, the parameters of the standard DEB model for Crangon crangon L. were estimated using available data sets. These were insufficient to allow a direct estimation, requiring a special protocol to achieve consistency between parameters. Next, the DEB model was validated by comparing simulations with published experimental data on shrimp growth in relation to water temperatures. Finally, the DEB model was applied to simulate growth under optimal food conditions using the prevailing water temperature conditions in the Wadden Sea. Results show clear differences between males and females whereby the fastest growth rates were observed in females. DEB model simulations of maximum growth in the Wadden Sea suggest that it is not the summer brood from the current year as Boddeke claimed, nor the previous winter generation as Kuipers and Dapper suggested, but more likely the summer generation from the previous year which contributes to the bulk of the fisheries recruits in autumn.

Importance of growth rate on mercury and polychlorinated biphenyl bioaccumulation in fish

USGS Publications Warehouse

Li, Jiajia; Haffner, G. Douglas; Patterson, Gordon; Walters, David M.; Burtnyk, Michael D.; Drouillard, Ken G.

2018-01-01

To evaluate the effect of fish growth on mercury (Hg) and polychlorinated biphenyl (PCB) bioaccumulation, a non–steady‐state toxicokinetic model, combined with a Wisconsin bioenergetics model, was developed to simulate Hg and PCB bioaccumulation in bluegill (Lepomis macrochirus). The model was validated by comparing observed with predicted Hg and PCB 180 concentrations across 5 age classes from 5 different waterbodies across North America. The non–steady‐state model generated accurate predictions for Hg and PCB bioaccumulation in 3 of 5 waterbodies: Apsey Lake (ON, Canada), Sharbot Lake (ON, Canada), and Stonelick Lake (OH, USA). The poor performance of the model for the Detroit River (MI, USA/ON, Canada) and Lake Hartwell (GA/SC, USA), which are 2 well‐known contaminated sites with possibly high heterogeneity in spatial contamination, was attributed to changes in feeding behavior and/or prey contamination. Model simulations indicate that growth dilution is a major component of contaminant bioaccumulation patterns in fish, especially during early life stages, and was predicted to be more important for hydrophobic PCBs than for Hg. Simulations that considered tissue‐specific growth provided some improvement in model performance particularly for PCBs in fish populations that exhibited changes in their whole‐body lipid content with age. Higher variation in lipid growth compared with that of lean dry protein was also observed between different bluegill populations, which partially explains the greater variation in PCB bioaccumulation slopes compared with Hg across sampling sites.

Reverse engineering the kidney: modelling calcium oxalate monohydrate crystallization in the nephron.

PubMed

Borissova, A; Goltz, G E; Kavanagh, J P; Wilkins, T A

2010-07-01

Crystallization of calcium oxalate monohydrate in a section of a single kidney nephron (distal convoluted tubule) is simulated using a model adapted from industrial crystallization. The nephron fluid dynamics is represented as a crystallizer/separator series with changing volume to allow for water removal along the tubule. The model integrates crystallization kinetics and crystal size distribution and allows the prediction of the calcium oxalate concentration profile and the nucleation and growth rates. The critical supersaturation ratio for the nucleation of calcium oxalate crystals has been estimated as 2 and the mean crystal size as 1 mum. The crystal growth order, determined as 2.2, indicates a surface integration mechanism of crystal growth and crystal growth dispersion. The model allows the exploration of the effect of varying the input calcium oxalate concentration and the rate of water extraction, simulating real life stressors for stone formation such as dietary loading and dehydration.

Simulating Thin Sheets: Buckling, Wrinkling, Folding and Growth

NASA Astrophysics Data System (ADS)

Vetter, Roman; Stoop, Norbert; Wittel, Falk K.; Herrmann, Hans J.

2014-03-01

Numerical simulations of thin sheets undergoing large deformations are computationally challenging. Depending on the scenario, they may spontaneously buckle, wrinkle, fold, or crumple. Nature's thin tissues often experience significant anisotropic growth, which can act as the driving force for such instabilities. We use a recently developed finite element model to simulate the rich variety of nonlinear responses of Kirchhoff-Love sheets. The model uses subdivision surface shape functions in order to guarantee convergence of the method, and to allow a finite element description of anisotropically growing sheets in the classical Rayleigh-Ritz formalism. We illustrate the great potential in this approach by simulating the inflation of airbags, the buckling of a stretched cylinder, as well as the formation and scaling of wrinkles at free boundaries of growing sheets. Finally, we compare the folding of spatially confined sheets subject to growth and shrinking confinement to find that the two processes are equivalent.

A model analysis of climate and CO2 controls on tree growth in a semi-arid woodland

NASA Astrophysics Data System (ADS)

Li, G.; Harrison, S. P.; Prentice, I. C.

2015-03-01

We used a light-use efficiency model of photosynthesis coupled with a dynamic carbon allocation and tree-growth model to simulate annual growth of the gymnosperm Callitris columellaris in the semi-arid Great Western Woodlands, Western Australia, over the past 100 years. Parameter values were derived from independent observations except for sapwood specific respiration rate, fine-root turnover time, fine-root specific respiration rate and the ratio of fine-root mass to foliage area, which were estimated by Bayesian optimization. The model reproduced the general pattern of interannual variability in radial growth (tree-ring width), including the response to the shift in precipitation regimes that occurred in the 1960s. Simulated and observed responses to climate were consistent. Both showed a significant positive response of tree-ring width to total photosynthetically active radiation received and to the ratio of modeled actual to equilibrium evapotranspiration, and a significant negative response to vapour pressure deficit. However, the simulations showed an enhancement of radial growth in response to increasing atmospheric CO2 concentration (ppm) ([CO2]) during recent decades that is not present in the observations. The discrepancy disappeared when the model was recalibrated on successive 30-year windows. Then the ratio of fine-root mass to foliage area increases by 14% (from 0.127 to 0.144 kg C m-2) as [CO2] increased while the other three estimated parameters remained constant. The absence of a signal of increasing [CO2] has been noted in many tree-ring records, despite the enhancement of photosynthetic rates and water-use efficiency resulting from increasing [CO2]. Our simulations suggest that this behaviour could be explained as a consequence of a shift towards below-ground carbon allocation.

Kinetic Monte Carlo simulations of nucleation and growth in electrodeposition.

PubMed

Guo, Lian; Radisic, Aleksandar; Searson, Peter C

2005-12-22

Nucleation and growth during bulk electrodeposition is studied using kinetic Monte Carlo (KMC) simulations. Ion transport in solution is modeled using Brownian dynamics, and the kinetics of nucleation and growth are dependent on the probabilities of metal-on-substrate and metal-on-metal deposition. Using this approach, we make no assumptions about the nucleation rate, island density, or island distribution. The influence of the attachment probabilities and concentration on the time-dependent island density and current transients is reported. Various models have been assessed by recovering the nucleation rate and island density from the current-time transients.

Simulation of Delamination Under High Cycle Fatigue in Composite Materials Using Cohesive Models

NASA Technical Reports Server (NTRS)

Camanho, Pedro P.; Turon, Albert; Costa, Josep; Davila, Carlos G.

2006-01-01

A new thermodynamically consistent damage model is proposed for the simulation of high-cycle fatigue crack growth. The basis for the formulation is an interfacial degradation law that links Fracture Mechanics and Damage Mechanics to relate the evolution of the damage variable, d, with the crack growth rate da/dN. The damage state is a function of the loading conditions (R and (Delta)G) as well as the experimentally-determined crack growth rates for the material. The formulation ensures that the experimental results can be reproduced by the analysis without the need of additional adjustment parameters.

Calibrating and testing a gap model for simulating forest management in the Oregon Coast Range

USGS Publications Warehouse

Pabst, R.J.; Goslin, M.N.; Garman, S.L.; Spies, T.A.

2008-01-01

The complex mix of economic and ecological objectives facing today's forest managers necessitates the development of growth models with a capacity for simulating a wide range of forest conditions while producing outputs useful for economic analyses. We calibrated the gap model ZELIG to simulate stand-level forest development in the Oregon Coast Range as part of a landscape-scale assessment of different forest management strategies. Our goal was to incorporate the predictive ability of an empirical model with the flexibility of a forest succession model. We emphasized the development of commercial-aged stands of Douglas-fir, the dominant tree species in the study area and primary source of timber. In addition, we judged that the ecological approach of ZELIG would be robust to the variety of other forest conditions and practices encountered in the Coast Range, including mixed-species stands, small-scale gap formation, innovative silvicultural methods, and reserve areas where forests grow unmanaged for long periods of time. We parameterized the model to distinguish forest development among two ecoregions, three forest types and two site productivity classes using three data sources: chronosequences of forest inventory data, long-term research data, and simulations from an empirical growth-and-yield model. The calibrated model was tested with independent, long-term measurements from 11 Douglas-fir plots (6 unthinned, 5 thinned), 3 spruce-hemlock plots, and 1 red alder plot. ZELIG closely approximated developmental trajectories of basal area and large trees in the Douglas-fir plots. Differences between simulated and observed conifer basal area for these plots ranged from -2.6 to 2.4 m2/ha; differences in the number of trees/ha ???50 cm dbh ranged from -8.8 to 7.3 tph. Achieving these results required the use of a diameter-growth multiplier, suggesting some underlying constraints on tree growth such as the temperature response function. ZELIG also tended to overestimate regeneration of shade-tolerant trees and underestimate total tree density (i.e., higher rates of tree mortality). However, comparisons with the chronosequences of forest inventory data indicated that the simulated data are within the range of variability observed in the Coast Range. Further exploration and improvement of ZELIG is warranted in three key areas: (1) modeling rapid rates of conifer tree growth without the need for a diameter-growth multiplier; (2) understanding and remedying rates of tree mortality that were higher than those observed in the independent data; and (3) improving the tree regeneration module to account for competition with understory vegetation. ?? 2008 Elsevier B.V.

A unified theory for ice vapor growth suitable for cloud models: Testing and implications for cold cloud evolution

NASA Astrophysics Data System (ADS)

Zhang, Chengzhu

A new microphysical model for the vapor growth and aspect ratio evolution of atmospheric ice crystals is presented. The method is based on the adaptive habit model of Chen and Lamb (1994), but is modified to include surface kinetic processes for crystal growth. Inclusion of surface kinetic effects is accomplished with a new theory that accounts for axis dependent growth. Deposition coefficients (growth efficiencies) are predicted for two axis directions based on laboratory-determined parameters for growth initiation (critical supersaturations) on each face. In essence, the new theory extends the adaptive habit approach of Chen and Lamb (1994) to ice saturation states below that of liquid saturation, where Chen and Lamb (1994) is likely most valid. The new model is used to simulate changes in crystal primary habit as a function of temperature and ice supersaturation. Predictions are compared with a detailed hexagonal growth model both in a single particle framework and in a Lagrangian parcel model to indicate the accuracy of the new method. Moreover, predictions of the ratio of the axis deposition coefficients match laboratory-generated data. A parameterization for predicting deposition coefficients is developed for the bulk microphysics frame work in Regional Atmospheric Modeling System (RAMS). Initial eddy-resolving model simulation is conducted to study the effect of surface kinetics on microphysical and dynamical processes in cold cloud development.

Local rules simulation of the kinetics of virus capsid self-assembly.

PubMed

Schwartz, R; Shor, P W; Prevelige, P E; Berger, B

1998-12-01

A computer model is described for studying the kinetics of the self-assembly of icosahedral viral capsids. Solution of this problem is crucial to an understanding of the viral life cycle, which currently cannot be adequately addressed through laboratory techniques. The abstract simulation model employed to address this is based on the local rules theory of. Proc. Natl. Acad. Sci. USA. 91:7732-7736). It is shown that the principle of local rules, generalized with a model of kinetics and other extensions, can be used to simulate complicated problems in self-assembly. This approach allows for a computationally tractable molecular dynamics-like simulation of coat protein interactions while retaining many relevant features of capsid self-assembly. Three simple simulation experiments are presented to illustrate the use of this model. These show the dependence of growth and malformation rates on the energetics of binding interactions, the tolerance of errors in binding positions, and the concentration of subunits in the examples. These experiments demonstrate a tradeoff within the model between growth rate and fidelity of assembly for the three parameters. A detailed discussion of the computational model is also provided.

Enhancing dendritic cell immunotherapy for melanoma using a simple mathematical model.

PubMed

Castillo-Montiel, E; Chimal-Eguía, J C; Tello, J Ignacio; Piñon-Zaráte, G; Herrera-Enríquez, M; Castell-Rodríguez, A E

2015-06-09

The immunotherapy using dendritic cells (DCs) against different varieties of cancer is an approach that has been previously explored which induces a specific immune response. This work presents a mathematical model of DCs immunotherapy for melanoma in mice based on work by Experimental Immunotherapy Laboratory of the Medicine Faculty in the Universidad Autonoma de Mexico (UNAM). The model is a five delay differential equation (DDEs) which represents a simplified view of the immunotherapy mechanisms. The mathematical model takes into account the interactions between tumor cells, dendritic cells, naive cytotoxic T lymphocytes cells (inactivated cytotoxic cells), effector cells (cytotoxic T activated cytotoxic cells) and transforming growth factor β cytokine (T G F-β). The model is validated comparing the computer simulation results with biological trial results of the immunotherapy developed by the research group of UNAM. The results of the growth of tumor cells obtained by the control immunotherapy simulation show a similar amount of tumor cell population than the biological data of the control immunotherapy. Moreover, comparing the increase of tumor cells obtained from the immunotherapy simulation and the biological data of the immunotherapy applied by the UNAM researchers obtained errors of approximately 10 %. This allowed us to use the model as a framework to test hypothetical treatments. The numerical simulations suggest that by using more doses of DCs and changing the infusion time, the tumor growth decays compared with the current immunotherapy. In addition, a local sensitivity analysis is performed; the results show that the delay in time " τ", the maximal growth rate of tumor "r" and the maximal efficiency of tumor cytotoxic cells rate "aT" are the most sensitive model parameters. By using this mathematical model it is possible to simulate the growth of the tumor cells with or without immunotherapy using the infusion protocol of the UNAM researchers, to obtain a good approximation of the biological trials data. It is worth mentioning that by manipulating the different parameters of the model the effectiveness of the immunotherapy may increase. This last suggests that different protocols could be implemented by the Immunotherapy Laboratory of UNAM in order to improve their results.

Integration of Genetic Algorithms and Fuzzy Logic for Urban Growth Modeling

NASA Astrophysics Data System (ADS)

Foroutan, E.; Delavar, M. R.; Araabi, B. N.

2012-07-01

Urban growth phenomenon as a spatio-temporal continuous process is subject to spatial uncertainty. This inherent uncertainty cannot be fully addressed by the conventional methods based on the Boolean algebra. Fuzzy logic can be employed to overcome this limitation. Fuzzy logic preserves the continuity of dynamic urban growth spatially by choosing fuzzy membership functions, fuzzy rules and the fuzzification-defuzzification process. Fuzzy membership functions and fuzzy rule sets as the heart of fuzzy logic are rather subjective and dependent on the expert. However, due to lack of a definite method for determining the membership function parameters, certain optimization is needed to tune the parameters and improve the performance of the model. This paper integrates genetic algorithms and fuzzy logic as a genetic fuzzy system (GFS) for modeling dynamic urban growth. The proposed approach is applied for modeling urban growth in Tehran Metropolitan Area in Iran. Historical land use/cover data of Tehran Metropolitan Area extracted from the 1988 and 1999 Landsat ETM+ images are employed in order to simulate the urban growth. The extracted land use classes of the year 1988 include urban areas, street, vegetation areas, slope and elevation used as urban growth physical driving forces. Relative Operating Characteristic (ROC) curve as an fitness function has been used to evaluate the performance of the GFS algorithm. The optimum membership function parameter is applied for generating a suitability map for the urban growth. Comparing the suitability map and real land use map of 1999 gives the threshold value for the best suitability map which can simulate the land use map of 1999. The simulation outcomes in terms of kappa of 89.13% and overall map accuracy of 95.58% demonstrated the efficiency and reliability of the proposed model.

Direct dynamic kinetic analysis and computer simulation of growth of Clostridium perfringens in cooked turkey during cooling

USDA-ARS?s Scientific Manuscript database

This research applied a new one-step methodology to directly construct a tertiary model for describing the growth of C. perfringens in cooked turkey meat under dynamically cooling conditions. The kinetic parameters of the growth models were determined by numerical analysis and optimization using mu...

The microcomputer scientific software series 6: ECOPHYS user's manual.

Treesearch

George E. Host; H. Michael Rauscher; J. G. Isebrands; Donald I. Dickmann; Richard E. Dickson; Thomas R. Crow; D.A. Michael

1990-01-01

ECOPHYS is an ecophysiological whole-tree growth process model designed to simulate the growth of poplar in the establishment year. This microcomputer-based model may be used to test the influence of genetically determined physiological or morphological attributes on plant growth. This manual describes the installation, file structures, and operational procedures for...

Meteorological Simulations of Ozone Episode Case Days during the 1996 Paso del Norte Ozone Study

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

Brown, M.J.; Costigan, K.; Muller, C.

1999-02-01

Meteorological simulations centered around the border cities of El Paso and Ciudad Juarez have been performed during an ozone episode that occurred on Aug. 13,1996 during the 1996 Paso del Norte Ozone Study field campaign. Simulations were petiormed using the HOTMAC mesoscale meteorological model using a 1,2,4, and 8 km horizontal grid size nested mesh system. Investigation of the vertical structure and evolution of the atmospheric boundary layer for the Aug. 11-13 time period is emphasized in this paper. Comparison of model-produced wind speed profiles to rawirisonde and radar profiler measurements shows reasonable agreement. A persistent upper-level jet was capturedmore » in the model simulations through data assimilation. In the evening hours, the model was not able to produce the strong wind direction shear seen in the radar wind profiles. Based on virtual potential temperature profile comparisons, the model appears to correctly simulate the daytime growth of the convective mixed layer. However, the model underestimates the cooling of the surface layer at night. We found that the upper-level jet significantly impacted the turbulence structure of the boundary layer, leading to relatively high turbulent kinetic energy (tke) values aloft at night. The model indicates that these high tke values aloft enhance the mid-morning growth of the boundary layer. No upper-level turbulence measurements were available to verify this finding, however. Radar profiler-derived mixing heights do indicate relatively rapid morning growth of the mixed layer.« less

Three dimensional modeling of cirrus during the 1991 FIRE IFO 2: Detailed process study

NASA Technical Reports Server (NTRS)

Jensen, Eric J.; Toon, Owen B.; Westphal, Douglas L.

1993-01-01

A three-dimensional model of cirrus cloud formation and evolution, including microphysical, dynamical, and radiative processes, was used to simulate cirrus observed in the FIRE Phase 2 Cirrus field program (13 Nov. - 7 Dec. 1991). Sulfate aerosols, solution drops, ice crystals, and water vapor are all treated as interactive elements in the model. Ice crystal size distributions are fully resolved based on calculations of homogeneous freezing of solution drops, growth by water vapor deposition, evaporation, aggregation, and vertical transport. Visible and infrared radiative fluxes, and radiative heating rates are calculated using the two-stream algorithm described by Toon et al. Wind velocities, diffusion coefficients, and temperatures were taken from the MAPS analyses and the MM4 mesoscale model simulations. Within the model, moisture is transported and converted to liquid or vapor by the microphysical processes. The simulated cloud bulk and microphysical properties are shown in detail for the Nov. 26 and Dec. 5 case studies. Comparisons with lidar, radar, and in situ data are used to determine how well the simulations reproduced the observed cirrus. The roles played by various processes in the model are described in detail. The potential modes of nucleation are evaluated, and the importance of small-scale variations in temperature and humidity are discussed. The importance of competing ice crystal growth mechanisms (water vapor deposition and aggregation) are evaluated based on model simulations. Finally, the importance of ice crystal shape for crystal growth and vertical transport of ice are discussed.

Growing C4 perennial grass for bioenergy using a new Agro-BGC ecosystem model

NASA Astrophysics Data System (ADS)

di Vittorio, A. V.; Anderson, R. S.; Miller, N. L.; Running, S. W.

2009-12-01

Accurate, spatially gridded estimates of bioenergy crop yields require 1) biophysically accurate crop growth models and 2) careful parameterization of unavailable inputs to these models. To meet the first requirement we have added the capacity to simulate C4 perennial grass as a bioenergy crop to the Biome-BGC ecosystem model. This new model, hereafter referred to as Agro-BGC, includes enzyme driven C4 photosynthesis, individual live and dead leaf, stem, and root carbon/nitrogen pools, separate senescence and litter fall processes, fruit growth, optional annual seeding, flood irrigation, a growing degree day phenology with a killing frost option, and a disturbance handler that effectively simulates fertilization, harvest, fire, and incremental irrigation. There are four Agro-BGC vegetation parameters that are unavailable for Panicum virgatum (switchgrass), and to meet the second requirement we have optimized the model across multiple calibration sites to obtain representative values for these parameters. We have verified simulated switchgrass yields against observations at three non-calibration sites in IL. Agro-BGC simulates switchgrass growth and yield at harvest very well at a single site. Our results suggest that a multi-site optimization scheme would be adequate for producing regional-scale estimates of bioenergy crop yields on high spatial resolution grids.

Compressible homogeneous shear: Simulation and modeling

NASA Technical Reports Server (NTRS)

Sarkar, S.; Erlebacher, G.; Hussaini, M. Y.

1992-01-01

Compressibility effects were studied on turbulence by direct numerical simulation of homogeneous shear flow. A primary observation is that the growth of the turbulent kinetic energy decreases with increasing turbulent Mach number. The sinks provided by compressible dissipation and the pressure dilatation, along with reduced Reynolds shear stress, are shown to contribute to the reduced growth of kinetic energy. Models are proposed for these dilatational terms and verified by direct comparison with the simulations. The differences between the incompressible and compressible fields are brought out by the examination of spectra, statistical moments, and structure of the rate of strain tensor.

Compressible homogeneous shear - Simulation and modeling

NASA Technical Reports Server (NTRS)

Sarkar, S.; Erlebacher, G.; Hussaini, M. Y.

1991-01-01

Compressibility effects were studied on turbulence by direct numerical simulation of homogeneous shear flow. A primary observation is that the growth of the turbulent kinetic energy decreases with increasing turbulent Mach number. The sinks provided by compressible dissipation and the pressure dilatation, along with reduced Reynolds shear stress, are shown to contribute to the reduced growth of kinetic energy. Models are proposed for these dilatational terms and verified by direct comparison with the simulations. The differences between the incompressible and compressible fields are brought out by the examination of spectra, statistical moments, and structure of the rate of strain tensor.

Kinetics modeling of precipitation with characteristic shape during post-implantation annealing

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

Li, Kun-Dar, E-mail: kundar@mail.nutn.edu.tw; Chen, Kwanyu

2015-11-15

In this study, we investigated the precipitation with characteristic shape in the microstructure during post-implantation annealing via a theoretical modeling approach. The processes of precipitates formation and evolution during phase separation were based on a nucleation and growth mechanism of atomic diffusion. Different stages of the precipitation, including the nucleation, growth and coalescence, were distinctly revealed in the numerical simulations. In addition, the influences of ion dose, temperature and crystallographic symmetry on the processes of faceted precipitation were also demonstrated. To comprehend the kinetic mechanism, the simulation results were further analyzed quantitatively by the Kolmogorov-Johnson-Mehl-Avrami (KJMA) equation. The Avrami exponentsmore » obtained from the regression curves varied from 1.47 to 0.52 for different conditions. With the increase of ion dose and temperature, the nucleation and growth of precipitations were expedited in accordance with the shortened incubation time and the raised coefficient of growth rate. A miscellaneous shape of precipitates in various crystallographic symmetry systems could be simulated through this anisotropic model. From the analyses of the kinetics, more fundamental information about the nucleation and growth mechanism of faceted precipitation during post-implantation annealing was acquired for future application.« less

An Object-Oriented Finite Element Framework for Multiphysics Phase Field Simulations

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

Michael R Tonks; Derek R Gaston; Paul C Millett

2012-01-01

The phase field approach is a powerful and popular method for modeling microstructure evolution. In this work, advanced numerical tools are used to create a phase field framework that facilitates rapid model development. This framework, called MARMOT, is based on Idaho National Laboratory's finite element Multiphysics Object-Oriented Simulation Environment. In MARMOT, the system of phase field partial differential equations (PDEs) are solved simultaneously with PDEs describing additional physics, such as solid mechanics and heat conduction, using the Jacobian-Free Newton Krylov Method. An object-oriented architecture is created by taking advantage of commonalities in phase fields models to facilitate development of newmore » models with very little written code. In addition, MARMOT provides access to mesh and time step adaptivity, reducing the cost for performing simulations with large disparities in both spatial and temporal scales. In this work, phase separation simulations are used to show the numerical performance of MARMOT. Deformation-induced grain growth and void growth simulations are included to demonstrate the muliphysics capability.« less

Influence of magnetic flutter on tearing growth in linear and nonlinear theory

NASA Astrophysics Data System (ADS)

Kreifels, L.; Hornsby, W. A.; Weikl, A.; Peeters, A. G.

2018-06-01

Recent simulations of tearing modes in turbulent regimes show an unexpected enhancement in the growth rate. In this paper the effect is investigated analytically. The enhancement is linked to the influence of turbulent magnetic flutter, which is modelled by diffusion terms in magnetohydrodynamics (MHD) momentum balance and Ohm’s law. Expressions for the linear growth rate as well as the island width in nonlinear theory for small amplitudes are derived. The results indicate an enhanced linear growth rate and a larger linear layer width compared with resistive MHD. Also the island width in the nonlinear regime grows faster in the diffusive model. These observations correspond well to simulations in which the effect of turbulence on the magnetic island width and tearing mode growth is analyzed.

Direct simulation Monte Carlo investigation of the Rayleigh-Taylor instability

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

Gallis, M. A.; Koehler, T. P.; Torczynski, J. R.

In this paper, the Rayleigh-Taylor instability (RTI) is investigated using the direct simulation Monte Carlo (DSMC) method of molecular gas dynamics. Here, fully resolved two-dimensional DSMC RTI simulations are performed to quantify the growth of flat and single-mode perturbed interfaces between two atmospheric-pressure monatomic gases as a function of the Atwood number and the gravitational acceleration. The DSMC simulations reproduce many qualitative features of the growth of the mixing layer and are in reasonable quantitative agreement with theoretical and empirical models in the linear, nonlinear, and self-similar regimes. In some of the simulations at late times, the instability enters themore » self-similar regime, in agreement with experimental observations. Finally, for the conditions simulated, diffusion can influence the initial instability growth significantly.« less

Direct simulation Monte Carlo investigation of the Rayleigh-Taylor instability

DOE PAGES

Gallis, M. A.; Koehler, T. P.; Torczynski, J. R.; ...

2016-08-31

In this paper, the Rayleigh-Taylor instability (RTI) is investigated using the direct simulation Monte Carlo (DSMC) method of molecular gas dynamics. Here, fully resolved two-dimensional DSMC RTI simulations are performed to quantify the growth of flat and single-mode perturbed interfaces between two atmospheric-pressure monatomic gases as a function of the Atwood number and the gravitational acceleration. The DSMC simulations reproduce many qualitative features of the growth of the mixing layer and are in reasonable quantitative agreement with theoretical and empirical models in the linear, nonlinear, and self-similar regimes. In some of the simulations at late times, the instability enters themore » self-similar regime, in agreement with experimental observations. Finally, for the conditions simulated, diffusion can influence the initial instability growth significantly.« less

Temporal slow-growth formulation for direct numerical simulation of compressible wall-bounded flows

NASA Astrophysics Data System (ADS)

Topalian, Victor; Oliver, Todd A.; Ulerich, Rhys; Moser, Robert D.

2017-08-01

A slow-growth formulation for DNS of wall-bounded turbulent flow is developed and demonstrated to enable extension of slow-growth modeling concepts to wall-bounded flows with complex physics. As in previous slow-growth approaches, the formulation assumes scale separation between the fast scales of turbulence and the slow evolution of statistics such as the mean flow. This separation enables the development of approaches where the fast scales of turbulence are directly simulated while the forcing provided by the slow evolution is modeled. The resulting model admits periodic boundary conditions in the streamwise direction, which avoids the need for extremely long domains and complex inflow conditions that typically accompany spatially developing simulations. Further, it enables the use of efficient Fourier numerics. Unlike previous approaches [Guarini, Moser, Shariff, and Wray, J. Fluid Mech. 414, 1 (2000), 10.1017/S0022112000008466; Maeder, Adams, and Kleiser, J. Fluid Mech. 429, 187 (2001), 10.1017/S0022112000002718; Spalart, J. Fluid Mech. 187, 61 (1988), 10.1017/S0022112088000345], the present approach is based on a temporally evolving boundary layer and is specifically tailored to give results for calibration and validation of Reynolds-averaged Navier-Stokes (RANS) turbulence models. The use of a temporal homogenization simplifies the modeling, enabling straightforward extension to flows with complicating features, including cold and blowing walls. To generate data useful for calibration and validation of RANS models, special care is taken to ensure that the mean slow-growth forcing is closed in terms of the mean and other quantities that appear in standard RANS models, ensuring that there is no confounding between typical RANS closures and additional closures required for the slow-growth problem. The performance of the method is demonstrated on two problems: an essentially incompressible, zero-pressure-gradient boundary layer and a transonic boundary layer over a cooled, transpiring wall. The results show that the approach produces flows that are qualitatively similar to other slow-growth methods as well as spatially developing simulations and that the method can be a useful tool in investigating wall-bounded flows with complex physics.

Growth model for uneven-aged loblolly pine stands : simulations and management implications

Treesearch

C.-R. Lin; J. Buongiorno; Jeffrey P. Prestemon; K. E. Skog

1998-01-01

A density-dependent matrix growth model of uneven-aged loblolly pine stands was developed with data from 991 permanent plots in the southern United States. The model predicts the number of pine, soft hardwood, and hard hardwood trees in 13 diameter classes, based on equations for ingrowth, upgrowth, and mortality. Projections of 6 to 10 years agreed with the growth...

FARSITE: a fire area simulator for fire managers

Treesearch

Mark A. Finney

1995-01-01

A fire growth model (FARSITE) has been developed for use on personal computers (PC’s). Because PC’s are commonly used by land and fire managers, this portable platform would be an accustomed means to bring fire growth modeling technology to management applications. The FARSITE model is intended for use in projecting the growth of prescribed natural fires for wilderness...

Modeling winter wheat phenological responses to water deficits in the Unified Plant Growth Model (UPGM) component of the spatially distributed Agricultural Ecosystem Services (AgES) model

USDA-ARS?s Scientific Manuscript database

Accurately predicting phenology in crop simulation models is critical for correctly simulating crop production. While extensive work in modeling phenology has focused on the temperature response function (resulting in robust phenology models), limited work on quantifying the phenological responses t...

Disentangling the Effects of Water Stress on Carbon Acquisition, Vegetative Growth, and Fruit Quality of Peach Trees by Means of the QualiTree Model.

PubMed

Rahmati, Mitra; Mirás-Avalos, José M; Valsesia, Pierre; Lescourret, Françoise; Génard, Michel; Davarynejad, Gholam H; Bannayan, Mohammad; Azizi, Majid; Vercambre, Gilles

2018-01-01

Climate change projections predict warmer and drier conditions. In general, moderate to severe water stress reduce plant vegetative growth and leaf photosynthesis. However, vegetative and reproductive growths show different sensitivities to water deficit. In fruit trees, water restrictions may have serious implications not only on tree growth and yield, but also on fruit quality, which might be improved. Therefore, it is of paramount importance to understand the complex interrelations among the physiological processes involved in within-tree carbon acquisition and allocation, water uptake and transpiration, organ growth, and fruit composition when affected by water stress. This can be studied using process-based models of plant functioning, which allow assessing the sensitivity of various physiological processes to water deficit and their relative impact on vegetative growth and fruit quality. In the current study, an existing fruit-tree model (QualiTree) was adapted for describing the water stress effects on peach ( Prunus persica L. Batsch) vegetative growth, fruit size and composition. First, an energy balance calculation at the fruit-bearing shoot level and a water transfer formalization within the plant were integrated into the model. Next, a reduction function of vegetative growth according to tree water status was added to QualiTree. Then, the model was parameterized and calibrated for a late-maturing peach cultivar ("Elberta") under semi-arid conditions, and for three different irrigation practices. Simulated vegetative and fruit growth variability over time was consistent with observed data. Sugar concentrations in fruit flesh were well simulated. Finally, QualiTree allowed for determining the relative importance of photosynthesis and vegetative growth reduction on carbon acquisition, plant growth and fruit quality under water constrains. According to simulations, water deficit impacted vegetative growth first through a direct effect on its sink strength, and; secondly, through an indirect reducing effect on photosynthesis. Fruit composition was moderately affected by water stress. The enhancements performed in the model broadened its predictive capabilities and proved that QualiTree allows for a better understanding of the water stress effects on fruit-tree functioning and might be useful for designing innovative horticultural practices in a changing climate scenario.

Ignoring Individual Differences in Times of Assessment in Growth Curve Modeling

ERIC Educational Resources Information Center

Coulombe, Patrick; Selig, James P.; Delaney, Harold D.

2016-01-01

Researchers often collect longitudinal data to model change over time in a phenomenon of interest. Inevitably, there will be some variation across individuals in specific time intervals between assessments. In this simulation study of growth curve modeling, we investigate how ignoring individual differences in time points when modeling change over…

Assessment of MARMOT Grain Growth Model

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

Fromm, B.; Zhang, Y.; Schwen, D.

2015-12-01

This report assesses the MARMOT grain growth model by comparing modeling predictions with experimental results from thermal annealing. The purpose here is threefold: (1) to demonstrate the validation approach of using thermal annealing experiments with non-destructive characterization, (2) to test the reconstruction capability and computation efficiency in MOOSE, and (3) to validate the grain growth model and the associated parameters that are implemented in MARMOT for UO 2. To assure a rigorous comparison, the 2D and 3D initial experimental microstructures of UO 2 samples were characterized using non-destructive Synchrotron x-ray. The same samples were then annealed at 2273K for grainmore » growth, and their initial microstructures were used as initial conditions for simulated annealing at the same temperature using MARMOT. After annealing, the final experimental microstructures were characterized again to compare with the results from simulations. So far, comparison between modeling and experiments has been done for 2D microstructures, and 3D comparison is underway. The preliminary results demonstrated the usefulness of the non-destructive characterization method for MARMOT grain growth model validation. A detailed analysis of the 3D microstructures is in progress to fully validate the current model in MARMOT.« less

A Gompertzian model with random effects to cervical cancer growth

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

Mazlan, Mazma Syahidatul Ayuni; Rosli, Norhayati

2015-05-15

In this paper, a Gompertzian model with random effects is introduced to describe the cervical cancer growth. The parameters values of the mathematical model are estimated via maximum likehood estimation. We apply 4-stage Runge-Kutta (SRK4) for solving the stochastic model numerically. The efficiency of mathematical model is measured by comparing the simulated result and the clinical data of the cervical cancer growth. Low values of root mean-square error (RMSE) of Gompertzian model with random effect indicate good fits.

Gompertzian stochastic model with delay effect to cervical cancer growth

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

Mazlan, Mazma Syahidatul Ayuni binti; Rosli, Norhayati binti; Bahar, Arifah

2015-02-03

In this paper, a Gompertzian stochastic model with time delay is introduced to describe the cervical cancer growth. The parameters values of the mathematical model are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic model numerically. The efficiency of mathematical model is measured by comparing the simulated result and the clinical data of cervical cancer growth. Low values of Mean-Square Error (MSE) of Gompertzian stochastic model with delay effect indicate good fits.

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

PubMed

Reilly, Anthony M; Briesen, Heiko

2012-01-21

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

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics.

PubMed

de Buyl, Pierre; Nies, Erik

2015-04-07

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics

NASA Astrophysics Data System (ADS)

de Buyl, Pierre; Nies, Erik

2015-04-01

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

Environmental influences on speleothem growth in southwestern Oregon during the last 380, 000 years

USGS Publications Warehouse

Ersek, Vasile; Hostetler, Steven W.; Cheng, Hai; Clark, Peter U.; Anslow, Faron S.; Mix, Alan C.; Edwards, R. Lawrence

2009-01-01

The growth of carbonate formations in caves (speleothems) is sensitive to changes in environmental conditions at the surface (temperature, precipitation and vegetation) and can provide useful paleoclimatic and paleoenvironmental information. We use 73 230Th dates from speleothems collected from a cave in southwestern Oregon (USA) to constrain speleothem growth for the past 380 000 years. Most speleothem growth occurred during interglacial periods, whereas little growth occurred during glacial intervals. To evaluate potential environmental controls on speleothem growth we use two new modeling approaches: i) a one-dimensional thermal advection–diffusion model to estimate cave temperatures during the last glacial cycle, and ii) a regional climate model simulation for the Last Glacial Maximum (21 000 years before present) that assesses a range of potential controls on speleothem growth under peak glacial conditions. The two models are mutually consistent in indicating that permafrost formation did not influence speleothem growth during glacial periods. Instead, the regional climate model simulation combined with proxy data suggest that the influence of the Laurentide and Cordilleran ice sheets on atmospheric circulation induced substantial changes in water balance in the Pacific Northwest and affected speleothem growth at our location. The overall drier conditions during glacial intervals and associated periods of frozen topsoil at times of maximum surface runoff likely induced drastic changes in cave recharge and limited speleothem growth. This mechanism could have affected speleothem growth in other mid-latitude caves without requiring the presence of permafrost.

A cellular automaton - finite volume method for the simulation of dendritic and eutectic growth in binary alloys using an adaptive mesh refinement

NASA Astrophysics Data System (ADS)

Dobravec, Tadej; Mavrič, Boštjan; Šarler, Božidar

2017-11-01

A two-dimensional model to simulate the dendritic and eutectic growth in binary alloys is developed. A cellular automaton method is adopted to track the movement of the solid-liquid interface. The diffusion equation is solved in the solid and liquid phases by using an explicit finite volume method. The computational domain is divided into square cells that can be hierarchically refined or coarsened using an adaptive mesh based on the quadtree algorithm. Such a mesh refines the regions of the domain near the solid-liquid interface, where the highest concentration gradients are observed. In the regions where the lowest concentration gradients are observed the cells are coarsened. The originality of the work is in the novel, adaptive approach to the efficient and accurate solution of the posed multiscale problem. The model is verified and assessed by comparison with the analytical results of the Lipton-Glicksman-Kurz model for the steady growth of a dendrite tip and the Jackson-Hunt model for regular eutectic growth. Several examples of typical microstructures are simulated and the features of the method as well as further developments are discussed.

Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

NASA Astrophysics Data System (ADS)

Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

2016-10-01

This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions in a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.

Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

DOE PAGES

Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; ...

2016-08-15

This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions inmore » a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Lastly, simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.« less

Predicting the impact of combined therapies on myeloma cell growth using a hybrid multi-scale agent-based model.

PubMed

Ji, Zhiwei; Su, Jing; Wu, Dan; Peng, Huiming; Zhao, Weiling; Nlong Zhao, Brian; Zhou, Xiaobo

2017-01-31

Multiple myeloma is a malignant still incurable plasma cell disorder. This is due to refractory disease relapse, immune impairment, and development of multi-drug resistance. The growth of malignant plasma cells is dependent on the bone marrow (BM) microenvironment and evasion of the host's anti-tumor immune response. Hence, we hypothesized that targeting tumor-stromal cell interaction and endogenous immune system in BM will potentially improve the response of multiple myeloma (MM). Therefore, we proposed a computational simulation of the myeloma development in the complicated microenvironment which includes immune cell components and bone marrow stromal cells and predicted the effects of combined treatment with multi-drugs on myeloma cell growth. We constructed a hybrid multi-scale agent-based model (HABM) that combines an ODE system and Agent-based model (ABM). The ODEs was used for modeling the dynamic changes of intracellular signal transductions and ABM for modeling the cell-cell interactions between stromal cells, tumor, and immune components in the BM. This model simulated myeloma growth in the bone marrow microenvironment and revealed the important role of immune system in this process. The predicted outcomes were consistent with the experimental observations from previous studies. Moreover, we applied this model to predict the treatment effects of three key therapeutic drugs used for MM, and found that the combination of these three drugs potentially suppress the growth of myeloma cells and reactivate the immune response. In summary, the proposed model may serve as a novel computational platform for simulating the formation of MM and evaluating the treatment response of MM to multiple drugs.

A mathematical model of a shallow and eutrophic lake (the Keszthely Basin, Lake Balaton) and simulation of restorative manipulations.

PubMed

Sagehashi, M; Sakoda, A; Suzuki, M

2001-05-01

Concern about the overall management of lakes has been growing, and a lake ecological model provides the guidelines necessary for such management. In this study, an ecological model describing the ecosystem of the Keszthely Basin, Lake Balaton, Hungary, one of the typical shallow and eutrophic lakes, was proposed. This model includes three types of zooplankton and two types of fish as well as two types of algae and nutrients. Parameters concerning the algae and fish were estimated based on observations in the basin between 1991 and 1995. The other parameters and the structure of the model were determined by our previous study. The parameters of the model were calibrated with the Monte Carlo technique, and its predictability was confirmed. The effects on the basin's ecosystem of three restorative manipulations, namely a biomanipulation, reduction of loading phosphorus, and dredging the sediment, were assessed by simulation studies using the proposed model. The simulation results indicated that a biomanipulation that removed 90% of the bream should suppress the growth of algae temporarily through bottom-up regulation; however, this effect seemed to not be perpetuated in this basin. The reduction of loading phosphorus seemed to be the most effective means to suppress algal growth, while dredging of sediment seemed to be the most desirable restoration method from the standpoint of the overall management of the lake, because it was expected to accelerate the growth of fish population as well as to suppress algal growth. Furthermore, the algal growth suppression mechanism of the dredging was discussed on the basis of the model calculations.

SIMULATION OF AEROSOL DYNAMICS: A COMPARATIVE REVIEW OF ALGORITHMS USED IN AIR QUALITY MODELS

EPA Science Inventory

A comparative review of algorithms currently used in air quality models to simulate aerosol dynamics is presented. This review addresses coagulation, condensational growth, nucleation, and gas/particle mass transfer. Two major approaches are used in air quality models to repres...

Modeling of time dependent localized flow shear stress and its impact on cellular growth within additive manufactured titanium implants

PubMed Central

Zhang, Ziyu; Yuan, Lang; Lee, Peter D; Jones, Eric; Jones, Julian R

2014-01-01

Bone augmentation implants are porous to allow cellular growth, bone formation and fixation. However, the design of the pores is currently based on simple empirical rules, such as minimum pore and interconnects sizes. We present a three-dimensional (3D) transient model of cellular growth based on the Navier–Stokes equations that simulates the body fluid flow and stimulation of bone precursor cellular growth, attachment, and proliferation as a function of local flow shear stress. The model's effectiveness is demonstrated for two additive manufactured (AM) titanium scaffold architectures. The results demonstrate that there is a complex interaction of flow rate and strut architecture, resulting in partially randomized structures having a preferential impact on stimulating cell migration in 3D porous structures for higher flow rates. This novel result demonstrates the potential new insights that can be gained via the modeling tool developed, and how the model can be used to perform what-if simulations to design AM structures to specific functional requirements. PMID:24664988

Contributions of muscle imbalance and impaired growth to postural and osseous shoulder deformity following brachial plexus birth palsy: a computational simulation analysis.

PubMed

Cheng, Wei; Cornwall, Roger; Crouch, Dustin L; Li, Zhongyu; Saul, Katherine R

2015-06-01

Two potential mechanisms leading to postural and osseous shoulder deformity after brachial plexus birth palsy are muscle imbalance between functioning internal rotators and paralyzed external rotators and impaired longitudinal growth of paralyzed muscles. Our goal was to evaluate the combined and isolated effects of these 2 mechanisms on transverse plane shoulder forces using a computational model of C5-6 brachial plexus injury. We modeled a C5-6 injury using a computational musculoskeletal upper limb model. Muscles expected to be denervated by C5-6 injury were classified as affected, with the remaining shoulder muscles classified as unaffected. To model muscle imbalance, affected muscles were given no resting tone whereas unaffected muscles were given resting tone at 30% of maximal activation. To model impaired growth, affected muscles were reduced in length by 30% compared with normal whereas unaffected muscles remained normal in length. Four scenarios were simulated: normal, muscle imbalance only, impaired growth only, and both muscle imbalance and impaired growth. Passive shoulder rotation range of motion and glenohumeral joint reaction forces were evaluated to assess postural and osseous deformity. All impaired scenarios exhibited restricted range of motion and increased and posteriorly directed compressive glenohumeral joint forces. Individually, impaired muscle growth caused worse restriction in range of motion and higher and more posteriorly directed glenohumeral forces than did muscle imbalance. Combined muscle imbalance and impaired growth caused the most restricted joint range of motion and the highest joint reaction force of all scenarios. Both muscle imbalance and impaired longitudinal growth contributed to range of motion and force changes consistent with clinically observed deformity, although the most substantial effects resulted from impaired muscle growth. Simulations suggest that treatment strategies emphasizing treatment of impaired longitudinal growth are warranted for reducing deformity after brachial plexus birth palsy. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

A numerical study of the effect of irrigation on land-atmosphere interactions in a spring wheat cropland in India using a coupled atmosphere-crop growth dynamics model

NASA Astrophysics Data System (ADS)

Kumari, S.; Sharma, P.; Srivastava, A.; Rastogi, D.; Sehgal, V. K.; Dhakar, R.; Roy, S. B.

2017-12-01

Vegetation dynamics and surface meteorology are tightly coupled through the exchange of momentum, moisture and heat between the land surface and the atmosphere. In this study, we use a recently developed coupled atmosphere-crop growth dynamics model to study these exchanges and their effects in a spring wheat cropland in northern India. In particular, we investigate the role of irrigation in controlling crop growth rates, surface meteorology, and sensible and latent heat fluxes. The model is developed by implementing a crop growth module based on the Simple and Universal Crop growth Simulator (SUCROS) model in the Weather Research Forecasting (WRF) mesoscale atmospheric model. The crop module calculates photosynthesis rates, carbon assimilation, and biomass partitioning as a function of environmental factors and crop development stage. The leaf area index (LAI) and root depth calculated by the crop module is then fed to the Noah-MP land module of WRF to calculate land-atmosphere fluxes. The crop model is calibrated using data from an experimental spring wheat crop site in the Indian Agriculture Research Institute. The coupled model is capable of simulating the observed spring wheat phenology. Irrigation is simulated by changing the soil moisture levels from 50% - 100% of field capacity. Results show that the yield first increases with increasing soil moisture and then starts decreasing as we further increase the soil moisture. Yield attains its maximum value with soil moisture at the level of 60% water of FC. At this level, high LAI values lead to a decrease in the Bowen Ratio because more energy is transferred to the atmosphere as latent heat rather than sensible heat resulting in a cooling effect on near-surface air temperatures. Apart from improving simulation of land-atmosphere interactions, this coupled modeling approach can form the basis for the seamless crop yield and seasonal scale weather outlook prediction system.

Simulation Studies of the Effect of Forest Spatial Structure on InSAR Signature

NASA Technical Reports Server (NTRS)

Sun, Guoqing; Liu, Dawei; Ranson, K. Jon; Koetz, Benjamin

2007-01-01

The height of scattering phase retrieved from InSAR data is considered being correlated with the tree height and the spatial structure of the forest stand. Though some researchers have used simple backscattering models to estimate tree height from the height of scattering center, the effect of forest spatial structure on InSAR data is not well understood yet. A three-dimensional coherent radar backscattering model for forest canopies based on realistic three-dimensional scene was used to investigate the effect in this paper. The realistic spatial structure of forest canopies was established either by field measurements (stem map) or through use of forest growth model. Field measurements or a forest growth model parameterized using local environmental parameters provides information of forest species composition and tree sizes in certain growth phases. A fractal tree model (L-system) was used to simulate individual 3- D tree structure of different ages or heights. Trees were positioned in a stand in certain patterns resulting in a 3-D medium of discrete scatterers. The radar coherent backscatter model took the 3-D forest scene as input and simulates the coherent radar backscattering signature. Interferometric SAR images of 3D scenes were simulated and heights of scattering phase centers were estimated from the simulated InSAR data. The effects of tree height, crown cover, crown depth, and the spatial distribution patterns of trees on the scattering phase center were analyzed. The results will be presented in the paper.

Understanding the barriers to crystal growth: dynamical simulation of the dissolution and growth of urea from aqueous solution.

PubMed

Piana, Stefano; Gale, Julian D

2005-02-16

Both the dissolution and growth of a molecular crystalline material, urea, has been studied using dynamical atomistic simulation. The kinetic steps of dissolution and growth are clearly identified, and the activation energies for each possible step are calculated. Our molecular dynamics simulations indicate that crystal growth on the [001] face is characterized by a nucleation and growth mechanism. Nucleation on the [001] urea crystal face is predicted to occur at a very high rate, followed by rapid propagation of the steps. The rate-limiting step for crystallization is actually found to be the removal of surface defects, rather than the initial formation of the next surface layer. Through kinetic Monte Carlo modeling of the surface growth, it is found that this crystal face evolves via a rough surface topography, rather than a clean layer-by-layer mechanism.

Calibrating and testing a gap model for simulating forest management in the Oregon Coast Range

Treesearch

Robert J. Pabst; Matthew N. Goslin; Steven L. Garman; Thomas A. Spies

2008-01-01

The complex mix of economic and ecological objectives facing today's forest managers necessitates the development of growth models with a capacity for simulating a wide range of forest conditions while producing outputs useful for economic analyses. We calibrated the gap model ZELIG to simulate stand level forest development in the Oregon Coast Range as part of a...

Direct identification of predator-prey dynamics in gyrokinetic simulations

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

Kobayashi, Sumire, E-mail: sumire.kobayashi@lpp.polytechnique.fr; Gürcan, Özgür D; Diamond, Patrick H.

2015-09-15

The interaction between spontaneously formed zonal flows and small-scale turbulence in nonlinear gyrokinetic simulations is explored in a shearless closed field line geometry. It is found that when clear limit cycle oscillations prevail, the observed turbulent dynamics can be quantitatively captured by a simple Lotka-Volterra type predator-prey model. Fitting the time traces of full gyrokinetic simulations by such a reduced model allows extraction of the model coefficients. Scanning physical plasma parameters, such as collisionality and density gradient, it was observed that the effective growth rates of turbulence (i.e., the prey) remain roughly constant, in spite of the higher and varyingmore » level of primary mode linear growth rates. The effective growth rate that was extracted corresponds roughly to the zonal-flow-modified primary mode growth rate. It was also observed that the effective damping of zonal flows (i.e., the predator) in the parameter range, where clear predator-prey dynamics is observed, (i.e., near marginal stability) agrees with the collisional damping expected in these simulations. This implies that the Kelvin-Helmholtz-like instability may be negligible in this range. The results imply that when the tertiary instability plays a role, the dynamics becomes more complex than a simple Lotka-Volterra predator prey.« less

Modeling Nitrogen Dynamics in a Waste Stabilization Pond System Using Flexible Modeling Environment with MCMC

PubMed Central

Mukhtar, Hussnain; Lin, Yu-Pin; Shipin, Oleg V.; Petway, Joy R.

2017-01-01

This study presents an approach for obtaining realization sets of parameters for nitrogen removal in a pilot-scale waste stabilization pond (WSP) system. The proposed approach was designed for optimal parameterization, local sensitivity analysis, and global uncertainty analysis of a dynamic simulation model for the WSP by using the R software package Flexible Modeling Environment (R-FME) with the Markov chain Monte Carlo (MCMC) method. Additionally, generalized likelihood uncertainty estimation (GLUE) was integrated into the FME to evaluate the major parameters that affect the simulation outputs in the study WSP. Comprehensive modeling analysis was used to simulate and assess nine parameters and concentrations of ON-N, NH3-N and NO3-N. Results indicate that the integrated FME-GLUE-based model, with good Nash–Sutcliffe coefficients (0.53–0.69) and correlation coefficients (0.76–0.83), successfully simulates the concentrations of ON-N, NH3-N and NO3-N. Moreover, the Arrhenius constant was the only parameter sensitive to model performances of ON-N and NH3-N simulations. However, Nitrosomonas growth rate, the denitrification constant, and the maximum growth rate at 20 °C were sensitive to ON-N and NO3-N simulation, which was measured using global sensitivity. PMID:28704958

A teleonomic model describing performance (body, milk and intake) during growth and over repeated reproductive cycles throughout the lifespan of dairy cattle. 1. Trajectories of life function priorities and genetic scaling.

PubMed

Martin, O; Sauvant, D

2010-12-01

The prediction of the control of nutrient partitioning, particularly energy, is a major issue in modelling dairy cattle performance. The proportions of energy channelled to physiological functions (growth, maintenance, gestation and lactation) change as the animal ages and reproduces, and according to its genotype and nutritional environment. This is the first of two papers describing a teleonomic model of individual performance during growth and over repeated reproductive cycles throughout the lifespan of dairy cattle. The conceptual framework is based on the coupling of a regulating sub-model providing teleonomic drives to govern the work of an operating sub-model scaled with genetic parameters. The regulating sub-model describes the dynamic partitioning of a mammal female's priority between life functions targeted to growth (G), ageing (A), balance of body reserves (R) and nutrient supply of the unborn (U), newborn (N) and suckling (S) calf. The so-called GARUNS dynamic pattern defines a trajectory of relative priorities, goal directed towards the survival of the individual for the continuation of the specie. The operating sub-model describes changes in body weight (BW) and composition, foetal growth, milk yield and composition and food intake in dairy cows throughout their lifespan, that is, during growth, over successive reproductive cycles and through ageing. This dynamic pattern of performance defines a reference trajectory of a cow under normal husbandry conditions and feed regimen. Genetic parameters are incorporated in the model to scale individual performance and simulate differences within and between breeds. The model was calibrated for dairy cows with literature data. The model was evaluated by comparison with simulations of previously published empirical equations of BW, body condition score, milk yield and composition and feed intake. This evaluation showed that the model adequately simulates these production variables throughout the lifespan, and across a range of dairy cattle genotypes.

Dual-scale phase-field simulation of Mg-Al alloy solidification

NASA Astrophysics Data System (ADS)

Monas, A.; Shchyglo, O.; Höche, D.; Tegeler, M.; Steinbach, I.

2015-06-01

Phase-field simulations of the nucleation and growth of primary α-Mg phase as well as secondary, β-phase of a Mg-Al alloy are presented. The nucleation model for α- and β-Mg phases is based on the “free growth model” by Greer et al.. After the α-Mg phase solidification we study a divorced eutectic growth of α- and β-Mg phases in a zoomed in melt channel between α-phase dendrites. The simulated cooling curves and final microstructures of α-grains are compared with experiments. In order to further enhance the resolution of the interdendritic region a high-performance computing approach has been used allowing significant simulation speed gain when using supercomputing facilities.

CCROP-Simulation model for container-grown nursery plant production.

USDA-ARS?s Scientific Manuscript database

Container Crop Resource Optimization Program (CCROP) is an integrative model which simulates the growth and water and nutrient requirements of a woody ornamental shrub grown in small (2.8–11.4 L) containers in a field environment with overhead sprinkler irrigation. The model was developed for produc...

Linking growth and yield and process models to estimate impact of environmental changes on growth of loblolly pine

Treesearch

V. Clark Baldwin; Harold E. Burkhart; James A. Westfall; Kelly D. Peterson

2001-01-01

PTAEDA2 is a distance-dependent, individual tree model that simulates the growth and yield of a plantation of loblolly pine (Pinus taeda L.)on an annual basis. The MAESTRO model utilizes an array of trees in a stand to calculate and integrate the effects of biological and physical variables on the photosynthesis and respiration processes of a target...

Stochastic Individual-Based Modeling of Bacterial Growth and Division Using Flow Cytometry.

PubMed

García, Míriam R; Vázquez, José A; Teixeira, Isabel G; Alonso, Antonio A

2017-01-01

A realistic description of the variability in bacterial growth and division is critical to produce reliable predictions of safety risks along the food chain. Individual-based modeling of bacteria provides the theoretical framework to deal with this variability, but it requires information about the individual behavior of bacteria inside populations. In this work, we overcome this problem by estimating the individual behavior of bacteria from population statistics obtained with flow cytometry. For this objective, a stochastic individual-based modeling framework is defined based on standard assumptions during division and exponential growth. The unknown single-cell parameters required for running the individual-based modeling simulations, such as cell size growth rate, are estimated from the flow cytometry data. Instead of using directly the individual-based model, we make use of a modified Fokker-Plank equation. This only equation simulates the population statistics in function of the unknown single-cell parameters. We test the validity of the approach by modeling the growth and division of Pediococcus acidilactici within the exponential phase. Estimations reveal the statistics of cell growth and division using only data from flow cytometry at a given time. From the relationship between the mother and daughter volumes, we also predict that P. acidilactici divide into two successive parallel planes.

An atomistic simulation scheme for modeling crystal formation from solution.

PubMed

Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk

2006-01-14

We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.

Model structure of the stream salmonid simulator (S3)—A dynamic model for simulating growth, movement, and survival of juvenile salmonids

USGS Publications Warehouse

Perry, Russell W.; Plumb, John M.; Jones, Edward C.; Som, Nicholas A.; Hetrick, Nicholas J.; Hardy, Thomas B.

2018-04-06

Fisheries and water managers often use population models to aid in understanding the effect of alternative water management or restoration actions on anadromous fish populations. We developed the Stream Salmonid Simulator (S3) to help resource managers evaluate the effect of management alternatives on juvenile salmonid populations. S3 is a deterministic stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and usable habitat area or carrying capacity. The physical characteristics of each habitat unit and the number of fish occupying each unit, in turn, drive survival and growth within each habitat unit and movement of fish among habitat units.The purpose of this report is to outline the underlying general structure of the S3 model that is common among different applications of the model. We have developed applications of the S3 model for juvenile fall Chinook salmon (Oncorhynchus tshawytscha) in the lower Klamath River. Thus, this report is a companion to current application of the S3 model to the Trinity River (in review). The general S3 model structure provides a biological and physical framework for the salmonid freshwater life cycle. This framework captures important demographics of juvenile salmonids aimed at translating management alternatives into simulated population responses. Although the S3 model is built on this common framework, the model has been constructed to allow much flexibility in application of the model to specific river systems. The ability for practitioners to include system-specific information for the physical stream structure, survival, growth, and movement processes ensures that simulations provide results that are relevant to the questions asked about the population under study.

Lysine production from methanol at 50 degrees C using Bacillus methanolicus: Modeling volume control, lysine concentration, and productivity using a three-phase continuous simulation.

PubMed

Lee, G H; Hur, W; Bremmon, C E; Flickinger, M C

1996-03-20

A simulation was developed based on experimental data obtained in a 14-L reactor to predict the growth and L-lysine accumulation kinetics, and change in volume of a large-scale (250-m(3)) Bacillus methanolicus methanol-based process. Homoserine auxotrophs of B. methanolicus MGA3 are unique methylotrophs because of the ability to secrete lysine during aerobic growth and threonine starvation at 50 degrees C. Dissolved methanol (100 mM), pH, dissolved oxygen tension (0.063 atm), and threonine levels were controlled to obtain threonine-limited conditions and high-cell density (25 g dry cell weight/L) in a 14-L reactor. As a fed-batch process, the additions of neat methanol (fed on demand), threonine, and other nutrients cause the volume of the fermentation to increase and the final lysine concentration to decrease. In addition, water produced as a result of methanol metabolism contributes to the increase in the volume of the reactor. A three-phase approach was used to predict the rate of change of culture volume based on carbon dioxide production and methanol consumption. This model was used for the evaluation of volume control strategies to optimize lysine productivity. A constant volume reactor process with variable feeding and continuous removal of broth and cells (VF(cstr)) resulted in higher lysine productivity than a fed-batch process without volume control. This model predicts the variation in productivity of lysine with changes in growth and in specific lysine productivity. Simple modifications of the model allows one to investigate other high-lysine-secreting strains with different growth and lysine productivity characteristics. Strain NOA2#13A5-2 which secretes lysine and other end-products were modeled using both growth and non-growth-associated lysine productivity. A modified version of this model was used to simulate the change in culture volume of another L-lysine producing mutant (NOA2#13A52-8A66) with reduced secretion of end-products. The modified simulation indicated that growth-associated production dominates in strain NOA2#13A52-8A66. (c) 1996 John Wiley & Sons, Inc.

Simulating carbon stocks and fluxes of an African tropical montane forest with an individual-based forest model.

PubMed

Fischer, Rico; Ensslin, Andreas; Rutten, Gemma; Fischer, Markus; Schellenberger Costa, David; Kleyer, Michael; Hemp, Andreas; Paulick, Sebastian; Huth, Andreas

2015-01-01

Tropical forests are carbon-dense and highly productive ecosystems. Consequently, they play an important role in the global carbon cycle. In the present study we used an individual-based forest model (FORMIND) to analyze the carbon balances of a tropical forest. The main processes of this model are tree growth, mortality, regeneration, and competition. Model parameters were calibrated using forest inventory data from a tropical forest at Mt. Kilimanjaro. The simulation results showed that the model successfully reproduces important characteristics of tropical forests (aboveground biomass, stem size distribution and leaf area index). The estimated aboveground biomass (385 t/ha) is comparable to biomass values in the Amazon and other tropical forests in Africa. The simulated forest reveals a gross primary production of 24 tcha(-1) yr(-1). Modeling above- and belowground carbon stocks, we analyzed the carbon balance of the investigated tropical forest. The simulated carbon balance of this old-growth forest is zero on average. This study provides an example of how forest models can be used in combination with forest inventory data to investigate forest structure and local carbon balances.

Processes influencing model-data mismatch in drought-stressed, fire-disturbed eddy flux sites

NASA Astrophysics Data System (ADS)

Mitchell, Stephen; Beven, Keith; Freer, Jim; Law, Beverly

2011-06-01

Semiarid forests are very sensitive to climatic change and among the most difficult ecosystems to accurately model. We tested the performance of the Biome-BGC model against eddy flux data taken from young (years 2004-2008), mature (years 2002-2008), and old-growth (year 2000) ponderosa pine stands at Metolius, Oregon, and subsequently examined several potential causes for model-data mismatch. We used the Generalized Likelihood Uncertainty Estimation methodology, which involved 500,000 model runs for each stand (1,500,000 total). Each simulation was run with randomly generated parameter values from a uniform distribution based on published parameter ranges, resulting in modeled estimates of net ecosystem CO2 exchange (NEE) that were compared to measured eddy flux data. Simulations for the young stand exhibited the highest level of performance, though they overestimated ecosystem C accumulation (-NEE) 99% of the time. Among the simulations for the mature and old-growth stands, 100% and 99% of the simulations underestimated ecosystem C accumulation. One obvious area of model-data mismatch is soil moisture, which was overestimated by the model in the young and old-growth stands yet underestimated in the mature stand. However, modeled estimates of soil water content and associated water deficits did not appear to be the primary cause of model-data mismatch; our analysis indicated that gross primary production can be accurately modeled even if soil moisture content is not. Instead, difficulties in adequately modeling ecosystem respiration, mainly autotrophic respiration, appeared to be the fundamental cause of model-data mismatch.

Processes influencing model-data mismatch in drought-stressed, fire-disturbed eddy flux sites

NASA Astrophysics Data System (ADS)

Mitchell, S. R.; Beven, K.; Freer, J. E.; Law, B. E.

2010-12-01

Semi-arid forests are very sensitive to climatic change and among the most difficult ecosystems to accurately model. We tested the performance of the Biome-BGC model against eddy flux data taken from young (years 2004-2008), mature (years 2002-2008), and old-growth (year 2000) Ponderosa pine stands at Metolius, Oregon, and subsequently examined several potential causes for model-data mismatch. We used the generalized likelihood uncertainty estimation (GLUE) methodology, which involved 500,000 model runs for each stand (1,500,000 total). Each simulation was run with randomly generated parameter values from a uniform distribution based on published parameter ranges, resulting in modeled estimates of net ecosystem CO2 exchange (NEE) that were compared to measured eddy flux data. Simulations for the young stand exhibited the highest level of performance, though they over-estimated ecosystem C accumulation (-NEE) 99% of the time. Among the simulations for the mature and old-growth stands, 100% and 99% of the simulations under-estimated ecosystem C accumulation. One obvious area of model-data mismatch is soil moisture, which was overestimated by the model in the young and old-growth stands yet underestimated in the mature stand. However, modeled estimates of soil water content and associated water deficits did not appear to be the primary cause of model-data mismatch; our analysis indicated that gross primary production can be accurately modeled even if soil moisture content is not. Instead, difficulties in adequately modeling ecosystem respiration, both autotrophic and heterotrophic, appeared to be fundamental causes of model-data mismatch.

Growth model for arc-deposited fullerene-like CNx nanoparticles.

PubMed

Veisz, Bernadett; Radnóczi, György

2005-06-01

Multiwall CNx nanotubes, nanoonions, and amorphous nanoballs were formed by carbon DC arc evaporation in a nitrogen atmosphere. The samples were investigated by conventional and high-resolution transmission electron microscopy. We propose a fragment-by-fragment growth mechanism for the formation of the nanoparticles. Accordingly, particles and aggregates of particles form in the vacuum ambient by the collisions between atomic species and small fragments. This growth model is supported by the discontinuous inner shells and disordered surface layers composed from graphene fragments. Image simulations confirm the detectability of dangling and back-folding surface layers in the experimental images. Further, the simulated images also confirm that the growth of nanoonions starts from a single fullerene-like seed. The amorphous nanoballs form when ordering of the building blocks during growth is hindered by the cross-linking nitrogen bonds. Copyright (c) 2005 Wiley-Liss, Inc.

Monte Carlo-based calibration and uncertainty analysis of a coupled plant growth and hydrological model

NASA Astrophysics Data System (ADS)

Houska, T.; Multsch, S.; Kraft, P.; Frede, H.-G.; Breuer, L.

2014-04-01

Computer simulations are widely used to support decision making and planning in the agriculture sector. On the one hand, many plant growth models use simplified hydrological processes and structures - for example, by the use of a small number of soil layers or by the application of simple water flow approaches. On the other hand, in many hydrological models plant growth processes are poorly represented. Hence, fully coupled models with a high degree of process representation would allow for a more detailed analysis of the dynamic behaviour of the soil-plant interface. We coupled two of such high-process-oriented independent models and calibrated both models simultaneously. The catchment modelling framework (CMF) simulated soil hydrology based on the Richards equation and the van Genuchten-Mualem model of the soil hydraulic properties. CMF was coupled with the plant growth modelling framework (PMF), which predicts plant growth on the basis of radiation use efficiency, degree days, water shortage and dynamic root biomass allocation. The Monte Carlo-based generalized likelihood uncertainty estimation (GLUE) method was applied to parameterize the coupled model and to investigate the related uncertainty of model predictions. Overall, 19 model parameters (4 for CMF and 15 for PMF) were analysed through 2 × 106 model runs randomly drawn from a uniform distribution. The model was applied to three sites with different management in Müncheberg (Germany) for the simulation of winter wheat (Triticum aestivum L.) in a cross-validation experiment. Field observations for model evaluation included soil water content and the dry matter of roots, storages, stems and leaves. The shape parameter of the retention curve n was highly constrained, whereas other parameters of the retention curve showed a large equifinality. We attribute this slightly poorer model performance to missing leaf senescence, which is currently not implemented in PMF. The most constrained parameters for the plant growth model were the radiation-use efficiency and the base temperature. Cross validation helped to identify deficits in the model structure, pointing out the need for including agricultural management options in the coupled model.

Peatland simulator connecting drainage, nutrient cycling, forest growth, economy and GHG efflux in boreal and tropical peatlands

NASA Astrophysics Data System (ADS)

Lauren, Ari; Hökkä, Hannu; Launiainen, Samuli; Palviainen, Marjo; Lehtonen, Aleksi

2016-04-01

Forest growth in peatlands is nutrient limited; principal source of nutrients is the decomposition of organic matter. Excess water decreases O2 diffusion and slows down the nutrient release. Drainage increases organic matter decomposition, CO2 efflux, and nutrient supply, and enhances the growth of forest. Profitability depends on costs, gained extra yield and its allocation into timber assortments, and the rate of interest. We built peatland simulator Susi to define and parameterize these interrelations. We applied Susi-simulator to compute water and nutrient processes, forest growth, and CO2 efflux of forested drained peatland. The simulator computes daily water fluxes and storages in two dimensions for a peatland forest strip located between drainage ditches. The CO2 efflux is made proportional to peat bulk density, soil temperature and O2 availability. Nutrient (N, P, K) release depends on decomposition and peat nutrient content. Growth limiting nutrient is detected by comparing the need and supply of nutrients. Increased supply of growth limiting nutrient is used to quantify the forest growth response to improved drainage. The extra yield is allocated into pulpwood and sawlogs based on volume of growing stock. The net present values of ditch cleaning operation and the gained extra yield are computed under different rates of interest to assess the profitability of the ditch cleaning. The hydrological sub-models of Susi-simulator were first parameterized using daily water flux data from Hyytiälä SMEAR II-site, after which the predictions were tested against independent hydrologic data from two drained peatland forests in Southern Finland. After verification of the hydrologic model, the CO2 efflux, nutrient release and forest growth proportionality hypothesis was tested and model performance validated against long-term forest growth and groundwater level data from 69 forested peatland sample plots in Central Finland. The results showed a clear relation between the stand growth, nutrient availability, and CO2 efflux. Potassium was the main limiting factor for the forest growth. This indicates that management aiming at decreasing heterotrophic CO2 efflux by raising the ground water table will decrease the forest growth. From the C balance perspective the growth rate of the tree stand becomes essential. Modelling approach enables a search for an optimal management schedule for producing timber in situation when there is a price given for release of C. Ditch network maintenance by ditch cleaning becomes profitable if: i) the initial drainage is very poor, ii) the availability of the critical nutrient is sufficient, iii) during prolonged rainy conditions, and iv) the tree stand is Scots pine (Pinus sylvestris) dominated and v) in a phase where most of the extra yield is allocated into sawlogs. The simulator and its holistic approach has been successfully implemented in both tropical pulpwood plantations in Sumatra, Indonesia and in Finnish boreal forests.

Comparison between phase field simulations and experimental data from intragranular bubble growth in UO{sub 2}

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

Tonks, M. R.; Biner, S. B.; Mille, P. C.

2013-07-01

In this work, we used the phase field method to simulate the post-irradiation annealing of UO{sub 2} described in the experimental work by Kashibe et al., 1993 [1]. The simulations were carried out in 2D and 3D using the MARMOT FEM-based phase-field modeling framework. The 2-D results compared fairly well with the experiments, in spite of the assumptions made in the model. The 3-D results compare even more favorably to experiments, indicating that diffusion in all three directions must be considered to accurate represent the bubble growth. (authors)

Modelling the effect of diffuse light on canopy photosynthesis in controlled environments

NASA Technical Reports Server (NTRS)

Cavazzoni, James; Volk, Tyler; Tubiello, Francesco; Monje, Oscar; Janes, H. W. (Principal Investigator)

2002-01-01

A layered canopy model was used to analyze the effects of diffuse light on canopy gross photosynthesis in controlled environment plant growth chambers, where, in contrast to the field, highly diffuse light can occur at high irradiance. The model suggests that high diffuse light fractions (approximately 0.7) and irradiance (1400 micromoles m-2 s-1) may enhance crop life-cycle canopy gross photosynthesis for hydroponic wheat by about 20% compared to direct light at the same irradiance. Our simulations suggest that high accuracy is not needed in specifying diffuse light fractions in chambers between approximately 0.7 and 1, because simulated photosynthesis for closed canopies plateau in this range. We also examined the effect of leaf angle distribution on canopy photosynthesis under growth chamber conditions, as these distributions determine canopy extinction coefficients for direct and diffuse light. We show that the spherical leaf angle distribution is not suitable for modeling photosynthesis of planophile canopies (e.g., soybean and peanut) in growth chambers. Also, the absorption of the light reflected from the surface below the canopy should generally be included in model simulations, as the corresponding albedo values in the photosynthetically active range may be quite high in growth chambers (e.g., approximately 0.5). In addition to the modeling implications, our results suggest that diffuse light conditions should be considered when drawing conclusions from experiments in controlled environments.

Global latitudinal-asymmetric vegetation growth trends and their driving mechanisms: 1982-2009

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

Mao, Jiafu; Shi, Xiaoying; Thornton, Peter E

2013-01-01

Using a recent Leaf Area Index (LAI) dataset and the Community Land Model version 4 (CLM4), we investigate percent changes and controlling factors of global vegetation growth for the period 1982 to 2009. Over that 28-year period, both the remote-sensing estimate and model simulation show a significant increasing trend in annual vegetation growth. Latitudinal asymmetry appeared in both products, with small increases in the Southern Hemisphere (SH) and larger increases at high latitudes in the Northern Hemisphere (NH). The south-to-north asymmetric land surface warming was assessed to be the principal driver of this latitudinal asymmetry of LAI trend. Heterogeneous precipitationmore » functioned to decrease this latitudinal LAI gradient, and considerably regulated the local LAI change. CO2 fertilization during the last three decades, was simulated to be the dominant cause for the enhanced vegetation growth. Our study, though limited by observational and modeling uncertainties, adds further insight into vegetation growth trends and environmental correlations. These validation exercises also provide new quantitative and objective metrics for evaluation of land ecosystem process models at multiple spatio-temporal scales.« less

Crop Model Improvement Reduces the Uncertainty of the Response to Temperature of Multi-Model Ensembles

NASA Technical Reports Server (NTRS)

Maiorano, Andrea; Martre, Pierre; Asseng, Senthold; Ewert, Frank; Mueller, Christoph; Roetter, Reimund P.; Ruane, Alex C.; Semenov, Mikhail A.; Wallach, Daniel; Wang, Enli

2016-01-01

To improve climate change impact estimates and to quantify their uncertainty, multi-model ensembles (MMEs) have been suggested. Model improvements can improve the accuracy of simulations and reduce the uncertainty of climate change impact assessments. Furthermore, they can reduce the number of models needed in a MME. Herein, 15 wheat growth models of a larger MME were improved through re-parameterization and/or incorporating or modifying heat stress effects on phenology, leaf growth and senescence, biomass growth, and grain number and size using detailed field experimental data from the USDA Hot Serial Cereal experiment (calibration data set). Simulation results from before and after model improvement were then evaluated with independent field experiments from a CIMMYT worldwide field trial network (evaluation data set). Model improvements decreased the variation (10th to 90th model ensemble percentile range) of grain yields simulated by the MME on average by 39% in the calibration data set and by 26% in the independent evaluation data set for crops grown in mean seasonal temperatures greater than 24 C. MME mean squared error in simulating grain yield decreased by 37%. A reduction in MME uncertainty range by 27% increased MME prediction skills by 47%. Results suggest that the mean level of variation observed in field experiments and used as a benchmark can be reached with half the number of models in the MME. Improving crop models is therefore important to increase the certainty of model-based impact assessments and allow more practical, i.e. smaller MMEs to be used effectively.

Aquatic Nutrient Simulation Modules (NSMs) Developed for Hydrologic and Hydraulic Models

DTIC Science & Technology

2016-02-01

effect of temperature on algal growth unitless FOxpi oxygen attenuation for algal respiration unitless FOxb oxygen attenuation for benthic algal... effect of temperature below T0p on benthic algal growth 0C-2 ktb2 effect of temperature above T0p on benthic algal growth 0C-2 ka(T) oxygen ...Si Silica SOD Sediment Oxygen Demand SO4 TEMP Sulfate Water Temperature Simulation Module TN Total Nitrogen TP Total Phosphorous TIC Total

Multiscale modelling and nonlinear simulation of vascular tumour growth

PubMed Central

Macklin, Paul; Anderson, Alexander R. A.; Chaplain, Mark A. J.; Cristini, Vittorio

2011-01-01

In this article, we present a new multiscale mathematical model for solid tumour growth which couples an improved model of tumour invasion with a model of tumour-induced angiogenesis. We perform nonlinear simulations of the multi-scale model that demonstrate the importance of the coupling between the development and remodeling of the vascular network, the blood flow through the network and the tumour progression. Consistent with clinical observations, the hydrostatic stress generated by tumour cell proliferation shuts down large portions of the vascular network dramatically affecting the flow, the subsequent network remodeling, the delivery of nutrients to the tumour and the subsequent tumour progression. In addition, extracellular matrix degradation by tumour cells is seen to have a dramatic affect on both the development of the vascular network and the growth response of the tumour. In particular, the newly developing vessels tend to encapsulate, rather than penetrate, the tumour and are thus less effective in delivering nutrients. PMID:18781303

Ensembles modeling approach to study Climate Change impacts on Wheat

NASA Astrophysics Data System (ADS)

Ahmed, Mukhtar; Claudio, Stöckle O.; Nelson, Roger; Higgins, Stewart

2017-04-01

Simulations of crop yield under climate variability are subject to uncertainties, and quantification of such uncertainties is essential for effective use of projected results in adaptation and mitigation strategies. In this study we evaluated the uncertainties related to crop-climate models using five crop growth simulation models (CropSyst, APSIM, DSSAT, STICS and EPIC) and 14 general circulation models (GCMs) for 2 representative concentration pathways (RCP) of atmospheric CO2 (4.5 and 8.5 W m-2) in the Pacific Northwest (PNW), USA. The aim was to assess how different process-based crop models could be used accurately for estimation of winter wheat growth, development and yield. Firstly, all models were calibrated for high rainfall, medium rainfall, low rainfall and irrigated sites in the PNW using 1979-2010 as the baseline period. Response variables were related to farm management and soil properties, and included crop phenology, leaf area index (LAI), biomass and grain yield of winter wheat. All five models were run from 2000 to 2100 using the 14 GCMs and 2 RCPs to evaluate the effect of future climate (rainfall, temperature and CO2) on winter wheat phenology, LAI, biomass, grain yield and harvest index. Simulated time to flowering and maturity was reduced in all models except EPIC with some level of uncertainty. All models generally predicted an increase in biomass and grain yield under elevated CO2 but this effect was more prominent under rainfed conditions than irrigation. However, there was uncertainty in the simulation of crop phenology, biomass and grain yield under 14 GCMs during three prediction periods (2030, 2050 and 2070). We concluded that to improve accuracy and consistency in simulating wheat growth dynamics and yield under a changing climate, a multimodel ensemble approach should be used.

Modeling of convection, temperature distribution and dendritic growth in glass-fluxed nickel melts

NASA Astrophysics Data System (ADS)

Gao, Jianrong; Kao, Andrew; Bojarevics, Valdis; Pericleous, Koulis; Galenko, Peter K.; Alexandrov, Dmitri V.

2017-08-01

Melt flow is often quoted as the reason for a discrepancy between experiment and theory on dendritic growth kinetics at low undercoolings. But this flow effect is not justified for glass-fluxed melts where the flow field is weaker. In the present work, we modeled the thermal history, flow pattern and dendritic structure of a glass-fluxed nickel sample by magnetohydrodynamics calculations. First, the temperature distribution and flow structure in the molten and undercooled melt were simulated by reproducing the observed thermal history of the sample prior to solidification. Then the dendritic structure and surface temperature of the recalescing sample were simulated. These simulations revealed a large thermal gradient crossing the sample, which led to an underestimation of the real undercooling for dendritic growth in the bulk volume of the sample. By accounting for this underestimation, we recalculated the dendritic tip velocities in the glass-fluxed nickel melt using a theory of three-dimensional dendritic growth with convection and concluded an improved agreement between experiment and theory.

Simulation of metastatic progression using a computer model including chemotherapy and radiation therapy.

PubMed

Bethge, Anja; Schumacher, Udo; Wedemann, Gero

2015-10-01

Despite considerable research efforts, the process of metastasis formation is still a subject of intense discussion, and even established models differ considerably in basic details and in the conclusions drawn from them. Mathematical and computational models add a new perspective to the research as they can quantitatively investigate the processes of metastasis and the effects of treatment. However, existing models look at only one treatment option at a time. We enhanced a previously developed computer model (called CaTSiT) that enables quantitative comparison of different metastasis formation models with clinical and experimental data, to include the effects of chemotherapy, external beam radiation, radioimmunotherapy and radioembolization. CaTSiT is based on a discrete event simulation procedure. The growth of the primary tumor and its metastases is modeled by a piecewise-defined growth function that describes the growth behavior of the primary tumor and metastases during various time intervals. The piecewise-defined growth function is composed of analytical functions describing the growth behavior of the tumor based on characteristics of the tumor, such as dormancy, or the effects of various therapies. The spreading of malignant cells into the blood is modeled by intravasation events, which are generated according to a rate function. Further events in the model describe the behavior of the released malignant cells until the formation of a new metastasis. The model is published under the GNU General Public License version 3. To demonstrate the application of the computer model, a case of a patient with a hepatocellular carcinoma and multiple metastases in the liver was simulated. Besides the untreated case, different treatments were simulated at two time points: one directly after diagnosis of the primary tumor and the other several months later. Except for early applied radioimmunotherapy, no treatment strategy was able to eliminate all metastases. These results emphasize the importance of early diagnosis and of proceeding with treatment even if no clinically detectable metastases are present at the time of diagnosis of the primary tumor. CaTSiT could be a valuable tool for quantitative investigation of the process of tumor growth and metastasis formation, including the effects of various treatment options. Copyright © 2015 Elsevier Inc. All rights reserved.

Stochastic growth logistic model with aftereffect for batch fermentation process

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

Rosli, Norhayati; Ayoubi, Tawfiqullah; Bahar, Arifah

2014-06-19

In this paper, the stochastic growth logistic model with aftereffect for the cell growth of C. acetobutylicum P262 and Luedeking-Piret equations for solvent production in batch fermentation system is introduced. The parameters values of the mathematical models are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic models numerically. The effciency of mathematical models is measured by comparing the simulated result and the experimental data of the microbial growth and solvent production in batch system. Low values of Root Mean-Square Error (RMSE) of stochastic models with aftereffect indicate good fits.

Stochastic growth logistic model with aftereffect for batch fermentation process

NASA Astrophysics Data System (ADS)

Rosli, Norhayati; Ayoubi, Tawfiqullah; Bahar, Arifah; Rahman, Haliza Abdul; Salleh, Madihah Md

2014-06-01

In this paper, the stochastic growth logistic model with aftereffect for the cell growth of C. acetobutylicum P262 and Luedeking-Piret equations for solvent production in batch fermentation system is introduced. The parameters values of the mathematical models are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic models numerically. The effciency of mathematical models is measured by comparing the simulated result and the experimental data of the microbial growth and solvent production in batch system. Low values of Root Mean-Square Error (RMSE) of stochastic models with aftereffect indicate good fits.

Planned Missing Designs to Optimize the Efficiency of Latent Growth Parameter Estimates

ERIC Educational Resources Information Center

Rhemtulla, Mijke; Jia, Fan; Wu, Wei; Little, Todd D.

2014-01-01

We examine the performance of planned missing (PM) designs for correlated latent growth curve models. Using simulated data from a model where latent growth curves are fitted to two constructs over five time points, we apply three kinds of planned missingness. The first is item-level planned missingness using a three-form design at each wave such…

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

Zhang, Damao; Wang, Zhien; Heymsfield, Andrew J.

Measurement of ice number concentration in clouds is important but still challenging. Stratiform mixed-phase clouds (SMCs) provide a simple scenario for retrieving ice number concentration from remote sensing measurements. The simple ice generation and growth pattern in SMCs offers opportunities to use cloud radar reflectivity (Ze) measurements and other cloud properties to infer ice number concentration quantitatively. To understand the strong temperature dependency of ice habit and growth rate quantitatively, we develop a 1-D ice growth model to calculate the ice diffusional growth along its falling trajectory in SMCs. The radar reflectivity and fall velocity profiles of ice crystals calculatedmore » from the 1-D ice growth model are evaluated with the Atmospheric Radiation Measurements (ARM) Climate Research Facility (ACRF) ground-based high vertical resolution radar measurements. Combining Ze measurements and 1-D ice growth model simulations, we develop a method to retrieve the ice number concentrations in SMCs at given cloud top temperature (CTT) and liquid water path (LWP). The retrieved ice concentrations in SMCs are evaluated with in situ measurements and with a three-dimensional cloud-resolving model simulation with a bin microphysical scheme. These comparisons show that the retrieved ice number concentrations are within an uncertainty of a factor of 2, statistically.« less

Numerical prediction of rail roughness growth on tangent railway tracks

NASA Astrophysics Data System (ADS)

Nielsen, J. C. O.

2003-10-01

Growth of railhead roughness (irregularities, waviness) is predicted through numerical simulation of dynamic train-track interaction on tangent track. The hypothesis is that wear is caused by longitudinal slip due to driven wheelsets, and that wear is proportional to the longitudinal frictional power in the contact patch. Emanating from an initial roughness spectrum corresponding to a new or a recent ground rail, an initial roughness profile is determined. Wheel-rail contact forces, creepages and wear for one wheelset passage are calculated in relation to location along a discretely supported track model. The calculated wear is scaled by a chosen number of wheelset passages, and is then added to the initial roughness profile. Field observations of rail corrugation on a Dutch track are used to validate the simulation model. Results from the simulations predict a large roughness growth rate for wavelengths around 30-40 mm. The large growth in this wavelength interval is explained by a low track receptance near the sleepers around the pinned-pinned resonance frequency, in combination with a large number of driven passenger wheelset passages at uniform speed. The agreement between simulations and field measurements is good with respect to dominating roughness wavelength and annual wear rate. Remedies for reducing roughness growth are discussed.

Long-range temporal correlations in the Kardar-Parisi-Zhang growth: numerical simulations

NASA Astrophysics Data System (ADS)

Song, Tianshu; Xia, Hui

2016-11-01

To analyze long-range temporal correlations in surface growth, we study numerically the (1  +  1)-dimensional Kardar-Parisi-Zhang (KPZ) equation driven by temporally correlated noise, and obtain the scaling exponents based on two different numerical methods. Our simulations show that the numerical results are in good agreement with the dynamic renormalization group (DRG) predictions, and are also consistent with the simulation results of the ballistic deposition (BD) model.

Kinetic Model of Growth of Arthropoda Populations

NASA Astrophysics Data System (ADS)

Ershov, Yu. A.; Kuznetsov, M. A.

2018-05-01

Kinetic equations were derived for calculating the growth of crustacean populations ( Crustacea) based on the biological growth model suggested earlier using shrimp ( Caridea) populations as an example. The development cycle of successive stages for populations can be represented in the form of quasi-chemical equations. The kinetic equations that describe the development cycle of crustaceans allow quantitative prediction of the development of populations depending on conditions. In contrast to extrapolation-simulation models, in the developed kinetic model of biological growth the kinetic parameters are the experimental characteristics of population growth. Verification and parametric identification of the developed model on the basis of the experimental data showed agreement with experiment within the error of the measurement technique.

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

TESP combines existing domain simulators in the electric power grid, with new transactive agents, growth models and evaluation scripts. The existing domain simulators include GridLAB-D for the distribution grid and single-family residential buildings, MATPOWER for transmission and bulk generation, and EnergyPlus for large buildings. More are planned for subsequent versions of TESP. The new elements are: TEAgents - simulate market participants and transactive systems for market clearing. Some of this functionality was extracted from GridLAB-D and implemented in Python for customization by PNNL and others; Growth Model - a means for simulating system changes over a multiyear period, including bothmore » normal load growth and specific investment decisions. Customizable in Python code; and Evaluation Script - a means of evaluating different transactive systems through customizable post-processing in Python code. TESP provides a method for other researchers and vendors to design transactive systems, and test them in a virtual environment. It allows customization of the key components by modifying Python code.« less

A Crack Growth Evaluation Method for Interacting Multiple Cracks

NASA Astrophysics Data System (ADS)

Kamaya, Masayuki

When stress corrosion cracking or corrosion fatigue occurs, multiple cracks are frequently initiated in the same area. According to section XI of the ASME Boiler and Pressure Vessel Code, multiple cracks are considered as a single combined crack in crack growth analysis, if the specified conditions are satisfied. In crack growth processes, however, no prescription for the interference between multiple cracks is given in this code. The JSME Post-Construction Code, issued in May 2000, prescribes the conditions of crack coalescence in the crack growth process. This study aimed to extend this prescription to more general cases. A simulation model was applied, to simulate the crack growth process, taking into account the interference between two cracks. This model made it possible to analyze multiple crack growth behaviors for many cases (e. g. different relative position and length) that could not be studied by experiment only. Based on these analyses, a new crack growth analysis method was suggested for taking into account the interference between multiple cracks.

Spontaneous chiral symmetry breaking in two-dimensional aggregation

NASA Astrophysics Data System (ADS)

Sandler, Ilya Moiseevich

Recently, unusual and strikingly beautiful seahorse-like growth patterns have been discovered. These patterns possess a spontaneously broken chiral (left/right) symmetry. To explain this spontaneous chiral symmetry breaking, we develop a model for the growth of the aggregate, assuming that the latter is charged, and that the incoming particles are polarizable, and hence drawn preferentially to regions of strong electric field. This model is used both for numerical simulation and theoretical analysis of the aggregation process. We find that the broken symmetry (typically, an 'S' shape) appears in our simulations for some parameter values. Its origin is the long-range interaction (competition and repulsion) among growing branches of the aggregate, such that a right or left side consistently dominates the growth process. We show that the electrostatic interaction may account for the other geometrical properties of the aggregates, such as the existence of only 2 main arms, and the "finned" external edge of the main arms. The results of our simulations of growth in the presence of the external electric field are also in a good agreement with the results of new experiments, motivated by our ideas. Thus, we believe that our growth model provides a plausible explanation of the origin of the broken symmetry in the experimental patterns.

Synchrotron characterization of nanograined UO 2 grain growth

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

Mo, Kun; Miao, Yinbin; Yun, Di

2015-09-30

This activity is supported by the US Nuclear Energy Advanced Modeling and Simulation (NEAMS) Fuels Product Line (FPL) and aims at providing experimental data for the validation of the mesoscale simulation code MARMOT. MARMOT is a mesoscale multiphysics code that predicts the coevolution of microstructure and properties within reactor fuel during its lifetime in the reactor. It is an important component of the Moose-Bison-Marmot (MBM) code suite that has been developed by Idaho National Laboratory (INL) to enable next generation fuel performance modeling capability as part of the NEAMS Program FPL. In order to ensure the accuracy of the microstructuremore » based materials models being developed within the MARMOT code, extensive validation efforts must be carried out. In this report, we summarize our preliminary synchrotron radiation experiments at APS to determine the grain size of nanograin UO 2. The methodology and experimental setup developed in this experiment can directly apply to the proposed in-situ grain growth measurements. The investigation of the grain growth kinetics was conducted based on isothermal annealing and grain growth characterization as functions of duration and temperature. The kinetic parameters such as activation energy for grain growth for UO 2 with different stoichiometry are obtained and compared with molecular dynamics (MD) simulations.« less

Supplying materials needed for grain growth characterizations of nano-grained UO 2

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

Mo, Kun; Miao, Yinbin; Yun, Di

2015-09-30

This activity is supported by the US Nuclear Energy Advanced Modeling and Simulation (NEAMS) Fuels Product Line (FPL) and aims at providing experimental data for the validation of the mesoscale simulation code MARMOT. MARMOT is a mesoscale multiphysics code that predicts the coevolution of microstructure and properties within reactor fuel during its lifetime in the reactor. It is an important component of the Moose-Bison-Marmot (MBM) code suite that has been developed by Idaho National Laboratory (INL) to enable next generation fuel performance modeling capability as part of the NEAMS Program FPL. In order to ensure the accuracy of the microstructuremore » based materials models being developed within the MARMOT code, extensive validation efforts must be carried out. In this report, we summarize our preliminary synchrotron radiation experiments at APS to determine the grain size of nanograin UO 2. The methodology and experimental setup developed in this experiment can directly apply to the proposed in-situ grain growth measurements. The investigation of the grain growth kinetics was conducted based on isothermal annealing and grain growth characterization as functions of duration and temperature. The kinetic parameters such as activation energy for grain growth for UO 2 with different stoichiometry are obtained and compared with molecular dynamics (MD) simulations.« less

Alternative approach to modeling bacterial lag time, using logistic regression as a function of time, temperature, pH, and sodium chloride concentration.

PubMed

Koseki, Shige; Nonaka, Junko

2012-09-01

The objective of this study was to develop a probabilistic model to predict the end of lag time (λ) during the growth of Bacillus cereus vegetative cells as a function of temperature, pH, and salt concentration using logistic regression. The developed λ model was subsequently combined with a logistic differential equation to simulate bacterial numbers over time. To develop a novel model for λ, we determined whether bacterial growth had begun, i.e., whether λ had ended, at each time point during the growth kinetics. The growth of B. cereus was evaluated by optical density (OD) measurements in culture media for various pHs (5.5 ∼ 7.0) and salt concentrations (0.5 ∼ 2.0%) at static temperatures (10 ∼ 20°C). The probability of the end of λ was modeled using dichotomous judgments obtained at each OD measurement point concerning whether a significant increase had been observed. The probability of the end of λ was described as a function of time, temperature, pH, and salt concentration and showed a high goodness of fit. The λ model was validated with independent data sets of B. cereus growth in culture media and foods, indicating acceptable performance. Furthermore, the λ model, in combination with a logistic differential equation, enabled a simulation of the population of B. cereus in various foods over time at static and/or fluctuating temperatures with high accuracy. Thus, this newly developed modeling procedure enables the description of λ using observable environmental parameters without any conceptual assumptions and the simulation of bacterial numbers over time with the use of a logistic differential equation.

Simulation of clustering and anisotropy due to Co step-edge segregation in vapor-deposited CoPt3

NASA Astrophysics Data System (ADS)

Maranville, B. B.; Schuerman, M.; Hellman, F.

2006-03-01

An atomistic mechanism is proposed for the creation of structural anisotropy and consequent large perpendicular magnetic anisotropy in vapor-deposited films of CoPt3 . Energetic considerations of bonding in Co-Pt suggest that Co segregates to step edges due to their low coordination, for all film orientations, while Pt segregates to the two low index surfaces. Coalescence of islands during growth cause these Co-rich step edges to become flat thin Co platelets in a Pt rich matrix, giving rise to the experimentally observed magnetic anisotropy. This proposed model is tested with kinetic Monte Carlo simulation of the vapor deposition growth. A tight-binding, second-moment approximation to the interatomic potential is used to calculate the probability of an atom hopping from one surface site to another, assuming an Arrhenius-like activation model of surface motion. Growth is simulated by allowing many hopping events per adatom. The simulated as-grown films show an asymmetry in Co-Co bonding between the in-plane and out-of-plane directions, in good agreement with experimental data. The growth temperature dependence found in the simulations is strong and similar to that seen in experiments, and an increase in Co edge segregation with increasing temperature is also observed.

Numerical Simulation and Experimental Casting of Nickel-Based Single-Crystal Superalloys by HRS and LMC Directional Solidification Processes

NASA Astrophysics Data System (ADS)

Yan, Xuewei; Wang, Run'nan; Xu, Qingyan; Liu, Baicheng

2017-04-01

Mathematical models for dynamic heat radiation and convection boundary in directional solidification processes are established to simulate the temperature fields. Cellular automaton (CA) method and Kurz-Giovanola-Trivedi (KGT) growth model are used to describe nucleation and growth. Primary dendritic arm spacing (PDAS) and secondary dendritic arm spacing (SDAS) are calculated by the Ma-Sham (MS) and Furer-Wunderlin (FW) models respectively. The mushy zone shape is investigated based on the temperature fields, for both high-rate solidification (HRS) and liquid metal cooling (LMC) processes. The evolution of the microstructure and crystallographic orientation are analyzed by simulation and electron back-scattered diffraction (EBSD) technique, respectively. Comparison of the simulation results from PDAS and SDAS with experimental results reveals a good agreement with each other. The results show that LMC process can provide both dendritic refinement and superior performance for castings due to the increased cooling rate and thermal gradient.

Regenerative life support system research

NASA Technical Reports Server (NTRS)

1988-01-01

Sections on modeling, experimental activities during the grant period, and topics under consideration for the future are contained. The sessions contain discussions of: four concurrent modeling approaches that were being integrated near the end of the period (knowledge-based modeling support infrastructure and data base management, object-oriented steady state simulations for three concepts, steady state mass-balance engineering tradeoff studies, and object-oriented time-step, quasidynamic simulations of generic concepts); interdisciplinary research activities, beginning with a discussion of RECON lab development and use, and followed with discussions of waste processing research, algae studies and subsystem modeling, low pressure growth testing of plants, subsystem modeling of plants, control of plant growth using lighting and CO2 supply as variables, search for and development of lunar soil simulants, preliminary design parameters for a lunar base life support system, and research considerations for food processing in space; and appendix materials, including a discussion of the CELSS Conference, detailed analytical equations for mass-balance modeling, plant modeling equations, and parametric data on existing life support systems for use in modeling.

Effect of Strain Restored Energy on Abnormal Grain Growth in Mg Alloy Simulated by Phase Field Methods

NASA Astrophysics Data System (ADS)

Wu, Yan; Huang, Yuan-yuan

2018-03-01

Abnormal grain growth of single phase AZ31 Mg alloy in the spatio-temporal process has been simulated by phase field models, and the influencing factors of abnormal grain growth are studied in order to find the ways to control secondary recrystallization in the microstructure. The study aims to find out the mechanisms for abnormal grain growth in real alloys. It is shown from the simulated results that the abnormal grain growth can be controlled by the strain restored energy. Secondary recrystallization after an annealing treatment can be induced if there are grains of a certain orientation in the microstructure with local high restored energy. However, if the value of the local restored energy at a certain grain orientation is not greater than 1.1E 0, there may be no abnormal grain growth in the microstructure.

Class Enumeration and Parameter Recovery of Growth Mixture Modeling and Second-Order Growth Mixture Modeling in the Presence of Measurement Noninvariance between Latent Classes

PubMed Central

Kim, Eun Sook; Wang, Yan

2017-01-01

Population heterogeneity in growth trajectories can be detected with growth mixture modeling (GMM). It is common that researchers compute composite scores of repeated measures and use them as multiple indicators of growth factors (baseline performance and growth) assuming measurement invariance between latent classes. Considering that the assumption of measurement invariance does not always hold, we investigate the impact of measurement noninvariance on class enumeration and parameter recovery in GMM through a Monte Carlo simulation study (Study 1). In Study 2, we examine the class enumeration and parameter recovery of the second-order growth mixture modeling (SOGMM) that incorporates measurement models at the first order level. Thus, SOGMM estimates growth trajectory parameters with reliable sources of variance, that is, common factor variance of repeated measures and allows heterogeneity in measurement parameters between latent classes. The class enumeration rates are examined with information criteria such as AIC, BIC, sample-size adjusted BIC, and hierarchical BIC under various simulation conditions. The results of Study 1 showed that the parameter estimates of baseline performance and growth factor means were biased to the degree of measurement noninvariance even when the correct number of latent classes was extracted. In Study 2, the class enumeration accuracy of SOGMM depended on information criteria, class separation, and sample size. The estimates of baseline performance and growth factor mean differences between classes were generally unbiased but the size of measurement noninvariance was underestimated. Overall, SOGMM is advantageous in that it yields unbiased estimates of growth trajectory parameters and more accurate class enumeration compared to GMM by incorporating measurement models. PMID:28928691

Modelling the competition of planktonic and sessile aerobic heterotrophs for complementary nutrients in biofilm reactor.

PubMed

Lu, T; Saikaly, P E; Oerther, D B

2007-01-01

A comprehensive, simplified microbial biofilm model was developed to evaluate the impact of bioreactor operating parameters on changes in microbial population abundance. Biofilm simulations were conducted using three special cases: fully penetrated, internal mass transfer resistance and external mass transfer resistance. The results of model simulations showed that for certain operating conditions, competition for growth limiting nutrients generated oscillations in the abundance of planktonic and sessile microbial populations. These oscillations resulted in the violation of the competitive exclusion principle where the number of microbial populations was greater than the number of growth limiting nutrients. However, the operating conditions which impacted microbial community diversity were different for the three special cases. Comparing the results of model simulations for dispersed-growth, biofilms and bioflocs showed that oscillations and microbial community diversity were a function of competition as well as other key features of the ecosystem. The significance of the current study is that it is the first to examine competition as a mechanism for controlling microbial community diversity in biofilm reactors.

Modeling seasonal variability of fecal coliform in natural surface waters using the modified SWAT

NASA Astrophysics Data System (ADS)

Cho, Kyung Hwa; Pachepsky, Yakov A.; Kim, Minjeong; Pyo, JongCheol; Park, Mi-Hyun; Kim, Young Mo; Kim, Jung-Woo; Kim, Joon Ha

2016-04-01

Fecal coliforms are indicators of pathogens and thereby, understanding of their fate and transport in surface waters is important to protect drinking water sources and public health. We compiled fecal coliform observations from four different sites in the USA and Korea and found a seasonal variability with a significant connection to temperature levels. In all observations, fecal coliform concentrations were relatively higher in summer and lower during the winter season. This could be explained by the seasonal dominance of growth or die-off of bacteria in soil and in-stream. Existing hydrologic models, however, have limitations in simulating the seasonal variability of fecal coliform. Soil and in-stream bacterial modules of the Soil and Water Assessment Tool (SWAT) model are oversimplified in that they exclude simulations of alternating bacterial growth. This study develops a new bacteria subroutine for the SWAT in an attempt to improve its prediction accuracy. We introduced critical temperatures as a parameter to simulate the onset of bacterial growth/die-off and to reproduce the seasonal variability of bacteria. The module developed in this study will improve modeling for environmental management schemes.

On the mechanics of growing thin biological membranes

NASA Astrophysics Data System (ADS)

Rausch, Manuel K.; Kuhl, Ellen

2014-02-01

Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression.

On the mechanics of growing thin biological membranes

PubMed Central

Rausch, Manuel K.; Kuhl, Ellen

2013-01-01

Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression. PMID:24563551

Erythroid cell growth and differentiation in vitro in the simulated microgravity environment of the NASA rotating wall vessel bioreactor

NASA Technical Reports Server (NTRS)

Sytkowski, A. J.; Davis, K. L.

2001-01-01

Prolonged exposure of humans and experimental animals to the altered gravitational conditions of space flight has adverse effects on the lymphoid and erythroid hematopoietic systems. Although some information is available regarding the cellular and molecular changes in lymphocytes exposed to microgravity, little is known about the erythroid cellular changes that may underlie the reduction in erythropoiesis and resultant anemia. We now report a reduction in erythroid growth and a profound inhibition of erythropoietin (Epo)-induced differentiation in a ground-based simulated microgravity model system. Rauscher murine erythroleukemia cells were grown either in tissue culture vessels at 1 x g or in the simulated microgravity environment of the NASA-designed rotating wall vessel (RWV) bioreactor. Logarithmic growth was observed under both conditions; however, the doubling time in simulated microgravity was only one-half of that seen at 1 x g. No difference in apoptosis was detected. Induction with Epo at the initiation of the culture resulted in differentiation of approximately 25% of the cells at 1 x g, consistent with our previous observations. In contrast, induction with Epo at the initiation of simulated microgravity resulted in only one-half of this degree of differentiation. Significantly, the growth of cells in simulated microgravity for 24 h prior to Epo induction inhibited the differentiation almost completely. The results suggest that the NASA RWV bioreactor may serve as a suitable ground-based microgravity simulator to model the cellular and molecular changes in erythroid cells observed in true microgravity.

Urban growth simulation from "first principles".

PubMed

Andersson, Claes; Lindgren, Kristian; Rasmussen, Steen; White, Roger

2002-08-01

General and mathematically transparent models of urban growth have so far suffered from a lack in microscopic realism. Physical models that have been used for this purpose, i.e., diffusion-limited aggregation, dielectric breakdown models, and correlated percolation all have microscopic dynamics for which analogies with urban growth appear stretched. Based on a Markov random field formulation we have developed a model that is capable of reproducing a variety of important characteristic urban morphologies and that has realistic microscopic dynamics. The results presented in this paper are particularly important in relation to "urban sprawl," an important aspect of which is aggressively spreading low-density land uses. This type of growth is increasingly causing environmental, social, and economical problems around the world. The microdynamics of our model, or its "first principles," can be mapped to human decisions and motivations and thus potentially also to policies and regulations. We measure statistical properties of macrostates generated by the urban growth mechanism that we propose, and we compare these to empirical measurements as well as to results from other models. To showcase the open-endedness of the model and to thereby relate our work to applied urban planning we have also included a simulated city consisting of a large number of land use classes in which also topographical data have been used.

Noah-MP-Crop: Introducing dynamic crop growth in the Noah-MP land surface model

NASA Astrophysics Data System (ADS)

Liu, Xing; Chen, Fei; Barlage, Michael; Zhou, Guangsheng; Niyogi, Dev

2016-12-01

Croplands are important in land-atmosphere interactions and in the modification of local and regional weather and climate; however, they are poorly represented in the current version of the coupled Weather Research and Forecasting/Noah with multiparameterization (Noah-MP) land surface modeling system. This study introduced dynamic corn (Zea mays) and soybean (Glycine max) growth simulations and field management (e.g., planting date) into Noah-MP and evaluated the enhanced model (Noah-MP-Crop) at field scales using crop biomass data sets, surface heat fluxes, and soil moisture observations. Compared to the generic dynamic vegetation and prescribed-leaf area index (LAI)-driven methods in Noah-MP, the Noah-MP-Crop showed improved performance in simulating leaf area index (LAI) and crop biomass. This model is able to capture the seasonal and annual variability of LAI and to differentiate corn and soybean in peak values of LAI as well as the length of growing seasons. Improved simulations of crop phenology in Noah-MP-Crop led to better surface heat flux simulations, especially in the early period of growing season where current Noah-MP significantly overestimated LAI. The addition of crop yields as model outputs expand the application of Noah-MP-Crop to regional agriculture studies. There are limitations in the use of current growing degree days (GDD) criteria to predict growth stages, and it is necessary to develop a new method that combines GDD with other environmental factors, to more accurately define crop growth stages. The capability introduced in Noah-MP allows further crop-related studies and development.

Multiscale simulations of the early stages of the growth of graphene on copper

NASA Astrophysics Data System (ADS)

Gaillard, P.; Chanier, T.; Henrard, L.; Moskovkin, P.; Lucas, S.

2015-07-01

We have performed multiscale simulations of the growth of graphene on defect-free copper (111) in order to model the nucleation and growth of graphene flakes during chemical vapour deposition and potentially guide future experimental work. Basic activation energies for atomic surface diffusion were determined by ab initio calculations. Larger scale growth was obtained within a kinetic Monte Carlo approach (KMC) with parameters based on the ab initio results. The KMC approach counts the first and second neighbours to determine the probability of surface diffusion. We report qualitative results on the size and shape of the graphene islands as a function of deposition flux. The dominance of graphene zigzag edges for low deposition flux, also observed experimentally, is explained by its larger dynamical stability that the present model fully reproduced.

Integrated Predictive Tools for Customizing Microstructure and Material Properties of Additively Manufactured Aerospace Components

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

Radhakrishnan, Balasubramaniam; Fattebert, Jean-Luc; Gorti, Sarma B.

Additive Manufacturing (AM) refers to a process by which digital three-dimensional (3-D) design data is converted to build up a component by depositing material layer-by-layer. United Technologies Corporation (UTC) is currently involved in fabrication and certification of several AM aerospace structural components made from aerospace materials. This is accomplished by using optimized process parameters determined through numerous design-of-experiments (DOE)-based studies. Certification of these components is broadly recognized as a significant challenge, with long lead times, very expensive new product development cycles and very high energy consumption. Because of these challenges, United Technologies Research Center (UTRC), together with UTC business unitsmore » have been developing and validating an advanced physics-based process model. The specific goal is to develop a physics-based framework of an AM process and reliably predict fatigue properties of built-up structures as based on detailed solidification microstructures. Microstructures are predicted using process control parameters including energy source power, scan velocity, deposition pattern, and powder properties. The multi-scale multi-physics model requires solution and coupling of governing physics that will allow prediction of the thermal field and enable solution at the microstructural scale. The state-of-the-art approach to solve these problems requires a huge computational framework and this kind of resource is only available within academia and national laboratories. The project utilized the parallel phase-fields codes at Oak Ridge National Laboratory (ORNL) and Lawrence Livermore National Laboratory (LLNL), along with the high-performance computing (HPC) capabilities existing at the two labs to demonstrate the simulation of multiple dendrite growth in threedimensions (3-D). The LLNL code AMPE was used to implement the UTRC phase field model that was previously developed for a model binary alloy, and the simulation results were compared against the UTRC simulation results, followed by extension of the UTRC model to simulate multiple dendrite growth in 3-D. The ORNL MEUMAPPS code was used to simulate dendritic growth in a model ternary alloy with the same equilibrium solidification range as the Ni-base alloy 718 using realistic model parameters, including thermodynamic integration with a Calphad based model for the ternary alloy. Implementation of the UTRC model in AMPE met with several numerical and parametric issues that were resolved and good comparison between the simulation results obtained by the two codes was demonstrated for two dimensional (2-D) dendrites. 3-D dendrite growth was then demonstrated with the AMPE code using nondimensional parameters obtained in 2-D simulations. Multiple dendrite growth in 2-D and 3-D were demonstrated using ORNL’s MEUMAPPS code using simple thermal boundary conditions. MEUMAPPS was then modified to incorporate the complex, time-dependent thermal boundary conditions obtained by UTRC’s thermal modeling of single track AM experiments to drive the phase field simulations. The results were in good agreement with UTRC’s experimental measurements.« less

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Tartakovsky, G. D.; Tartakovsky, A. M.; Scheibe, T. D.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2013-09-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Tartakovsky, G.; Tartakovsky, A. M.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2012-12-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

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

Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2013-09-07

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated withmore » microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).« less

Molecular dynamics modeling and simulation of void growth in two dimensions

NASA Astrophysics Data System (ADS)

Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.

2013-10-01

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

Particle-Size-Grouping Model of Precipitation Kinetics in Microalloyed Steels

NASA Astrophysics Data System (ADS)

Xu, Kun; Thomas, Brian G.

2012-03-01

The formation, growth, and size distribution of precipitates greatly affects the microstructure and properties of microalloyed steels. Computational particle-size-grouping (PSG) kinetic models based on population balances are developed to simulate precipitate particle growth resulting from collision and diffusion mechanisms. First, the generalized PSG method for collision is explained clearly and verified. Then, a new PSG method is proposed to model diffusion-controlled precipitate nucleation, growth, and coarsening with complete mass conservation and no fitting parameters. Compared with the original population-balance models, this PSG method saves significant computation and preserves enough accuracy to model a realistic range of particle sizes. Finally, the new PSG method is combined with an equilibrium phase fraction model for plain carbon steels and is applied to simulate the precipitated fraction of aluminum nitride and the size distribution of niobium carbide during isothermal aging processes. Good matches are found with experimental measurements, suggesting that the new PSG method offers a promising framework for the future development of realistic models of precipitation.

Penalty-Based Interface Technology for Prediction of Delamination Growth in Laminated Structures

NASA Technical Reports Server (NTRS)

Averill, Ronald C.

2004-01-01

An effective interface element technology has been developed for connecting and simulating crack growth between independently modeled finite element subdomains (e.g., composite plies). This method has been developed using penalty constraints and allows coupling of finite element models whose nodes do not necessarily coincide along their common interface. Additionally, the present formulation leads to a computational approach that is very efficient and completely compatible with existing commercial software. The present interface element has been implemented in the commercial finite element code ABAQUS as a User Element Subroutine (UEL), making it easy to test the approach for a wide range of problems. The interface element technology has been formulated to simulate delamination growth in composite laminates. Thanks to its special features, the interface element approach makes it possible to release portions of the interface surface whose length is smaller than that of the finite elements. In addition, the penalty parameter can vary within the interface element, allowing the damage model to be applied to a desired fraction of the interface between the two meshes. Results for double cantilever beam DCB, end-loaded split (ELS) and fixed-ratio mixed mode (FRMM) specimens are presented. These results are compared to measured data to assess the ability of the present damage model to simulate crack growth.

Simulation of the ultrasound-induced growth and collapse of a near-wall bubble

NASA Astrophysics Data System (ADS)

Boyd, Bradley; Becker, Sid

2017-11-01

In this study, we consider the acoustically driven growth and collapse of a cavitation bubble in a fluid medium exposed to an ultrasound field. The bubble dynamics are modelled using a compressible, inviscid, multiphase model. The numerical scheme consists of a conservative interface capturing scheme which uses the fifth-order WENO reconstruction with a maximum-principle-satisfying and positivity-preserving limiter, and the HLLC approximate Riemann flux. To model the ultrasound input, a moving boundary oscillates through a fixed grid of finite-volume cells. The growth phase of the simulation shows the rapid non-spherical growth of the near-wall bubble. Once the bubble reaches its maximum size and the collapse phase begins, the simulation shows the formation of a jet which penetrates the bubble towards the wall at the later stages of the collapse. For a bubble with an initial radius of 50 μ m and an ultrasound pressure amplitude of 200 kPa, the pressure experienced by the wall increased rapidly nearing the end of the collapse, reaching a peak pressure of 13 MPa. This model is an important development in the field as it represents the physics of acoustic cavitation in more detail than before. This work was supported by the Royal Society of New Zealand's Marsden Fund.

Simulation of crop yield variability by improved root-soil-interaction modelling

NASA Astrophysics Data System (ADS)

Duan, X.; Gayler, S.; Priesack, E.

2009-04-01

Understanding the processes and factors that govern the within-field variability in crop yield has attached great importance due to applications in precision agriculture. Crop response to environment at field scale is a complex dynamic process involving the interactions of soil characteristics, weather conditions and crop management. The numerous static factors combined with temporal variations make it very difficult to identify and manage the variability pattern. Therefore, crop simulation models are considered to be useful tools in analyzing separately the effects of change in soil or weather conditions on the spatial variability, in order to identify the cause of yield variability and to quantify the spatial and temporal variation. However, tests showed that usual crop models such as CERES-Wheat and CERES-Maize were not able to quantify the observed within-field yield variability, while their performance on crop growth simulation under more homogeneous and mainly non-limiting conditions was sufficent to simulate average yields at the field-scale. On a study site in South Germany, within-field variability in crop growth has been documented since years. After detailed analysis and classification of the soil patterns, two site specific factors, the plant-available-water and the O2 deficiency, were considered as the main causes of the crop growth variability in this field. Based on our measurement of root distribution in the soil profile, we hypothesize that in our case the insufficiency of the applied crop models to simulate the yield variability can be due to the oversimplification of the involved root models which fail to be sensitive to different soil conditions. In this study, the root growth model described by Jones et al. (1991) was adapted by using data of root distributions in the field and linking the adapted root model to the CERES crop model. The ability of the new root model to increase the sensitivity of the CERES crop models to different enviromental conditions was then evaluated by means of comparison of the simualtion results with measured data and by scenario calculations.

Effects of simulated weightlessness on fish otolith growth: Clinostat versus Rotating-Wall Vessel

NASA Astrophysics Data System (ADS)

Brungs, Sonja; Hauslage, Jens; Hilbig, Reinhard; Hemmersbach, Ruth; Anken, Ralf

2011-09-01

Stimulus dependence is a general feature of developing sensory systems. It has been shown earlier that the growth of inner ear heavy stones (otoliths) of late-stage Cichlid fish ( Oreochromis mossambicus) and Zebrafish ( Danio rerio) is slowed down by hypergravity, whereas microgravity during space flight yields an opposite effect, i.e. larger than 1 g otoliths, in Swordtail ( Xiphophorus helleri) and in Cichlid fish late-stage embryos. These and related studies proposed that otolith growth is actively adjusted via a feedback mechanism to produce a test mass of the appropriate physical capacity. Using ground-based techniques to apply simulated weightlessness, long-term clinorotation (CR; exposure on a fast-rotating Clinostat with one axis of rotation) led to larger than 1 g otoliths in late-stage Cichlid fish. Larger than normal otoliths were also found in early-staged Zebrafish embryos after short-term Wall Vessel Rotation (WVR; also regarded as a method to simulate weightlessness). These results are basically in line with the results obtained on Swordtails from space flight. Thus, the growth of fish inner ear otoliths seems to be an appropriate parameter to assess the quality of "simulated weightlessness" provided by a particular simulation device. Since CR and WVR are in worldwide use to simulate weightlessness conditions on ground using small-sized specimens, we were prompted to directly compare the effects of CR and WVR on otolith growth using developing Cichlids as model organism. Animals were simultaneously subjected to CR and WVR from a point of time when otolith primordia had begun to calcify both within the utricle (gravity perception) and the saccule (hearing); the respective otoliths are the lapilli and the sagittae. Three such runs were subsequently carried out, using three different batches of fish. The runs were discontinued when the animals began to hatch. In the course of all three runs performed, CR led to larger than normal lapilli, whereas WVR had no effect on the growth of these otoliths. Regarding sagittae, CR resulted in larger than normal stones in one of the three runs. The other CR runs and all WVR runs had no effect on sagittal growth. These results clearly indicate that CR rather than WVR can be regarded as a device to simulate weightlessness using the Cichlid as model organism. Since WVR has earlier been shown to affect otolith growth in Zebrafish, the lifestyle of an animal (mouth-breeding versus egg-laying) seems to be of considerable importance. Further studies using a variety of simulation techniques (including, e.g. magnetic levitation and random positioning) and various species are needed in order to identify the most appropriate technique to simulate weightlessness regarding a particular model organism.

Modeling Gypsy Moth-Related Tree Mortality Under Different Outbreak Scenarios in Interior Highlands Forests

Treesearch

Kurt W. Gottschalk; James M. Guldin; Jimmie J. Colbert

2004-01-01

A simulation was conducted to determine how growth of forests in the Interior Highlands would change under attack by the gypsy moth (Lymantria dispar L.). Simulations were conducted for three different outbreak intensities using the Gypsy Moth Stand-Damage Model. Forest Inventory and Analysis (FIA) inventory data were used as input for the simulation...

Defect, Kinetics and Heat Transfer of CDTE Bridgman Growth without Wall Contact

NASA Technical Reports Server (NTRS)

Larson, D. J., Jr.; Zhang, H.

2003-01-01

A detached growth mechanism has been proposed, which is similar to that proposed by Duffar et al. and used to study the current detached growth system. From numerical results, we can conclude that detached growth will more likely appear if the growth and wetting angles are large and meniscus is flat. Detached thickness is dependent on growth angle, wetting angle, and gap width and shape of the fins. The model can also explain why the detached growth will not happen for metals in which the growth angle is almost zero. Since the growth angle of CdZnTe cannot be changed, to promote detached growth, the number density of the fins should be low and the wetting angle should be high. Also, a much smaller gap width of the fins should be used in the ground experiment and the detached gap width is much smaller. The shape of the fins has minor influence on detached growth. An integrated numerical model for detached solidification has been developed combining a global heat transfer sub-model and a wall contact sub-model. The global heat transfer sub-model accounts for heat and mass transfer in the multiphase system, convection in the melt, macro-segregation, and interface dynamics. The location and dynamics of the solidification interface are accurately tracked by a multizone adaptive grid generation scheme. The wall contact sub-model accounts for the meniscus dynamics at the three-phase boundary. Simulations have been performed for crystal growth in a conventional ampoule and a designed ampoule to understand the benefits of detached solidification and its impacts on crystalline structural quality, e.g., stoichiometry, macro-segregation, and stress. From simulation results, both the Grashof and Marangoni numbers will have significant effects on the shape of growth front, Zn concentration distribution, and radial segregation. The integrated model can be used in designing apparatus and determining the optimal geometry for detached solidification in space and on the ground.

Using Growth and Arrest of Richtmyer-Meshkov Instabilities and Lagrangian Simulations to Study High-Rate Material Strength

NASA Astrophysics Data System (ADS)

Prime, Michael; Vaughan, Diane; Preston, Dean; Oro, David; Buttler, William

2013-06-01

Rayleigh-Taylor instabilities have been widely used to study the deviatoric (flow) strength of solids at high strain rates. More recently, experiments applying a supported shock through mating surfaces (Atwood number = 1) with geometrical perturbations have been proposed for studying strength at strain rates up to 107/sec using Richtmyer-Meshkov (RM) instabilities. Buttler et al. [J. Fluid Mech., 2012] recently reported experimental results for RM instability growth but with an unsupported shock applied by high explosives and the geometrical perturbations on the opposite free surface (Atwood number = -1). This novel configuration allowed detailed experimental observation of the instability growth and arrest. We present results and detailed interpretation from numerical simulations of the Buttler experiments on copper. Highly-resolved, two-dimensional simulations were performed using a Lagrangian hydrocode and the Preston-Tonks-Wallace (PTW) strength model. The model predictions show good agreement with the data in spite of the PTW model being calibrated on lower strain rate data. The numerical simulations are used to 1) examine various assumptions previously made in an analytical model, 2) to estimate the sensitivity of such experiments to material strength and 3) to explore the possibility of extracting meaningful strength information in the face of complicated spatial and temporal variations of stress, pressure, and temperature during the experiments.

Simulating magnetic resonance images based on a model of tumor growth incorporating microenvironment

NASA Astrophysics Data System (ADS)

Jackson, Pamela R.; Hawkins-Daarud, Andrea; Partridge, Savannah C.; Kinahan, Paul E.; Swanson, Kristin R.

2018-03-01

Glioblastoma (GBM), the most aggressive primary brain tumor, is primarily diagnosed and monitored using gadoliniumenhanced T1-weighted and T2-weighted (T2W) magnetic resonance imaging (MRI). Hyperintensity on T2W images is understood to correspond with vasogenic edema and infiltrating tumor cells. GBM's inherent heterogeneity and resulting non-specific MRI image features complicate assessing treatment response. To better understand treatment response, we propose creating a patient-specific untreated virtual imaging control (UVIC), which represents an individual tumor's growth if it had not been treated, for comparison with actual post-treatment images. We generated a T2W MRI UVIC by combining a patient-specific mathematical model of tumor growth with a multi-compartmental MRI signal equation. GBM growth was mathematically modeled using the previously developed Proliferation-Invasion-Hypoxia-Necrosis- Angiogenesis-Edema (PIHNA-E) model, which simulated tumor as being comprised of three cellular phenotypes: normoxic, hypoxic and necrotic cells interacting with a vasculature species, angiogenic factors and extracellular fluid. Within the PIHNA-E model, both hypoxic and normoxic cells emitted angiogenic factors, which recruited additional vessels and caused the vessels to leak, allowing fluid, or edema, to escape into the extracellular space. The model's output was spatial volume fraction maps for each glioma cell type and edema/extracellular space. Volume fraction maps and corresponding T2 values were then incorporated into a multi-compartmental Bloch signal equation to create simulated T2W images. T2 values for individual compartments were estimated from the literature and a normal volunteer. T2 maps calculated from simulated images had normal white matter, normal gray matter, and tumor tissue T2 values within range of literature values.

A one-dimensional sectional model to simulate multicomponent aerosol dynamics in the marine boundary layer 3. Numerical methods and comparisons with exact solutions

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

Gelbard, F.; Fitzgerald, J.W.; Hoppel, W.A.

1998-07-01

We present the theoretical framework and computational methods that were used by {ital Fitzgerald} {ital et al.} [this issue (a), (b)] describing a one-dimensional sectional model to simulate multicomponent aerosol dynamics in the marine boundary layer. The concepts and limitations of modeling spatially varying multicomponent aerosols are elucidated. New numerical sectional techniques are presented for simulating multicomponent aerosol growth, settling, and eddy transport, coupled to time-dependent and spatially varying condensing vapor concentrations. Comparisons are presented with new exact solutions for settling and particle growth by simultaneous dynamic condensation of one vapor and by instantaneous equilibration with a spatially varying secondmore » vapor. {copyright} 1998 American Geophysical Union« less

Identification of a constitutive law for trabecular bone samples under remodeling in the framework of irreversible thermodynamics

NASA Astrophysics Data System (ADS)

Louna, Zineeddine; Goda, Ibrahim; Ganghoffer, Jean-François

2018-01-01

We construct in the present paper constitutive models for bone remodeling based on micromechanical analyses at the scale of a representative unit cell (RUC) including a porous trabecular microstructure. The time evolution of the microstructure is simulated as a surface remodeling process by relating the surface growth remodeling velocity to a surface driving force incorporating a (surface) Eshelby tensor. Adopting the framework of irreversible thermodynamics, a 2D constitutive model based on the setting up of the free energy density and a dissipation potential is identified from FE simulations performed over a unit cell representative of the trabecular architecture obtained from real bone microstructures. The static and evolutive effective properties of bone at the scale of the RUC are obtained by combining a methodology for the evaluation of the average kinematic and static variables over a prototype unit cell and numerical simulations with controlled imposed first gradient rates. The formulated effective growth constitutive law at the scale of the homogenized set of trabeculae within the RUC is of viscoplastic type and relates the average growth strain rate to the homogenized stress tensor. The postulated model includes a power law function of an effective stress chosen to depend on the first and second stress invariants. The model coefficients are calibrated from a set of virtual testing performed over the RUC subjected to a sequence of loadings. Numerical simulations show that overall bone growth does not show any growth kinematic hardening. The obtained results quantify the strength and importance of different types of external loads (uniaxial tension, simple shear, and biaxial loading) on the overall remodeling process and the development of elastic deformations within the RUC.

Phototropic growth control of nanoscale pattern formation in photoelectrodeposited Se–Te films

PubMed Central

Sadtler, Bryce; Burgos, Stanley P.; Batara, Nicolas A.; Beardslee, Joseph A.; Atwater, Harry A.; Lewis, Nathan S.

2013-01-01

Photoresponsive materials that adapt their morphologies, growth directions, and growth rates dynamically in response to the local incident electromagnetic field would provide a remarkable route to the synthesis of complex 3D mesostructures via feedback between illumination and the structure that develops under optical excitation. We report the spontaneous development of ordered, nanoscale lamellar patterns in electrodeposited selenium–tellurium (Se–Te) alloy films grown under noncoherent, uniform illumination on unpatterned substrates in an isotropic electrolyte solution. These inorganic nanostructures exhibited phototropic growth in which lamellar stripes grew toward the incident light source, adopted an orientation parallel to the light polarization direction with a period controlled by the illumination wavelength, and showed an increased growth rate with increasing light intensity. Furthermore, the patterns responded dynamically to changes during growth in the polarization, wavelength, and angle of the incident light, enabling the template-free and pattern-free synthesis, on a variety of substrates, of woodpile, spiral, branched, or zigzag structures, along with dynamically directed growth toward a noncoherent, uniform intensity light source. Full-wave electromagnetic simulations in combination with Monte Carlo growth simulations were used to model light–matter interactions in the Se–Te films and produced a model for the morphological evolution of the lamellar structures under phototropic growth conditions. The experiments and simulations are consistent with a phototropic growth mechanism in which the optical near-field intensity profile selects and reinforces the dominant morphological mode in the emergent nanoscale patterns. PMID:24218617

Phototropic growth control of nanoscale pattern formation in photoelectrodeposited Se-Te films.

PubMed

Sadtler, Bryce; Burgos, Stanley P; Batara, Nicolas A; Beardslee, Joseph A; Atwater, Harry A; Lewis, Nathan S

2013-12-03

Photoresponsive materials that adapt their morphologies, growth directions, and growth rates dynamically in response to the local incident electromagnetic field would provide a remarkable route to the synthesis of complex 3D mesostructures via feedback between illumination and the structure that develops under optical excitation. We report the spontaneous development of ordered, nanoscale lamellar patterns in electrodeposited selenium-tellurium (Se-Te) alloy films grown under noncoherent, uniform illumination on unpatterned substrates in an isotropic electrolyte solution. These inorganic nanostructures exhibited phototropic growth in which lamellar stripes grew toward the incident light source, adopted an orientation parallel to the light polarization direction with a period controlled by the illumination wavelength, and showed an increased growth rate with increasing light intensity. Furthermore, the patterns responded dynamically to changes during growth in the polarization, wavelength, and angle of the incident light, enabling the template-free and pattern-free synthesis, on a variety of substrates, of woodpile, spiral, branched, or zigzag structures, along with dynamically directed growth toward a noncoherent, uniform intensity light source. Full-wave electromagnetic simulations in combination with Monte Carlo growth simulations were used to model light-matter interactions in the Se-Te films and produced a model for the morphological evolution of the lamellar structures under phototropic growth conditions. The experiments and simulations are consistent with a phototropic growth mechanism in which the optical near-field intensity profile selects and reinforces the dominant morphological mode in the emergent nanoscale patterns.

Growth and yield models for central hardwoods

Treesearch

Martin E. Dale; Donald E. Hilt

1989-01-01

Over the last 20 years computers have become an efficient tool to estimate growth and yield. Computerized yield estimates vary from simple approximation or interpolation of traditional normal yield tables to highly sophisticated programs that simulate the growth and yield of each individual tree.

A Systematic Investigation of Within-Subject and Between-Subject Covariance Structures in Growth Mixture Models

ERIC Educational Resources Information Center

Liu, Junhui

2012-01-01

The current study investigated how between-subject and within-subject variance-covariance structures affected the detection of a finite mixture of unobserved subpopulations and parameter recovery of growth mixture models in the context of linear mixed-effects models. A simulation study was conducted to evaluate the impact of variance-covariance…

Modeling of time dependent localized flow shear stress and its impact on cellular growth within additive manufactured titanium implants.

PubMed

Zhang, Ziyu; Yuan, Lang; Lee, Peter D; Jones, Eric; Jones, Julian R

2014-11-01

Bone augmentation implants are porous to allow cellular growth, bone formation and fixation. However, the design of the pores is currently based on simple empirical rules, such as minimum pore and interconnects sizes. We present a three-dimensional (3D) transient model of cellular growth based on the Navier-Stokes equations that simulates the body fluid flow and stimulation of bone precursor cellular growth, attachment, and proliferation as a function of local flow shear stress. The model's effectiveness is demonstrated for two additive manufactured (AM) titanium scaffold architectures. The results demonstrate that there is a complex interaction of flow rate and strut architecture, resulting in partially randomized structures having a preferential impact on stimulating cell migration in 3D porous structures for higher flow rates. This novel result demonstrates the potential new insights that can be gained via the modeling tool developed, and how the model can be used to perform what-if simulations to design AM structures to specific functional requirements. © 2014 Wiley Periodicals, Inc.

Comparing crop growth and carbon budgets simulated across AmeriFlux agricultural sites using the community land model (CLM)

USDA-ARS?s Scientific Manuscript database

Improving process-based crop models is needed to achieve high fidelity forecasts of regional energy, water, and carbon exchange. However, most state-of-the-art Land Surface Models (LSMs) assessed in the fifth phase of the Coupled Model Inter-comparison project (CMIP5) simulated crops as simple C3 or...

Simulations of reactive transport and precipitation with smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Tartakovsky, Alexandre M.; Meakin, Paul; Scheibe, Timothy D.; Eichler West, Rogene M.

2007-03-01

A numerical model based on smoothed particle hydrodynamics (SPH) was developed for reactive transport and mineral precipitation in fractured and porous materials. Because of its Lagrangian particle nature, SPH has several advantages for modeling Navier-Stokes flow and reactive transport including: (1) in a Lagrangian framework there is no non-linear term in the momentum conservation equation, so that accurate solutions can be obtained for momentum dominated flows and; (2) complicated physical and chemical processes such as surface growth due to precipitation/dissolution and chemical reactions are easy to implement. In addition, SPH simulations explicitly conserve mass and linear momentum. The SPH solution of the diffusion equation with fixed and moving reactive solid-fluid boundaries was compared with analytical solutions, Lattice Boltzmann [Q. Kang, D. Zhang, P. Lichtner, I. Tsimpanogiannis, Lattice Boltzmann model for crystal growth from supersaturated solution, Geophysical Research Letters, 31 (2004) L21604] simulations and diffusion limited aggregation (DLA) [P. Meakin, Fractals, scaling and far from equilibrium. Cambridge University Press, Cambridge, UK, 1998] model simulations. To illustrate the capabilities of the model, coupled three-dimensional flow, reactive transport and precipitation in a fracture aperture with a complex geometry were simulated.

Evaluating Modeled Impact Metrics for Human Health, Agriculture Growth, and Near-Term Climate

NASA Astrophysics Data System (ADS)

Seltzer, K. M.; Shindell, D. T.; Faluvegi, G.; Murray, L. T.

2017-12-01

Simulated metrics that assess impacts on human health, agriculture growth, and near-term climate were evaluated using ground-based and satellite observations. The NASA GISS ModelE2 and GEOS-Chem models were used to simulate the near-present chemistry of the atmosphere. A suite of simulations that varied by model, meteorology, horizontal resolution, emissions inventory, and emissions year were performed, enabling an analysis of metric sensitivities to various model components. All simulations utilized consistent anthropogenic global emissions inventories (ECLIPSE V5a or CEDS), and an evaluation of simulated results were carried out for 2004-2006 and 2009-2011 over the United States and 2014-2015 over China. Results for O3- and PM2.5-based metrics featured minor differences due to the model resolutions considered here (2.0° × 2.5° and 0.5° × 0.666°) and model, meteorology, and emissions inventory each played larger roles in variances. Surface metrics related to O3 were consistently high biased, though to varying degrees, demonstrating the need to evaluate particular modeling frameworks before O3 impacts are quantified. Surface metrics related to PM2.5 were diverse, indicating that a multimodel mean with robust results are valuable tools in predicting PM2.5-related impacts. Oftentimes, the configuration that captured the change of a metric best over time differed from the configuration that captured the magnitude of the same metric best, demonstrating the challenge in skillfully simulating impacts. These results highlight the strengths and weaknesses of these models in simulating impact metrics related to air quality and near-term climate. With such information, the reliability of historical and future simulations can be better understood.

Block Oriented Simulation System (BOSS)

NASA Technical Reports Server (NTRS)

Ratcliffe, Jaimie

1988-01-01

Computer simulation is assuming greater importance as a flexible and expedient approach to modeling system and subsystem behavior. Simulation has played a key role in the growth of complex, multiple access space communications such as those used by the space shuttle and the TRW-built Tracking and Data Relay Satellites (TDRS). A powerful new simulator for use in designing and modeling the communication system of NASA's planned Space Station is being developed. Progress to date on the Block (Diagram) Oriented Simulation System (BOSS) is described.

Validating Hydrodynamic Growth in National Ignition Facility Implosions

NASA Astrophysics Data System (ADS)

Peterson, J. Luc

2014-10-01

The hydrodynamic growth of capsule imperfections can threaten the success of inertial confinement fusion implosions. Therefore, it is important to design implosions that are robust to hydrodynamic instabilities. However, the numerical simulation of interacting Rayleigh-Taylor and Richtmyer-Meshkov growth in these implosions is sensitive to modeling uncertainties such as radiation drive and material equations of state, the effects of which are especially apparent at high mode number (small perturbation wavelength) and high convergence ratio (small capsule radius). A series of validation experiments were conducted at the National Ignition Facility to test the ability to model hydrodynamic growth in spherically converging ignition-relevant implosions. These experiments on the Hydro-Growth Radiography platform constituted direct measurements of the growth of pre-imposed imperfections up to Legendre mode 160 and a convergence ratio of greater than four using two different laser drives: a ``low-foot'' drive used during the National Ignition Campaign and a larger adiabat ``high-foot'' drive that is modeled to be relatively more robust to ablation front hydrodynamic growth. We will discuss these experiments and how their results compare to numerical simulations and analytic theories of hydrodynamic growth, as well as their implications for the modeling of future designs. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Coupled hydrodynamic and ecological simulation for prognosticating land reclamation impacts in river estuaries

NASA Astrophysics Data System (ADS)

Xu, Yan; Cai, Yanpeng; Sun, Tao; Yang, Zhifeng; Hao, Yan

2018-03-01

A multiphase finite-element hydrodynamic model and a phytoplankton simulation approach are coupled into a general modeling framework. It can help quantify impacts of land reclamation. Compared with previous studies, it has the following improvements: a) reflection of physical currents and suitable growth areas for phytoplankton, (b) advancement of a simulation method to describe the suitability of phytoplankton in the sea water. As the results, water velocity is 16.7% higher than that of original state without human disturbances. The related filling engineering has shortened sediment settling paths, weakened the vortex flow and reduced the capacity of material exchange. Additionally, coastal reclamation lead to decrease of the growth suitability index (GSI), thus it cut down the stability of phytoplankton species approximately 4-12%. The proposed GSI can be applied to the management of coastal reclamation for minimizing ecological impacts. It will be helpful for facilitating identifying suitable phytoplankton growth areas.

Implementation of Combined Feather and Surface-Normal Ice Growth Models in LEWICE/X

NASA Technical Reports Server (NTRS)

Velazquez, M. T.; Hansman, R. J., Jr.

1995-01-01

Experimental observations have shown that discrete rime ice growths called feathers, which grow in approximately the direction of water droplet impingement, play an important role in the growth of ice on accreting surfaces for some thermodynamic conditions. An improved physical model of ice accretion has been implemented in the LEWICE 2D panel-based ice accretion code maintained by the NASA Lewis Research Center. The LEWICE/X model of ice accretion explicitly simulates regions of feather growth within the framework of the LEWICE model. Water droplets impinging on an accreting surface are withheld from the normal LEWICE mass/energy balance and handled in a separate routine; ice growth resulting from these droplets is performed with enhanced convective heat transfer approximately along droplet impingement directions. An independent underlying ice shape is grown along surface normals using the unmodified LEWICE method. The resulting dual-surface ice shape models roughness-induced feather growth observed in icing wind tunnel tests. Experiments indicate that the exact direction of feather growth is dependent on external conditions. Data is presented to support a linear variation of growth direction with temperature and cloud water content. Test runs of LEWICE/X indicate that the sizes of surface regions containing feathers are influenced by initial roughness element height. This suggests that a previous argument that feather region size is determined by boundary layer transition may be incorrect. Simulation results for two typical test cases give improved shape agreement over unmodified LEWICE.

Simulating wall and corner fire tests on wood products with the OSU room fire model

Treesearch

H. C. Tran

1994-01-01

This work demonstrates the complexity of modeling wall and corner fires in a compartment. The model chosen for this purpose is the Ohio State University (OSU) room fire model. This model was designed to simulate fire growth on walls in a compartment and therefore lends itself to direct comparison with standard room test results. The model input were bench-scale data...

Evaluation of a kinetic model for computer simulation of growth and fermentation by Scheffersomyces (Pichia) stipitis fed D-xylose

USDA-ARS?s Scientific Manuscript database

Scheffersomyces (formly Pichia) stipitis is a potential biocatalyst for converting lignocelluloses to ethanol because the yeast natively ferments xylose. An unstructured kinetic model based upon a system of linear differential equations has been formulated that describes growth and ethanol productio...

NASA Experimental Program to Stimulate Competitive Research: South Carolina

NASA Technical Reports Server (NTRS)

Sutton, Michael A.

2004-01-01

The use of an appropriate relationship model is critical for reliable prediction of future urban growth. Identification of proper variables and mathematic functions and determination of the weights or coefficients are the key tasks for building such a model. Although the conventional logistic regression model is appropriate for handing land use problems, it appears insufficient to address the issue of interdependency of the predictor variables. This study used an alternative approach to simulation and modeling urban growth using artificial neural networks. It developed an operational neural network model trained using a robust backpropagation method. The model was applied in the Myrtle Beach region of South Carolina, and tested with both global datasets and areal datasets to examine the strength of both regional models and areal models. The results indicate that the neural network model not only has many theoretic advantages over other conventional mathematic models in representing the complex urban systems, but also is practically superior to the logistic model in its capability to predict urban growth with better - accuracy and less variation. The neural network model is particularly effective in terms of successfully identifying urban patterns in the rural areas where the logistic model often falls short. It was also found from the area-based tests that there are significant intra-regional differentiations in urban growth with different rules and rates. This suggests that the global modeling approach, or one model for the entire region, may not be adequate for simulation of a urban growth at the regional scale. Future research should develop methods for identification and subdivision of these areas and use a set of area-based models to address the issues of multi-centered, intra- regionally differentiated urban growth.

Process model simulations of the divergence effect

NASA Astrophysics Data System (ADS)

Anchukaitis, K. J.; Evans, M. N.; D'Arrigo, R. D.; Smerdon, J. E.; Hughes, M. K.; Kaplan, A.; Vaganov, E. A.

2007-12-01

We explore the extent to which the Vaganov-Shashkin (VS) model of conifer tree-ring formation can explain evidence for changing relationships between climate and tree growth over recent decades. The VS model is driven by daily environmental forcing (temperature, soil moisture, and solar radiation), and simulates tree-ring growth cell-by-cell as a function of the most limiting environmental control. This simplified representation of tree physiology allows us to examine using a selection of case studies whether instances of divergence may be explained in terms of changes in limiting environmental dependencies or transient climate change. Identification of model-data differences permits further exploration of the effects of tree-ring standardization, atmospheric composition, and additional non-climatic factors.

The Photochemical Reflectance Index from Directional Cornfield Reflectances: Observations and Simulations

NASA Technical Reports Server (NTRS)

Cheng, Yen-Ben; Middleton, Elizabeth M.; Zhang, Qingyuan; Corp, Lawrence A.; Dandois, Jonathan; Kustas, William P.

2012-01-01

The two-layer Markov chain Analytical Canopy Reflectance Model (ACRM) was linked with in situ hyperspectral leaf optical properties to simulate the Photochemical Reflectance Index (PRI) for a corn crop canopy at three different growth stages. This is an extended study after a successful demonstration of PRI simulations for a cornfield previously conducted at an early vegetative growth stage. Consistent with previous in situ studies, sunlit leaves exhibited lower PRI values than shaded leaves. Since sunlit (shaded) foliage dominates the canopy in the reflectance hotspot (coldspot), the canopy PRI derived from field hyperspectral observations displayed sensitivity to both view zenith angle and relative azimuth angle at all growth stages. Consequently, sunlit and shaded canopy sectors were most differentiated when viewed along the azimuth matching the solar principal plane. These directional PRI responses associated with sunlit/shaded foliage were successfully reproduced by the ACRM. As before, the simulated PRI values from the current study were closer to in situ values when both sunlit and shaded leaves were utilized as model input data in a two-layer mode, instead of a one-layer mode with sunlit leaves only. Model performance as judged by correlation between in situ and simulated values was strongest for the mature corn crop (r = 0.87, RMSE = 0.0048), followed by the early vegetative stage (r = 0.78; RMSE = 0.0051) and the early senescent stage (r = 0.65; RMSE = 0.0104). Since the benefit of including shaded leaves in the scheme varied across different growth stages, a further analysis was conducted to investigate how variable fractions of sunlit/shaded leaves affect the canopy PRI values expected for a cornfield, with implications for 20 remote sensing monitoring options. Simulations of the sunlit to shaded canopy ratio near 50/50 +/- 10 (e.g., 60/40) matching field observations at all growth stages were examined. Our results suggest in the importance of the sunlit/shaded fraction and canopy structure in understanding and interpreting PRI.

A Monte Carlo Simulation Comparing the Statistical Precision of Two High-Stakes Teacher Evaluation Methods: A Value-Added Model and a Composite Measure

ERIC Educational Resources Information Center

Spencer, Bryden

2016-01-01

Value-added models are a class of growth models used in education to assign responsibility for student growth to teachers or schools. For value-added models to be used fairly, sufficient statistical precision is necessary for accurate teacher classification. Previous research indicated precision below practical limits. An alternative approach has…

Performance of the SEAPROG prognosis variant of the forest vegetation simulator.

Treesearch

Michael H. McClellan; Frances E. Biles

2003-01-01

This paper reports the first phase of a recent effort to evaluate the performance and use of the FVS-SEAPROG vegetation growth model. In this paper, we present our evaluation of SEAPROG’s performance in modeling the growth of even-aged stands regenerated by clearcutting, windthrow, or fire. We evaluated the model by comparing model predictions to observed values from...

Extended Eden model reproduces growth of an acellular slime mold.

PubMed

Wagner, G; Halvorsrud, R; Meakin, P

1999-11-01

A stochastic growth model was used to simulate the growth of the acellular slime mold Physarum polycephalum on substrates where the nutrients were confined in separate drops. Growth of Physarum on such substrates was previously studied experimentally and found to produce a range of different growth patterns [Phys. Rev. E 57, 941 (1998)]. The model represented the aging of cluster sites and differed from the original Eden model in that the occupation probability of perimeter sites depended on the time of occupation of adjacent cluster sites. This feature led to a bias in the selection of growth directions. A moderate degree of persistence was found to be crucial to reproduce the biological growth patterns under various conditions. Persistence in growth combined quick propagation in heterogeneous environments with a high probability of locating sources of nutrients.

Extended Eden model reproduces growth of an acellular slime mold

NASA Astrophysics Data System (ADS)

Wagner, Geri; Halvorsrud, Ragnhild; Meakin, Paul

1999-11-01

A stochastic growth model was used to simulate the growth of the acellular slime mold Physarum polycephalum on substrates where the nutrients were confined in separate drops. Growth of Physarum on such substrates was previously studied experimentally and found to produce a range of different growth patterns [Phys. Rev. E 57, 941 (1998)]. The model represented the aging of cluster sites and differed from the original Eden model in that the occupation probability of perimeter sites depended on the time of occupation of adjacent cluster sites. This feature led to a bias in the selection of growth directions. A moderate degree of persistence was found to be crucial to reproduce the biological growth patterns under various conditions. Persistence in growth combined quick propagation in heterogeneous environments with a high probability of locating sources of nutrients.

Does spatial variation in environmental conditions affect recruitment? A study using a 3-D model of Peruvian anchovy

NASA Astrophysics Data System (ADS)

Xu, Yi; Rose, Kenneth A.; Chai, Fei; Chavez, Francisco P.; Ayón, Patricia

2015-11-01

We used a 3-dimensional individual-based model (3-D IBM) of Peruvian anchovy to examine how spatial variation in environmental conditions affects larval and juvenile growth and survival, and recruitment. Temperature, velocity, and phytoplankton and zooplankton concentrations generated from a coupled hydrodynamic Nutrients-Phytoplankton-Zooplankton-Detritus (NPZD) model, mapped to a three dimensional rectangular grid, were used to simulate anchovy populations. The IBM simulated individuals as they progressed from eggs to recruitment at 10 cm. Eggs and yolk-sac larvae were followed hourly through the processes of development, mortality, and movement (advection), and larvae and juveniles were followed daily through the processes of growth, mortality, and movement (advection plus behavior). A bioenergetics model was used to grow larvae and juveniles. The NPZD model provided prey fields which influence both food consumption rate as well as behavior mediated movement with individuals going to grids cells having optimal growth conditions. We compared predicted recruitment for monthly cohorts for 1990 through 2004 between the full 3-D IBM and a point (0-D) model that used spatially-averaged environmental conditions. The 3-D and 0-D versions generated similar interannual patterns in monthly recruitment for 1991-2004, with the 3-D results yielding consistently higher survivorship. Both versions successfully captured the very poor recruitment during the 1997-1998 El Niño event. Higher recruitment in the 3-D simulations was due to higher survival during the larval stage resulting from individuals searching for more favorable temperatures that lead to faster growth rates. The strong effect of temperature was because both model versions provided saturating food conditions for larval and juvenile anchovies. We conclude with a discussion of how explicit treatment of spatial variation affected simulated recruitment, other examples of fisheries modeling analyses that have used a similar approach to assess the influence of spatial variation, and areas for further model development.

Porcine spine finite element model: a complementary tool to experimental scoliosis fusionless instrumentation.

PubMed

Hachem, Bahe; Aubin, Carl-Eric; Parent, Stefan

2017-06-01

Developing fusionless devices to treat pediatric scoliosis necessitates lengthy and expensive animal trials. The objective was to develop and validate a porcine spine numerical model as an alternative platform to assess fusionless devices. A parametric finite element model (FEM) of an osseoligamentous porcine spine and rib cage, including the epiphyseal growth plates, was developed. A follower-type load replicated physiological and gravitational loads. Vertebral growth and its modulation were programmed based on the Hueter-Volkmann principle, stipulating growth reduction/promotion due to increased compressive/tensile stresses. Scoliosis induction via a posterior tether and 5-level rib tethering, was simulated over 10 weeks along with its subsequent correction via a contralateral anterior custom tether (20 weeks). Scoliosis induction was also simulated using two experimentally tested compression-based fusionless implants (hemi- and rigid staples) over 12- and 8-weeks growth, respectively. Resulting simulated Cobb and sagittal angles, apical vertebral wedging, and left/right height alterations were compared to reported studies. Simulated induced Cobb and vertebral wedging were 48.4° and 7.6° and corrected to 21° and 5.4°, respectively, with the contralateral anterior tether. Apical rotation (15.6°) was corrected to 7.4°. With the hemi- and rigid staples, Cobb angle was 11.2° and 11.8°, respectively, with 3.7° and 2.0° vertebral wedging. Sagittal plane was within the published range. Convex/concave-side vertebral height difference was 3.1 mm with the induction posterior tether and reduced to 2.3 with the contralateral anterior tether, with 1.4 and 0.8 for the hemi- and rigid staples. The FEM represented growth-restraining effects and growth modulation with Cobb and vertebral wedging within 0.6° and 1.9° of experimental animal results, while it was within 5° for the two simulated staples. Ultimately, the model would serve as a time- and cost-effective tool to assess the biomechanics and long-term effect of compression-based fusionless devices prior to animal trials, assisting the transfer towards treating scoliosis in the growing spine.

Improved simulation of poorly drained forests using Biome-BGC.

PubMed

Bond-Lamberty, Ben; Gower, Stith T; Ahl, Douglas E

2007-05-01

Forested wetlands and peatlands are important in boreal and terrestrial biogeochemical cycling, but most general-purpose forest process models are designed and parameterized for upland systems. We describe changes made to Biome-BGC, an ecophysiological process model, that improve its ability to simulate poorly drained forests. Model changes allowed for: (1) lateral water inflow from a surrounding watershed, and variable surface and subsurface drainage; (2) adverse effects of anoxic soil on decomposition and nutrient mineralization; (3) closure of leaf stomata in flooded soils; and (4) growth of nonvascular plants (i.e., bryophytes). Bryophytes were treated as ectohydric broadleaf evergreen plants with zero stomatal conductance, whose cuticular conductance to CO(2) was dependent on plant water content. Individual model changes were parameterized with published data, and ecosystem-level model performance was assessed by comparing simulated output to field data from the northern BOREAS site in Manitoba, Canada. The simulation of the poorly drained forest model exhibited reduced decomposition and vascular plant growth (-90%) compared with that of the well-drained forest model; the integrated bryophyte photosynthetic response accorded well with published data. Simulated net primary production, biomass and soil carbon accumulation broadly agreed with field measurements, although simulated net primary production was higher than observed data in well-drained stands. Simulated net primary production in the poorly drained forest was most sensitive to oxygen restriction on soil processes, and secondarily to stomatal closure in flooded conditions. The modified Biome-BGC remains unable to simulate true wetlands that are subject to prolonged flooding, because it does not track organic soil formation, water table changes, soil redox potential or anaerobic processes.

Comprehensive computational model for combining fluid hydrodynamics, light transport and biomass growth in a Taylor vortex algal photobioreactor: Lagrangian approach.

PubMed

Gao, Xi; Kong, Bo; Vigil, R Dennis

2017-01-01

A comprehensive quantitative model incorporating the effects of fluid flow patterns, light distribution, and algal growth kinetics on biomass growth rate is developed in order to predict the performance of a Taylor vortex algal photobioreactor for culturing Chlorella vulgaris. A commonly used Lagrangian strategy for coupling the various factors influencing algal growth was employed whereby results from computational fluid dynamics and radiation transport simulations were used to compute numerous microorganism light exposure histories, and this information in turn was used to estimate the global biomass specific growth rate. The simulations provide good quantitative agreement with experimental data and correctly predict the trend in reactor performance as a key reactor operating parameter is varied (inner cylinder rotation speed). However, biomass growth curves are consistently over-predicted and potential causes for these over-predictions and drawbacks of the Lagrangian approach are addressed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Monitoring growth condition of spring maize in Northeast China using a process-based model

NASA Astrophysics Data System (ADS)

Wang, Peijuan; Zhou, Yuyu; Huo, Zhiguo; Han, Lijuan; Qiu, Jianxiu; Tan, Yanjng; Liu, Dan

2018-04-01

Early and accurate assessment of the growth condition of spring maize, a major crop in China, is important for the national food security. This study used a process-based Remote-Sensing-Photosynthesis-Yield Estimation for Crops (RS-P-YEC) model, driven by satellite-derived leaf area index and ground-based meteorological observations, to simulate net primary productivity (NPP) of spring maize in Northeast China from the first ten-day (FTD) of May to the second ten-day (STD) of August during 2001-2014. The growth condition of spring maize in 2014 in Northeast China was monitored and evaluated spatially and temporally by comparison with 5- and 13-year averages, as well as 2009 and 2013. Results showed that NPP simulated by the RS-P-YEC model, with consideration of multi-scattered radiation inside the crop canopy, could reveal the growth condition of spring maize more reasonably than the Boreal Ecosystem Productivity Simulator. Moreover, NPP outperformed other commonly used vegetation indices (e.g., Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI)) for monitoring and evaluating the growth condition of spring maize. Compared with the 5- and 13-year averages, the growth condition of spring maize in 2014 was worse before the STD of June and after the FTD of August, and it was better from the third ten-day (TTD) of June to the TTD of July across Northeast China. Spatially, regions with slightly worse and worse growth conditions in the STD of August 2014 were concentrated mainly in central Northeast China, and they accounted for about half of the production area of spring maize in Northeast China. This study confirms that NPP is a good indicator for monitoring and evaluating growth condition because of its capacity to reflect the physiological characteristics of crops. Meanwhile, the RS-P-YEC model, driven by remote sensing and ground-based meteorological data, is effective for monitoring crop growth condition over large areas in a near real time.

A potential-energy scaling model to simulate the initial stages of thin-film growth

NASA Technical Reports Server (NTRS)

Heinbockel, J. H.; Outlaw, R. A.; Walker, G. H.

1983-01-01

A solid on solid (SOS) Monte Carlo computer simulation employing a potential energy scaling technique was used to model the initial stages of thin film growth. The model monitors variations in the vertical interaction potential that occur due to the arrival or departure of selected adatoms or impurities at all sites in the 400 sq. ft. array. Boltzmann ordered statistics are used to simulate fluctuations in vibrational energy at each site in the array, and the resulting site energy is compared with threshold levels of possible atomic events. In addition to adsorption, desorption, and surface migration, adatom incorporation and diffusion of a substrate atom to the surface are also included. The lateral interaction of nearest, second nearest, and third nearest neighbors is also considered. A series of computer experiments are conducted to illustrate the behavior of the model.

Simulating Carbon Stocks and Fluxes of an African Tropical Montane Forest with an Individual-Based Forest Model

PubMed Central

Fischer, Rico; Ensslin, Andreas; Rutten, Gemma; Fischer, Markus; Schellenberger Costa, David; Kleyer, Michael; Hemp, Andreas; Paulick, Sebastian; Huth, Andreas

2015-01-01

Tropical forests are carbon-dense and highly productive ecosystems. Consequently, they play an important role in the global carbon cycle. In the present study we used an individual-based forest model (FORMIND) to analyze the carbon balances of a tropical forest. The main processes of this model are tree growth, mortality, regeneration, and competition. Model parameters were calibrated using forest inventory data from a tropical forest at Mt. Kilimanjaro. The simulation results showed that the model successfully reproduces important characteristics of tropical forests (aboveground biomass, stem size distribution and leaf area index). The estimated aboveground biomass (385 t/ha) is comparable to biomass values in the Amazon and other tropical forests in Africa. The simulated forest reveals a gross primary production of 24 tcha-1yr-1. Modeling above- and belowground carbon stocks, we analyzed the carbon balance of the investigated tropical forest. The simulated carbon balance of this old-growth forest is zero on average. This study provides an example of how forest models can be used in combination with forest inventory data to investigate forest structure and local carbon balances. PMID:25915854

Coupling sensing to crop models for closed-loop plant production in advanced life support systems

NASA Astrophysics Data System (ADS)

Cavazzoni, James; Ling, Peter P.

1999-01-01

We present a conceptual framework for coupling sensing to crop models for closed-loop analysis of plant production for NASA's program in advanced life support. Crop status may be monitored through non-destructive observations, while models may be independently applied to crop production planning and decision support. To achieve coupling, environmental variables and observations are linked to mode inputs and outputs, and monitoring results compared with model predictions of plant growth and development. The information thus provided may be useful in diagnosing problems with the plant growth system, or as a feedback to the model for evaluation of plant scheduling and potential yield. In this paper, we demonstrate this coupling using machine vision sensing of canopy height and top projected canopy area, and the CROPGRO crop growth model. Model simulations and scenarios are used for illustration. We also compare model predictions of the machine vision variables with data from soybean experiments conducted at New Jersey Agriculture Experiment Station Horticulture Greenhouse Facility, Rutgers University. Model simulations produce reasonable agreement with the available data, supporting our illustration.

Microstructure development in Kolmogorov, Johnson-Mehl, and Avrami nucleation and growth kinetics

NASA Astrophysics Data System (ADS)

Pineda, Eloi; Crespo, Daniel

1999-08-01

A statistical model with the ability to evaluate the microstructure developed in nucleation and growth kinetics is built in the framework of the Kolmogorov, Johnson-Mehl, and Avrami theory. A populational approach is used to compute the observed grain-size distribution. The impingement process which delays grain growth is analyzed, and the effective growth rate of each population is estimated considering the previous grain history. The proposed model is integrated for a wide range of nucleation and growth protocols, including constant nucleation, pre-existing nuclei, and intermittent nucleation with interface or diffusion-controlled grain growth. The results are compared with Monte Carlo simulations, giving quantitative agreement even in cases where previous models fail.

Evaluating Forest Vegetation Simulator predictions for southern Appalachian upland hardwoods with a modified mortality model

Treesearch

Philip J. Radtke; Nathan D. Herring; David L. Loftis; Chad E. Keyser

2012-01-01

Prediction accuracy for projected basal area and trees per acre was assessed for the growth and yield model of the Forest Vegetation Simulator Southern Variant (FVS-Sn). Data for comparison with FVS-Sn predictions were compiled from a collection of n

Growth process and model simulation of three different classes of Schima superba in a natural subtropical forest in China

NASA Astrophysics Data System (ADS)

Wei, Hui; Deng, Xiangwen; Ouyang, Shuai; Chen, Lijun; Chu, Yonghe

2017-01-01

Schima superba is an important fire-resistant, high-quality timber species in southern China. Growth in height, diameter at breast height (DBH), and volume of the three different classes (overtopped, average and dominant) of S. superba were examined in a natural subtropical forest. Four growth models (Richards, edited Weibull, Logistic and Gompertz) were selected to fit the growth of the three different classes of trees. The results showed that there was a fluctuation phenomenon in height and DBH current annual growth process of all three classes. Multiple intersections were found between current annual increment (CAI) and mean annual increment (MAI) curves of both height and DBH, but there was no intersection between volume CAI and MAI curves. All selected models could be used to fit the growth of the three classes of S. superba, with determinant coefficients above 0.9637. However, the edited Weibull model performed best with the highest R2 and the lowest root of mean square error (RMSE). S. superba is a fast-growing tree with a higher growth rate during youth. The height and DBH CAIs of overtopped, average and dominant trees reached growth peaks at ages 5-10, 10-15 and 15-20 years, respectively. According to model simulation, the volume CAIs of overtopped, average and dominant trees reached growth peaks at ages 17, 55 and 76 years, respectively. The biological rotation ages of the overtopped, average and dominant trees of S. superba were 29, 85 and 128 years, respectively.

Simulating historical variability in the amount of old forests in the Oregon Coast Range.

Treesearch

M.C. Wimberly; T.M. Spies; C.J. Long; C. Whitlock

2000-01-01

We developed the landscape age-class demographics simulator (LADS) to model historical variability in the amount of old-growth and late-successional forest in the Oregon Coast Range over the past 3,000 years. The model simulated temporal and spatial patterns of forest fires along with the resulting fluctuations in the distribution of forest age classes across the...

Optimization of space system development resources

NASA Astrophysics Data System (ADS)

Kosmann, William J.; Sarkani, Shahram; Mazzuchi, Thomas

2013-06-01

NASA has had a decades-long problem with cost growth during the development of space science missions. Numerous agency-sponsored studies have produced average mission level cost growths ranging from 23% to 77%. A new study of 26 historical NASA Science instrument set developments using expert judgment to reallocate key development resources has an average cost growth of 73.77%. Twice in history, a barter-based mechanism has been used to reallocate key development resources during instrument development. The mean instrument set development cost growth was -1.55%. Performing a bivariate inference on the means of these two distributions, there is statistical evidence to support the claim that using a barter-based mechanism to reallocate key instrument development resources will result in a lower expected cost growth than using the expert judgment approach. Agent-based discrete event simulation is the natural way to model a trade environment. A NetLogo agent-based barter-based simulation of science instrument development was created. The agent-based model was validated against the Cassini historical example, as the starting and ending instrument development conditions are available. The resulting validated agent-based barter-based science instrument resource reallocation simulation was used to perform 300 instrument development simulations, using barter to reallocate development resources. The mean cost growth was -3.365%. A bivariate inference on the means was performed to determine that additional significant statistical evidence exists to support a claim that using barter-based resource reallocation will result in lower expected cost growth, with respect to the historical expert judgment approach. Barter-based key development resource reallocation should work on spacecraft development as well as it has worked on instrument development. A new study of 28 historical NASA science spacecraft developments has an average cost growth of 46.04%. As barter-based key development resource reallocation has never been tried in a spacecraft development, no historical results exist, and a simulation of using that approach must be developed. The instrument development simulation should be modified to account for spacecraft development market participant differences. The resulting agent-based barter-based spacecraft resource reallocation simulation would then be used to determine if significant statistical evidence exists to prove a claim that using barter-based resource reallocation will result in lower expected cost growth.

ForCent Model Development and Testing using the Enriched Background Isotope Study (EBIS) Experiment

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

Parton, William; Hanson, Paul J; Swanston, Chris

The ForCent forest ecosystem model was developed by making major revisions to the DayCent model including: (1) adding a humus organic pool, (2) incorporating a detailed root growth model, and (3) including plant phenological growth patterns. Observed plant production and soil respiration data from 1993 to 2000 were used to demonstrate that the ForCent model could accurately simulate ecosystem carbon dynamics for the Oak Ridge National Laboratory deciduous forest. A comparison of ForCent versus observed soil pool 14C signature (? 14C) data from the Enriched Background Isotope Study 14C experiment (1999-2006) shows that the model correctly simulates the temporal dynamicsmore » of the 14C label as it moved from the surface litter and roots into the mineral soil organic matter pools. ForCent model validation was performed by comparing the observed Enriched Background Isotope Study experimental data with simulated live and dead root biomass ? 14C data, and with soil respiration ? 14C (mineral soil, humus layer, leaf litter layer, and total soil respiration) data. Results show that the model correctly simulates the impact of the Enriched Background Isotope Study 14C experimental treatments on soil respiration ? 14C values for the different soil organic matter pools. Model results suggest that a two-pool root growth model correctly represents root carbon dynamics and inputs to the soil. The model fitting process and sensitivity analysis exposed uncertainty in our estimates of the fraction of mineral soil in the slow and passive pools, dissolved organic carbon flux out of the litter layer into the mineral soil, and mixing of the humus layer into the mineral soil layer.« less

Monte Carlo Based Calibration and Uncertainty Analysis of a Coupled Plant Growth and Hydrological Model

NASA Astrophysics Data System (ADS)

Houska, Tobias; Multsch, Sebastian; Kraft, Philipp; Frede, Hans-Georg; Breuer, Lutz

2014-05-01

Computer simulations are widely used to support decision making and planning in the agriculture sector. On the one hand, many plant growth models use simplified hydrological processes and structures, e.g. by the use of a small number of soil layers or by the application of simple water flow approaches. On the other hand, in many hydrological models plant growth processes are poorly represented. Hence, fully coupled models with a high degree of process representation would allow a more detailed analysis of the dynamic behaviour of the soil-plant interface. We used the Python programming language to couple two of such high process oriented independent models and to calibrate both models simultaneously. The Catchment Modelling Framework (CMF) simulated soil hydrology based on the Richards equation and the Van-Genuchten-Mualem retention curve. CMF was coupled with the Plant growth Modelling Framework (PMF), which predicts plant growth on the basis of radiation use efficiency, degree days, water shortage and dynamic root biomass allocation. The Monte Carlo based Generalised Likelihood Uncertainty Estimation (GLUE) method was applied to parameterize the coupled model and to investigate the related uncertainty of model predictions to it. Overall, 19 model parameters (4 for CMF and 15 for PMF) were analysed through 2 x 106 model runs randomly drawn from an equally distributed parameter space. Three objective functions were used to evaluate the model performance, i.e. coefficient of determination (R2), bias and model efficiency according to Nash Sutcliffe (NSE). The model was applied to three sites with different management in Muencheberg (Germany) for the simulation of winter wheat (Triticum aestivum L.) in a cross-validation experiment. Field observations for model evaluation included soil water content and the dry matters of roots, storages, stems and leaves. Best parameter sets resulted in NSE of 0.57 for the simulation of soil moisture across all three sites. The shape parameter of the retention curve n was highly constrained whilst other parameters of the retention curve showed a large equifinality. The root and storage dry matter observations were predicted with a NSE of 0.94, a low bias of 58.2 kg ha-1 and a high R2 of 0.98. Dry matters of stem and leaves were predicted with less, but still high accuracy (NSE=0.79, bias=221.7 kg ha-1, R2=0.87). We attribute this slightly poorer model performance to missing leaf senescence which is currently not implemented in PMF. The most constrained parameters for the plant growth model were the radiation-use-efficiency and the base temperature. Cross validation helped to identify deficits in the model structure, pointing out the need of including agricultural management options in the coupled model.

Monte Carlo based calibration and uncertainty analysis of a coupled plant growth and hydrological model

NASA Astrophysics Data System (ADS)

Houska, T.; Multsch, S.; Kraft, P.; Frede, H.-G.; Breuer, L.

2013-12-01

Computer simulations are widely used to support decision making and planning in the agriculture sector. On the one hand, many plant growth models use simplified hydrological processes and structures, e.g. by the use of a small number of soil layers or by the application of simple water flow approaches. On the other hand, in many hydrological models plant growth processes are poorly represented. Hence, fully coupled models with a high degree of process representation would allow a more detailed analysis of the dynamic behaviour of the soil-plant interface. We used the Python programming language to couple two of such high process oriented independent models and to calibrate both models simultaneously. The Catchment Modelling Framework (CMF) simulated soil hydrology based on the Richards equation and the van-Genuchten-Mualem retention curve. CMF was coupled with the Plant growth Modelling Framework (PMF), which predicts plant growth on the basis of radiation use efficiency, degree days, water shortage and dynamic root biomass allocation. The Monte Carlo based Generalised Likelihood Uncertainty Estimation (GLUE) method was applied to parameterize the coupled model and to investigate the related uncertainty of model predictions to it. Overall, 19 model parameters (4 for CMF and 15 for PMF) were analysed through 2 × 106 model runs randomly drawn from an equally distributed parameter space. Three objective functions were used to evaluate the model performance, i.e. coefficient of determination (R2), bias and model efficiency according to Nash Sutcliffe (NSE). The model was applied to three sites with different management in Muencheberg (Germany) for the simulation of winter wheat (Triticum aestivum L.) in a cross-validation experiment. Field observations for model evaluation included soil water content and the dry matters of roots, storages, stems and leaves. Best parameter sets resulted in NSE of 0.57 for the simulation of soil moisture across all three sites. The shape parameter of the retention curve n was highly constrained whilst other parameters of the retention curve showed a large equifinality. The root and storage dry matter observations were predicted with a NSE of 0.94, a low bias of -58.2 kg ha-1 and a high R2 of 0.98. Dry matters of stem and leaves were predicted with less, but still high accuracy (NSE = 0.79, bias = 221.7 kg ha-1, R2 = 0.87). We attribute this slightly poorer model performance to missing leaf senescence which is currently not implemented in PMF. The most constrained parameters for the plant growth model were the radiation-use-efficiency and the base temperature. Cross validation helped to identify deficits in the model structure, pointing out the need of including agricultural management options in the coupled model.

Cellular Automaton Study of Hydrogen Porosity Evolution Coupled with Dendrite Growth During Solidification in the Molten Pool of Al-Cu Alloys

NASA Astrophysics Data System (ADS)

Gu, Cheng; Wei, Yanhong; Yu, Fengyi; Liu, Xiangbo; She, Lvbo

2017-09-01

Welding porosity defects significantly reduce the mechanical properties of welded joints. In this paper, the hydrogen porosity evolution coupled with dendrite growth during solidification in the molten pool of Al-4.0 wt pct Cu alloy was modeled and simulated. Three phases, including a liquid phase, a solid phase, and a gas phase, were considered in this model. The growth of dendrites and hydrogen gas pores was reproduced using a cellular automaton (CA) approach. The diffusion of solute and hydrogen was calculated using the finite difference method (FDM). Columnar and equiaxed dendrite growth with porosity evolution were simulated. Competitive growth between different dendrites and porosities was observed. Dendrite morphology was influenced by porosity formation near dendrites. After solidification, when the porosities were surrounded by dendrites, they could not escape from the liquid, and they made pores that existed in the welded joints. With the increase in the cooling rate, the average diameter of porosities decreased, and the average number of porosities increased. The average diameter of porosities and the number of porosities in the simulation results had the same trend as the experimental results.

Predictive modeling of low solubility semiconductor alloys

NASA Astrophysics Data System (ADS)

Rodriguez, Garrett V.; Millunchick, Joanna M.

2016-09-01

GaAsBi is of great interest for applications in high efficiency optoelectronic devices due to its highly tunable bandgap. However, the experimental growth of high Bi content films has proven difficult. Here, we model GaAsBi film growth using a kinetic Monte Carlo simulation that explicitly takes cation and anion reactions into account. The unique behavior of Bi droplets is explored, and a sharp decrease in Bi content upon Bi droplet formation is demonstrated. The high mobility of simulated Bi droplets on GaAsBi surfaces is shown to produce phase separated Ga-Bi droplets as well as depressions on the film surface. A phase diagram for a range of growth rates that predicts both Bi content and droplet formation is presented to guide the experimental growth of high Bi content GaAsBi films.

Modeling the effects of forest management on in situ and ex situ longleaf pine forest carbon stocks

Treesearch

C.A. Gonzalez-Benecke; L.J. Samuelson; T.A. Martin; W.P. Cropper Jr; Kurt Johnsen; T.A. Stokes; John Butnor; P.H. Anderson

2015-01-01

Assessment of forest carbon storage dynamics requires a variety of techniques including simulation models. We developed a hybrid model to assess the effects of silvicultural management systems on carbon (C) budgets in longleaf pine (Pinus palustris Mill.) plantations in the southeastern U.S. To simulate in situ C pools, the model integrates a growth and yield model...

Analytical approximation of a stochastic, spatial simulation model of fire and forest landscape dynamics

Treesearch

A.J. Tepley; E.A. Thomann

2012-01-01

Recent increases in computation power have prompted enormous growth in the use of simulation models in ecological research. These models are valued for their ability to account for much of the ecological complexity found in field studies, but this ability usually comes at the cost of losing transparency into how the models work. In order to foster greater understanding...

Terrestrial Microgravity Model and Threshold Gravity Simulation sing Magnetic Levitation

NASA Technical Reports Server (NTRS)

Ramachandran, N.

2005-01-01

What is the threshold gravity (minimum gravity level) required for the nominal functioning of the human system? What dosage is required? Do human cell lines behave differently in microgravity in response to an external stimulus? The critical need for such a gravity simulator is emphasized by recent experiments on human epithelial cells and lymphocytes on the Space Shuttle clearly showing that cell growth and function are markedly different from those observed terrestrially. Those differences are also dramatic between cells grown in space and those in Rotating Wall Vessels (RWV), or NASA bioreactor often used to simulate microgravity, indicating that although morphological growth patterns (three dimensional growth) can be successiblly simulated using RWVs, cell function performance is not reproduced - a critical difference. If cell function is dramatically affected by gravity off-loading, then cell response to stimuli such as radiation, stress, etc. can be very different from terrestrial cell lines. Yet, we have no good gravity simulator for use in study of these phenomena. This represents a profound shortcoming for countermeasures research. We postulate that we can use magnetic levitation of cells and tissue, through the use of strong magnetic fields and field gradients, as a terrestrial microgravity model to study human cells. Specific objectives of the research are: 1. To develop a tried, tested and benchmarked terrestrial microgravity model for cell culture studies; 2. Gravity threshold determination; 3. Dosage (magnitude and duration) of g-level required for nominal functioning of cells; 4. Comparisons of magnetic levitation model to other models such as RWV, hind limb suspension, etc. and 5. Cellular response to reduced gravity levels of Moon and Mars.

A Comparative Study of Foreign Direct Investment Flow Using Diffusion Models

NASA Astrophysics Data System (ADS)

Li, Yiming; Chiang, Yi-Hui; Yu, Shao-Ming; Chiang, Su-Yun; Hung, C.-H.

2007-12-01

In this work, we apply an improvement dynamic model of the foreign direct investment (FDI) flow to analyze the evolution of FDI flow. In comparison with the fundamental growth model of FDI, the simulation result is further accurate if the asymmetric growth pattern and heterogeneity of the potential adopters are considered. According to the result, the internal influence dominates the growth of FDI flow from Taiwan to China during 2001-2006, taking the electronics industry for example.

A Linked Model for Simulating Stand Development and Growth Processes of Loblolly Pine

Treesearch

V. Clark Baldwin; Phillip M. Dougherty; Harold E. Burkhart

1998-01-01

Linking models of different scales (e.g., process, tree-stand-ecosystem) is essential for furthering our understanding of stand, climatic, and edaphic effects on tree growth and forest productivity. Moreover, linking existing models that differ in scale and levels of resolution quickly identifies knowledge gaps in information required to scale from one level to another...

Earth surface modeling for education: How effective is it? Latest classroom tests with Web-based Interactive Landform Simulation Model - Grand Canyon (WILSIM-GC)

NASA Astrophysics Data System (ADS)

Luo, W.; Pelletier, J. D.; Smith, T.; Whalley, K.; Shelhamer, A.; Darling, A.; Ormand, C. J.; Duffin, K.; Hung, W. C.; Iverson, E. A. R.; Shernoff, D.; Zhai, X.; Chiang, J. L.; Lotter, N.

2016-12-01

The Web-based Interactive Landform Simulation Model - Grand Canyon (WILSIM-GC, http://serc.carleton.edu/landform/) is a simplified version of a physically-based model that simulates bedrock channel erosion, cliff retreat, and base level change. Students can observe the landform evolution in animation under different scenarios by changing parameter values. In addition, cross-sections and profiles at different time intervals can be displayed and saved for further quantitative analysis. Students were randomly assigned to a treatment group (using WILSIM-GC simulation) or a control group (using traditional paper-based material). Pre- and post-tests were administered to measure students' understanding of the concepts and processes related to Grand Canyon formation and evolution. Results from the ANOVA showed that for both groups there were statistically significant growth in scores from pre-test to post-test [F(1, 47) = 25.82, p < .001], but the growth in scores between the two groups was not statistically significant [F(1, 47) = 0.08, p =.774]. In semester 1, the WILSIM-GC group showed greater growth, while in semester 2, the paper-based group showed greater growth. Additionally, a significant time × group × gender × semester interaction effect was observed [F(1, 47) = 4.76, p =.034]. Here, in semester 1 female students were more strongly advantaged by the WILSIM-GC intervention than male students, while in semester 2, female students were less strongly advantaged than male students. The new results are consistent with our initial findings (Luo et al., 2016) and others reported in the literature, i.e., simulation approach is at least equally effective as traditional paper-based method in teaching students about landform evolution. Survey data indicate that students favor the simulation approach. Further study is needed to investigate the reasons for the difference by gender.

Agent-Based Modeling of Cancer Stem Cell Driven Solid Tumor Growth.

PubMed

Poleszczuk, Jan; Macklin, Paul; Enderling, Heiko

2016-01-01

Computational modeling of tumor growth has become an invaluable tool to simulate complex cell-cell interactions and emerging population-level dynamics. Agent-based models are commonly used to describe the behavior and interaction of individual cells in different environments. Behavioral rules can be informed and calibrated by in vitro assays, and emerging population-level dynamics may be validated with both in vitro and in vivo experiments. Here, we describe the design and implementation of a lattice-based agent-based model of cancer stem cell driven tumor growth.

Multi-scale finite element model of growth plate damage during the development of slipped capital femoral epiphysis.

PubMed

Farzaneh, S; Paseta, O; Gómez-Benito, M J

2015-04-01

Slipped capital femoral epiphysis (SCFE) is one of the most common disorders of adolescent hips. A number of works have related the development of SCFE to mechanical factors. Due to the difficulty of diagnosing SCFE in its early stages, the disorder often progresses over time, resulting in serious side effects. Therefore, the development of a tool to predict the initiation of damage in the growth plate is needed. Because the growth plate is a heterogeneous structure, to develop a precise and reliable model, it is necessary to consider this structure from both macro- and microscale perspectives. Thus, the main objective of this work is to develop a numerical multi-scale model that links damage occurring at the microscale to damage occurring at the macroscale. The use of this model enables us to predict which regions of the growth plate are at high risk of damage. First, we have independently analyzed the microscale to simulate the microstructure under shear and tensile tests to calibrate the damage model. Second, we have employed the model to simulate damage occurring in standardized healthy and affected femurs during the heel-strike stage of stair climbing. Our results indicate that on the macroscale, damage is concentrated in the medial region of the growth plate in both healthy and affected femurs. Furthermore, damage to the affected femur is greater than damage to the healthy femur from both the micro- and macrostandpoints. Maximal damage is observed in territorial matrices. Furthermore, simulations illustrate that little damage occurs in the reserve zone. These findings are consistent with previous findings reported in well-known experimental works.

Evolution of the potential distribution area of french mediterranean forests under global warming

NASA Astrophysics Data System (ADS)

Gaucherel, C.; Guiot, J.; Misson, L.

2008-02-01

This work aims at understanding future spatial and temporal distributions of tree species in the Mediterranean region of France under various climates. We focused on two different species (Pinus Halepensis and Quercus Ilex) and compared their growth under the IPCC-B2 climate scenario in order to quantify significant changes between present and future. The influence of environmental factors such as atmospheric CO2 increase and topography on the tree growth has also been quantified. We modeled species growths with the help of a process-based model (MAIDEN), previously calibrated over measured ecophysiological and dendrochronological series with a Bayesian scheme. The model was fed with the ARPEGE - MeteoFrance climate model, combined with an explicit increase in CO2 atmospheric concentration. The main output of the model gives the carbon allocation in boles and thus tree production. Our results show that the MAIDEN model is correctly able to simulate pine and oak production in space and time, after detailed calibration and validation stages. Yet, these simulations, mainly based on climate, are indicative and not predictive. The comparison of simulated growth at end of 20 and 21 centuries, show a shift of the pine production optimum from about 650 to 950 m due to 2.5°K temperature increase, while no optimum has been found for oak. With the direct effect of CO2 increase taken into account, both species show a significant increase in productivity (+26 and +43% for pine and oak, respectively) at the end of the 21 century. While both species have complementary growth mechanisms, they have a good chance to extend their spatial distribution and their elevation in the Alps during the 21 century under the IPCC-B2 climate scenario. This extension is mainly due to the CO2 fertilization effect.

Numerical analysis of thermal stress and dislocation density distributions in large size multi-crystalline silicon ingots during the seeded growth process

NASA Astrophysics Data System (ADS)

Nguyen, Thi Hoai Thu; Chen, Jyh-Chen; Hu, Chieh; Chen, Chun-Hung; Huang, Yen-Hao; Lin, Huang-Wei; Yu, Andy; Hsu, Bruce

2017-06-01

In this study, a global transient numerical simulation of silicon growth from the beginning of the solidification process until the end of the cooling process is carried out modeling the growth of an 800 kg ingot in an industrial seeded directional solidification furnace. The standard furnace is modified by the addition of insulating blocks in the hot zone. The simulation results show that there is a significant decrease in the thermal stress and dislocation density in the modified model as compared to the standard one (a maximal decrease of 23% and 75% along the center line of ingot for thermal stress and dislocation density, respectively). This modification reduces the heating power consumption for solidification of the silicon melt by about 17% and shortens the growth time by about 2.5 h. Moreover, it is found that adjusting the operating conditions of modified model to obtain the lower growth rate during the early stages of the solidification process can lower dislocation density and total heater power.

Analysing and modelling the growth behaviour of Listeria monocytogenes on RTE cooked meat products after a high pressure treatment at 400 MPa.

PubMed

Hereu, A; Dalgaard, P; Garriga, M; Aymerich, T; Bover-Cid, S

2014-09-01

Various predictive models are available for high pressure inactivation of Listeria monocytogenes in food, but currently available models do not consider the growth kinetics of surviving cells during the subsequent storage of products. Therefore, we characterised the growth of L. monocytogenes in sliced cooked meat products after a pressurization treatment. Two inoculum levels (10(7) or 10(4) CFU/g) and two physiological states before pressurization (freeze-stressed or cold-adapted) were evaluated. Samples of cooked ham and mortadella were inoculated, high pressure processed (400 MPa, 5 min) and subsequently stored at 4, 8 and 12 °C. The Logistic model with delay was used to estimate lag phase (λ) and maximum specific growth rate (μmax) values from the obtained growth curves. The effect of storage temperature on μmax and λ was modelled using the Ratkowsky square root model and the relative lag time (RLT) concept. Compared with cold-adapted cells the freeze-stressed cells were more pressure-resistant and showed a much longer lag phase during growth after the pressure treatment. Interestingly, for high-pressure inactivation and subsequent growth, the time to achieve a concentration of L. monocytogenes 100-fold (2-log) higher than the cell concentration prior to the pressure treatment was similar for the two studied physiological states of the inoculum. Two secondary models were necessary to describe the different growth behaviour of L. monocytogenes on ready-to-eat cooked ham (lean product) and mortadella (fatty product). This supported the need of a product-oriented approach to assess growth after high pressure processing. The performance of the developed predictive models for the growth of L. monocytogenes in high-pressure processed cooked ham and mortadella was evaluated by comparison with available data from the literature and by using the Acceptable Simulation Zone approach. Overall, 91% of the relative errors fell into the Acceptable Simulation Zone. Copyright © 2014 Elsevier B.V. All rights reserved.

Towards a consensus-based biokinetic model for green microalgae - The ASM-A.

PubMed

Wágner, Dorottya S; Valverde-Pérez, Borja; Sæbø, Mariann; Bregua de la Sotilla, Marta; Van Wagenen, Jonathan; Smets, Barth F; Plósz, Benedek Gy

2016-10-15

Cultivation of microalgae in open ponds and closed photobioreactors (PBRs) using wastewater resources offers an opportunity for biochemical nutrient recovery. Effective reactor system design and process control of PBRs requires process models. Several models with different complexities have been developed to predict microalgal growth. However, none of these models can effectively describe all the relevant processes when microalgal growth is coupled with nutrient removal and recovery from wastewaters. Here, we present a mathematical model developed to simulate green microalgal growth (ASM-A) using the systematic approach of the activated sludge modelling (ASM) framework. The process model - identified based on a literature review and using new experimental data - accounts for factors influencing photoautotrophic and heterotrophic microalgal growth, nutrient uptake and storage (i.e. Droop model) and decay of microalgae. Model parameters were estimated using laboratory-scale batch and sequenced batch experiments using the novel Latin Hypercube Sampling based Simplex (LHSS) method. The model was evaluated using independent data obtained in a 24-L PBR operated in sequenced batch mode. Identifiability of the model was assessed. The model can effectively describe microalgal biomass growth, ammonia and phosphate concentrations as well as the phosphorus storage using a set of average parameter values estimated with the experimental data. A statistical analysis of simulation and measured data suggests that culture history and substrate availability can introduce significant variability on parameter values for predicting the reaction rates for bulk nitrate and the intracellularly stored nitrogen state-variables, thereby requiring scenario specific model calibration. ASM-A was identified using standard cultivation medium and it can provide a platform for extensions accounting for factors influencing algal growth and nutrient storage using wastewater resources. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structure, Function, and Applications of the Georgetown-Einstein (GE) Breast Cancer Simulation Model.

PubMed

Schechter, Clyde B; Near, Aimee M; Jayasekera, Jinani; Chandler, Young; Mandelblatt, Jeanne S

2018-04-01

The Georgetown University-Albert Einstein College of Medicine breast cancer simulation model (Model GE) has evolved over time in structure and function to reflect advances in knowledge about breast cancer, improvements in early detection and treatment technology, and progress in computing resources. This article describes the model and provides examples of model applications. The model is a discrete events microsimulation of single-life histories of women from multiple birth cohorts. Events are simulated in the absence of screening and treatment, and interventions are then applied to assess their impact on population breast cancer trends. The model accommodates differences in natural history associated with estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) biomarkers, as well as conventional breast cancer risk factors. The approach for simulating breast cancer natural history is phenomenological, relying on dates, stage, and age of clinical and screen detection for a tumor molecular subtype without explicitly modeling tumor growth. The inputs to the model are regularly updated to reflect current practice. Numerous technical modifications, including the use of object-oriented programming (C++), and more efficient algorithms, along with hardware advances, have increased program efficiency permitting simulations of large samples. The model results consistently match key temporal trends in US breast cancer incidence and mortality. The model has been used in collaboration with other CISNET models to assess cancer control policies and will be applied to evaluate clinical trial design, recurrence risk, and polygenic risk-based screening.

Applicability of land use models for the Houston area test site

NASA Technical Reports Server (NTRS)

Petersburg, R. K.; Bradford, L. H.

1973-01-01

Descriptions of land use models are presented which were considered for their applicability to the Houston Area Test Site. These models are representative both of the prevailing theories of land use dynamics and of basic approaches to simulation. The models considered are: a model of metropolis, land use simulation model, emperic land use forecasting model, a probabilistic model for residential growth, and the regional environmental management allocation process. Sources of environmental/resource information are listed.

L3.PHI.CTF.P10.02-rev2 Coupling of Subchannel T/H (CTF) and CRUD Chemistry (MAMBA1D)

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

Salko, Robert K.; Palmtag, Scott; Collins, Benjamin S.

2015-05-15

The purpose of this milestone is to create a preliminary capability for modeling light water reactor (LWR) thermal-hydraulic (T/H) and CRUD growth using the CTF subchannel code and the subgrid version of the MAMBA CRUD chemistry code, MAMBA1D. In part, this is a follow-on to Milestone L3.PHI.VCS.P9.01, which is documented in Report CASL-U-2014-0188-000, titled "Development of CTF Capability for Modeling Reactor Operating Cycles with Crud Growth". As the title suggests, the previous milestone set up a framework for modeling reactor operation cycles with CTF. The framework also facilitated coupling to a CRUD chemistry capability for modeling CRUD growth throughout themore » reactor operating cycle. To demonstrate the capability, a simple CRUD \\surrogate" tool was developed and coupled to CTF; however, it was noted that CRUD growth predictions by the surrogate were not considered realistic. This milestone builds on L3.PHI.VCS.P9.01 by replacing this simple surrogate tool with the more advanced MAMBA1D CRUD chemistry code. Completing this task involves addressing unresolved tasks from Milestone L3.PHI.VCS.P9.01, setting up an interface to MAMBA1D, and extracting new T/H information from CTF that was not previously required in the simple surrogate tool. Speci c challenges encountered during this milestone include (1) treatment of the CRUD erosion model, which requires local turbulent kinetic energy (TKE) (a value that CTF does not calculate) and (2) treatment of the MAMBA1D CRUD chimney boiling model in the CTF rod heat transfer solution. To demonstrate this new T/H, CRUD modeling capability, two sets of simulations were performed: (1) an 18 month cycle simulation of a quarter symmetry model of Watts Bar and (2) a simulation of Assemblies G69 and G70 from Seabrook Cycle 5. The Watts Bar simulation is merely a demonstration of the capability. The simulation of the Seabrook cycle, which had experienced CRUD-related fuel rod failures, had actual CRUD-scrape data to compare with results. As results show, the initial CTF/MAMBA1D-predicted CRUD thicknesses were about half of their expected values, so further investigation will be required for this simulation.« less

Growth Simulation and Discrimination of Botrytis cinerea, Rhizopus stolonifer and Colletotrichum acutatum Using Hyperspectral Reflectance Imaging

PubMed Central

Gu, Xinzhe; Wang, Zhenjie; Huang, Yangmin; Wei, Yingying; Zhang, Miaomiao; Tu, Kang

2015-01-01

This research aimed to develop a rapid and nondestructive method to model the growth and discrimination of spoilage fungi, like Botrytis cinerea, Rhizopus stolonifer and Colletotrichum acutatum, based on hyperspectral imaging system (HIS). A hyperspectral imaging system was used to measure the spectral response of fungi inoculated on potato dextrose agar plates and stored at 28°C and 85% RH. The fungi were analyzed every 12 h over two days during growth, and optimal simulation models were built based on HIS parameters. The results showed that the coefficients of determination (R2) of simulation models for testing datasets were 0.7223 to 0.9914, and the sum square error (SSE) and root mean square error (RMSE) were in a range of 2.03–53.40×10−4 and 0.011–0.756, respectively. The correlation coefficients between the HIS parameters and colony forming units of fungi were high from 0.887 to 0.957. In addition, fungi species was discriminated by partial least squares discrimination analysis (PLSDA), with the classification accuracy of 97.5% for the test dataset at 36 h. The application of this method in real food has been addressed through the analysis of Botrytis cinerea, Rhizopus stolonifer and Colletotrichum acutatum inoculated in peaches, demonstrating that the HIS technique was effective for simulation of fungal infection in real food. This paper supplied a new technique and useful information for further study into modeling the growth of fungi and detecting fruit spoilage caused by fungi based on HIS. PMID:26642054

An individual based computational model of intestinal crypt fission and its application to predicting unrestrictive growth of the intestinal epithelium.

PubMed

Pin, Carmen; Parker, Aimee; Gunning, A Patrick; Ohta, Yuki; Johnson, Ian T; Carding, Simon R; Sato, Toshiro

2015-02-01

Intestinal crypt fission is a homeostatic phenomenon, observable in healthy adult mucosa, but which also plays a pathological role as the main mode of growth of some intestinal polyps. Building on our previous individual based model for the small intestinal crypt and on in vitro cultured intestinal organoids, we here model crypt fission as a budding process based on fluid mechanics at the individual cell level and extrapolated predictions for growth of the intestinal epithelium. Budding was always observed in regions of organoids with abundant Paneth cells. Our data support a model in which buds are biomechanically initiated by single stem cells surrounded by Paneth cells which exhibit greater resistance to viscoelastic deformation, a hypothesis supported by atomic force measurements of single cells. Time intervals between consecutive budding events, as simulated by the model and observed in vitro, were 2.84 and 2.62 days, respectively. Predicted cell dynamics was unaffected within the original crypt which retained its full capability of providing cells to the epithelium throughout fission. Mitotic pressure in simulated primary crypts forced upward migration of buds, which simultaneously grew into new protruding crypts at a rate equal to 1.03 days(-1) in simulations and 0.99 days(-1) in cultured organoids. Simulated crypts reached their final size in 4.6 days, and required 6.2 days to migrate to the top of the primary crypt. The growth of the secondary crypt is independent of its migration along the original crypt. Assuming unrestricted crypt fission and multiple budding events, a maximal growth rate of the intestinal epithelium of 0.10 days(-1) is predicted and thus approximately 22 days are required for a 10-fold increase of polyp size. These predictions are in agreement with the time reported to develop macroscopic adenomas in mice after loss of Apc in intestinal stem cells.

Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

NASA Astrophysics Data System (ADS)

Miecnikowski, Matthew T.; Sturdevant, Benjamin J.; Chen, Yang; Parker, Scott E.

2018-05-01

Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. This work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

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

PubMed Central

Xu, Guanghua; Yang, Junjie; Li, Guoqing

2013-01-01

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

Growth/reflectance model interface for wheat and corresponding model

NASA Technical Reports Server (NTRS)

Suits, G. H.; Sieron, R.; Odenweller, J.

1984-01-01

The use of modeling to explore the possibility of discovering new and useful crop condition indicators which might be available from the Thematic Mapper and to connect these symptoms to the biological causes in the crop is discussed. A crop growth model was used to predict the day to day growth features of the crop as it responds biologically to the various environmental factors. A reflectance model was used to predict the character of the interaction of daylight with the predicted growth features. An atmospheric path radiance was added to the reflected daylight to simulate the radiance appearing at the sensor. Finally, the digitized data sent to a ground station were calculated. The crop under investigation is wheat.

Simulation of Bacillus subtilis biofilm growth on agar plate by diffusion-reaction based continuum model

NASA Astrophysics Data System (ADS)

Zhang, Xianlong; Wang, Xiaoling; Nie, Kai; Li, Mingpeng; Sun, Qingping

2016-08-01

Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm’s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

Simulation of Bacillus subtilis biofilm growth on agar plate by diffusion-reaction based continuum model.

PubMed

Zhang, Xianlong; Wang, Xiaoling; Nie, Kai; Li, Mingpeng; Sun, Qingping

2016-07-19

Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm's shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

A Computational Model Predicting Disruption of Blood Vessel Development

PubMed Central

Kleinstreuer, Nicole; Dix, David; Rountree, Michael; Baker, Nancy; Sipes, Nisha; Reif, David; Spencer, Richard; Knudsen, Thomas

2013-01-01

Vascular development is a complex process regulated by dynamic biological networks that vary in topology and state across different tissues and developmental stages. Signals regulating de novo blood vessel formation (vasculogenesis) and remodeling (angiogenesis) come from a variety of biological pathways linked to endothelial cell (EC) behavior, extracellular matrix (ECM) remodeling and the local generation of chemokines and growth factors. Simulating these interactions at a systems level requires sufficient biological detail about the relevant molecular pathways and associated cellular behaviors, and tractable computational models that offset mathematical and biological complexity. Here, we describe a novel multicellular agent-based model of vasculogenesis using the CompuCell3D (http://www.compucell3d.org/) modeling environment supplemented with semi-automatic knowledgebase creation. The model incorporates vascular endothelial growth factor signals, pro- and anti-angiogenic inflammatory chemokine signals, and the plasminogen activating system of enzymes and proteases linked to ECM interactions, to simulate nascent EC organization, growth and remodeling. The model was shown to recapitulate stereotypical capillary plexus formation and structural emergence of non-coded cellular behaviors, such as a heterologous bridging phenomenon linking endothelial tip cells together during formation of polygonal endothelial cords. Molecular targets in the computational model were mapped to signatures of vascular disruption derived from in vitro chemical profiling using the EPA's ToxCast high-throughput screening (HTS) dataset. Simulating the HTS data with the cell-agent based model of vascular development predicted adverse effects of a reference anti-angiogenic thalidomide analog, 5HPP-33, on in vitro angiogenesis with respect to both concentration-response and morphological consequences. These findings support the utility of cell agent-based models for simulating a morphogenetic series of events and for the first time demonstrate the applicability of these models for predictive toxicology. PMID:23592958

Supplemental oxygen attenuates the increase in wound bacterial growth during simulated aeromedical evacuation in goats.

PubMed

Earnest, Ryan E; Sonnier, Dennis I; Makley, Amy T; Campion, Eric M; Wenke, Joseph C; Bailey, Stephanie R; Dorlac, Warren C; Lentsch, Alex B; Pritts, Timothy A

2012-07-01

Bacterial growth in soft tissue and open fractures is a known risk factor for tissue loss and complications in contaminated musculoskeletal wounds. Current care for battlefield casualties with soft tissue and musculoskeletal wounds includes tactical and strategic aeromedical evacuation (AE). This exposes patients to a hypobaric, hypoxic environment. In this study, we sought to determine whether exposure to AE alters bacterial growth in contaminated complex musculoskeletal wounds and whether supplemental oxygen had any effect on wound infections during simulated AE. A caprine model of a contaminated complex musculoskeletal wound was used. Complex musculoskeletal wounds were created and inoculated with bioluminescent Pseudomonas aeruginosa. Goats were divided into three experimental groups: ground control, simulated AE, and simulated AE with supplemental oxygen. Simulated AE was induced in a hypobaric chamber pressurized to 8,800 feet for 7 hours. Bacterial luminescence was measured using a photon counting camera at three time points: preflight (20 hours postsurgery), postflight (7 hours from preflight and 27 hours postsurgery), and necropsy (24 hours from preflight and 44 hours postsurgery). There was a significant increase in bacterial growth in the AE group compared with the ground control group measured postflight and at necropsy. Simulated AE induced hypoxia with oxygen saturation less than 93%. Supplemental oxygen corrected the hypoxia and significantly reduced bacterial growth in wounds at necropsy. Hypoxia induced during simulated AE enhances bacterial growth in complex musculoskeletal wounds which can be prevented with the application of supplemental oxygen to the host.

A probabilistic fatigue analysis of multiple site damage

NASA Technical Reports Server (NTRS)

Rohrbaugh, S. M.; Ruff, D.; Hillberry, B. M.; Mccabe, G.; Grandt, A. F., Jr.

1994-01-01

The variability in initial crack size and fatigue crack growth is incorporated in a probabilistic model that is used to predict the fatigue lives for unstiffened aluminum alloy panels containing multiple site damage (MSD). The uncertainty of the damage in the MSD panel is represented by a distribution of fatigue crack lengths that are analytically derived from equivalent initial flaw sizes. The variability in fatigue crack growth rate is characterized by stochastic descriptions of crack growth parameters for a modified Paris crack growth law. A Monte-Carlo simulation explicitly describes the MSD panel by randomly selecting values from the stochastic variables and then grows the MSD cracks with a deterministic fatigue model until the panel fails. Different simulations investigate the influences of the fatigue variability on the distributions of remaining fatigue lives. Six cases that consider fixed and variable conditions of initial crack size and fatigue crack growth rate are examined. The crack size distribution exhibited a dominant effect on the remaining fatigue life distribution, and the variable crack growth rate exhibited a lesser effect on the distribution. In addition, the probabilistic model predicted that only a small percentage of the life remains after a lead crack develops in the MSD panel.

An Individual-Tree Growth and Yield Prediction System for Even-Aged Natural Shortleaf Pine Forests

Treesearch

Thomas B. Lynch; Kenneth L. Hitch; Michael M. Huebschmann; Paul A. Murphy

1999-01-01

The development of a system of equations that model the growth and development of even-aged natural shortleaf (Pinus echinata Mill.) pine forests is described. The growth prediction system is a distance-independent individual-tree simulator containing equations that predict basal-area growth, survival, total and merchantable heights, and total and...

Using Geostatistical Data Fusion Techniques and MODIS Data to Upscale Simulated Wheat Yield

NASA Astrophysics Data System (ADS)

Castrignano, A.; Buttafuoco, G.; Matese, A.; Toscano, P.

2014-12-01

Population growth increases food request. Assessing food demand and predicting the actual supply for a given location are critical components of strategic food security planning at regional scale. Crop yield can be simulated using crop models because is site-specific and determined by weather, management, length of growing season and soil properties. Crop models require reliable location-specific data that are not generally available. Obtaining these data at a large number of locations is time-consuming, costly and sometimes simply not feasible. An upscaling method to extend coverage of sparse estimates of crop yield to an appropriate extrapolation domain is required. This work is aimed to investigate the applicability of a geostatistical data fusion approach for merging remote sensing data with the predictions of a simulation model of wheat growth and production using ground-based data. The study area is Capitanata plain (4000 km2) located in Apulia Region, mostly cropped with durum wheat. The MODIS EVI/NDVI data products for Capitanata plain were downloaded from the Land Processes Distributed Active Archive Center (LPDAAC) remote for the whole crop cycle of durum wheat. Phenological development, biomass growth and grain quantity of durum wheat were simulated by the Delphi system, based on a crop simulation model linked to a database including soil properties, agronomical and meteorological data. Multicollocated cokriging was used to integrate secondary exhaustive information (multi-spectral MODIS data) with primary variable (sparsely distributed biomass/yield model predictions of durum wheat). The model estimates looked strongly spatially correlated with the radiance data (red and NIR bands) and the fusion data approach proved to be quite suitable and flexible to integrate data of different type and support.

Terrestrial Microgravity Model and Threshold Gravity Simulation using Magnetic Levitation

NASA Technical Reports Server (NTRS)

Ramachandran, N.

2005-01-01

What is the threshold gravity (minimum gravity level) required for the nominal functioning of the human system? What dosage is required? Do human cell lines behave differently in microgravity in response to an external stimulus? The critical need for such a gravity simulator is emphasized by recent experiments on human epithelial cells and lymphocytes on the Space Shuttle clearly showing that cell growth and function are markedly different from those observed terrestrially. Those differences are also dramatic between cells grown in space and those in Rotating Wall Vessels (RWV), or NASA bioreactor often used to simulate microgravity, indicating that although morphological growth patterns (three dimensional growth) can be successfully simulated using RWVs, cell function performance is not reproduced - a critical difference. If cell function is dramatically affected by gravity off-loading, then cell response to stimuli such as radiation, stress, etc. can be very different from terrestrial cell lines. Yet, we have no good gravity simulator for use in study of these phenomena. This represents a profound shortcoming for countermeasures research. We postulate that we can use magnetic levitation of cells and tissue, through the use of strong magnetic fields and field gradients, as a terrestrial microgravity model to study human cells. Specific objectives of the research are: 1. To develop a tried, tested and benchmarked terrestrial microgravity model for cell culture studies; 2. Gravity threshold determination; 3. Dosage (magnitude and duration) of g-level required for nominal functioning of cells; 4. Comparisons of magnetic levitation model to other models such as RWV, hind limb suspension, etc. and 5. Cellular response to reduced gravity levels of Moon and Mars. The paper will discuss experiments md modeling work to date in support of this project.

Experimental and computational models of neurite extension at a choice point in response to controlled diffusive gradients

NASA Astrophysics Data System (ADS)

Catig, G. C.; Figueroa, S.; Moore, M. J.

2015-08-01

Ojective. Axons are guided toward desired targets through a series of choice points that they navigate by sensing cues in the cellular environment. A better understanding of how microenvironmental factors influence neurite growth during development can inform strategies to address nerve injury. Therefore, there is a need for biomimetic models to systematically investigate the influence of guidance cues at such choice points. Approach. We ran an adapted in silico biased turning axon growth model under the influence of nerve growth factor (NGF) and compared the results to corresponding in vitro experiments. We examined if growth simulations were predictive of neurite population behavior at a choice point. We used a biphasic micropatterned hydrogel system consisting of an outer cell restrictive mold that enclosed a bifurcated cell permissive region and placed a well near a bifurcating end to allow proteins to diffuse and form a gradient. Experimental diffusion profiles in these constructs were used to validate a diffusion computational model that utilized experimentally measured diffusion coefficients in hydrogels. The computational diffusion model was then used to establish defined soluble gradients within the permissive region of the hydrogels and maintain the profiles in physiological ranges for an extended period of time. Computational diffusion profiles informed the neurite growth model, which was compared with neurite growth experiments in the bifurcating hydrogel constructs. Main results. Results indicated that when applied to the constrained choice point geometry, the biased turning model predicted experimental behavior closely. Results for both simulated and in vitro neurite growth studies showed a significant chemoattractive response toward the bifurcated end containing an NGF gradient compared to the control, though some neurites were found in the end with no NGF gradient. Significance. The integrated model of neurite growth we describe will allow comparison of experimental studies against growth cone guidance computational models applied to axon pathfinding at choice points.

Modelling the cancer growth process by Stochastic Differential Equations with the effect of Chondroitin Sulfate (CS) as anticancer therapeutics

NASA Astrophysics Data System (ADS)

Syahidatul Ayuni Mazlan, Mazma; Rosli, Norhayati; Jauhari Arief Ichwan, Solachuddin; Suhaity Azmi, Nina

2017-09-01

A stochastic model is introduced to describe the growth of cancer affected by anti-cancer therapeutics of Chondroitin Sulfate (CS). The parameters values of the stochastic model are estimated via maximum likelihood function. The numerical method of Euler-Maruyama will be employed to solve the model numerically. The efficiency of the stochastic model is measured by comparing the simulated result with the experimental data.

Crystal-melt interface mobility in bcc Fe: Linking molecular dynamics to phase-field and phase-field crystal modeling

NASA Astrophysics Data System (ADS)

Guerdane, M.; Berghoff, M.

2018-04-01

By combining molecular dynamics (MD) simulations with phase-field (PF) and phase-field crystal (PFC) modeling we study collision-controlled growth kinetics from the melt for pure Fe. The MD/PF comparison shows, on the one hand, that the PF model can be properly designed to reproduce quantitatively different aspects of the growth kinetics and anisotropy of planar and curved solid-liquid interfaces. On the other hand, this comparison demonstrates the ability of classical MD simulations to predict morphology and dynamics of moving curved interfaces up to a length scale of about 0.15 μ m . After mapping the MD model to the PF one, the latter permits to analyze the separate contribution of different anisotropies to the interface morphology. The MD/PFC agreement regarding the growth anisotropy and morphology extends the trend already observed for the here used PFC model in describing structural and elastic properties of bcc Fe.

Modeling complexity in engineered infrastructure system: Water distribution network as an example

NASA Astrophysics Data System (ADS)

Zeng, Fang; Li, Xiang; Li, Ke

2017-02-01

The complex topology and adaptive behavior of infrastructure systems are driven by both self-organization of the demand and rigid engineering solutions. Therefore, engineering complex systems requires a method balancing holism and reductionism. To model the growth of water distribution networks, a complex network model was developed following the combination of local optimization rules and engineering considerations. The demand node generation is dynamic and follows the scaling law of urban growth. The proposed model can generate a water distribution network (WDN) similar to reported real-world WDNs on some structural properties. Comparison with different modeling approaches indicates that a realistic demand node distribution and co-evolvement of demand node and network are important for the simulation of real complex networks. The simulation results indicate that the efficiency of water distribution networks is exponentially affected by the urban growth pattern. On the contrary, the improvement of efficiency by engineering optimization is limited and relatively insignificant. The redundancy and robustness, on another aspect, can be significantly improved through engineering methods.

A computational model of cerebral cortex folding.

PubMed

Nie, Jingxin; Guo, Lei; Li, Gang; Faraco, Carlos; Stephen Miller, L; Liu, Tianming

2010-05-21

The geometric complexity and variability of the human cerebral cortex have long intrigued the scientific community. As a result, quantitative description of cortical folding patterns and the understanding of underlying folding mechanisms have emerged as important research goals. This paper presents a computational 3D geometric model of cerebral cortex folding initialized by MRI data of a human fetal brain and deformed under the governance of a partial differential equation modeling cortical growth. By applying different simulation parameters, our model is able to generate folding convolutions and shape dynamics of the cerebral cortex. The simulations of this 3D geometric model provide computational experimental support to the following hypotheses: (1) Mechanical constraints of the skull regulate the cortical folding process. (2) The cortical folding pattern is dependent on the global cell growth rate of the whole cortex. (3) The cortical folding pattern is dependent on relative rates of cell growth in different cortical areas. (4) The cortical folding pattern is dependent on the initial geometry of the cortex. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

FVS out of the box - assembly required

Treesearch

Don Vandendriesche

2010-01-01

The Forest Vegetation Simulator (FVS) is a prominent growth and yield model used for forecasting stand dynamics. However, users need to be aware of model behavior regarding stocking density, tree senescence, and understory recruitment; otherwise over long projections, FVS tends to concentrate substantial growth on few survivor trees. If the intent is to forecast...

Characterizing the reproduction number of epidemics with early subexponential growth dynamics

PubMed Central

Viboud, Cécile; Simonsen, Lone; Moghadas, Seyed M.

2016-01-01

Early estimates of the transmission potential of emerging and re-emerging infections are increasingly used to inform public health authorities on the level of risk posed by outbreaks. Existing methods to estimate the reproduction number generally assume exponential growth in case incidence in the first few disease generations, before susceptible depletion sets in. In reality, outbreaks can display subexponential (i.e. polynomial) growth in the first few disease generations, owing to clustering in contact patterns, spatial effects, inhomogeneous mixing, reactive behaviour changes or other mechanisms. Here, we introduce the generalized growth model to characterize the early growth profile of outbreaks and estimate the effective reproduction number, with no need for explicit assumptions about the shape of epidemic growth. We demonstrate this phenomenological approach using analytical results and simulations from mechanistic models, and provide validation against a range of empirical disease datasets. Our results suggest that subexponential growth in the early phase of an epidemic is the rule rather the exception. Mechanistic simulations show that slight modifications to the classical susceptible–infectious–removed model result in subexponential growth, and in turn a rapid decline in the reproduction number within three to five disease generations. For empirical outbreaks, the generalized-growth model consistently outperforms the exponential model for a variety of directly and indirectly transmitted diseases datasets (pandemic influenza, measles, smallpox, bubonic plague, cholera, foot-and-mouth disease, HIV/AIDS and Ebola) with model estimates supporting subexponential growth dynamics. The rapid decline in effective reproduction number predicted by analytical results and observed in real and synthetic datasets within three to five disease generations contrasts with the expectation of invariant reproduction number in epidemics obeying exponential growth. The generalized-growth concept also provides us a compelling argument for the unexpected extinction of certain emerging disease outbreaks during the early ascending phase. Overall, our approach promotes a more reliable and data-driven characterization of the early epidemic phase, which is important for accurate estimation of the reproduction number and prediction of disease impact. PMID:27707909

Urban change analysis and future growth of Istanbul.

PubMed

Akın, Anıl; Sunar, Filiz; Berberoğlu, Süha

2015-08-01

This study is aimed at analyzing urban change within Istanbul and assessing the city's future growth potential using appropriate approach modeling for the year 2040. Urban growth is a major driving force of land-use change, and spatial and temporal components of urbanization can be identified through accurate spatial modeling. In this context, widely used urban modeling approaches, such as the Markov chain and logistic regression based on cellular automata (CA), were used to simulate urban growth within Istanbul. The distance from each pixel to the urban and road classes, elevation, and slope, together with municipality and land use maps (as an excluded layer), were identified as factors. Calibration data were obtained from remotely sensed data recorded in 1972, 1986, and 2013. Validation was performed by overlaying the simulated and actual 2013 urban maps, and a kappa index of agreement was derived. The results indicate that urban expansion will influence mainly forest areas during the time period of 2013-2040. The urban expansion was predicted as 429 and 327 km(2) with the Markov chain and logistic regression models, respectively.

Symplectic multiparticle tracking model for self-consistent space-charge simulation

DOE PAGES

Qiang, Ji

2017-01-23

Symplectic tracking is important in accelerator beam dynamics simulation. So far, to the best of our knowledge, there is no self-consistent symplectic space-charge tracking model available in the accelerator community. In this paper, we present a two-dimensional and a three-dimensional symplectic multiparticle spectral model for space-charge tracking simulation. This model includes both the effect from external fields and the effect of self-consistent space-charge fields using a split-operator method. Such a model preserves the phase space structure and shows much less numerical emittance growth than the particle-in-cell model in the illustrative examples.

Symplectic multiparticle tracking model for self-consistent space-charge simulation

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

Qiang, Ji

Symplectic tracking is important in accelerator beam dynamics simulation. So far, to the best of our knowledge, there is no self-consistent symplectic space-charge tracking model available in the accelerator community. In this paper, we present a two-dimensional and a three-dimensional symplectic multiparticle spectral model for space-charge tracking simulation. This model includes both the effect from external fields and the effect of self-consistent space-charge fields using a split-operator method. Such a model preserves the phase space structure and shows much less numerical emittance growth than the particle-in-cell model in the illustrative examples.

Simulating ectomycorrhiza in boreal forests: implementing ectomycorrhizal fungi model MYCOFON in CoupModel (v5)

NASA Astrophysics Data System (ADS)

He, Hongxing; Meyer, Astrid; Jansson, Per-Erik; Svensson, Magnus; Rütting, Tobias; Klemedtsson, Leif

2018-02-01

The symbiosis between plants and Ectomycorrhizal fungi (ECM) is shown to considerably influence the carbon (C) and nitrogen (N) fluxes between the soil, rhizosphere, and plants in boreal forest ecosystems. However, ECM are either neglected or presented as an implicit, undynamic term in most ecosystem models, which can potentially reduce the predictive power of models.

In order to investigate the necessity of an explicit consideration of ECM in ecosystem models, we implement the previously developed MYCOFON model into a detailed process-based, soil-plant-atmosphere model, Coup-MYCOFON, which explicitly describes the C and N fluxes between ECM and roots. This new Coup-MYCOFON model approach (ECM explicit) is compared with two simpler model approaches: one containing ECM implicitly as a dynamic uptake of organic N considering the plant roots to represent the ECM (ECM implicit), and the other a static N approach in which plant growth is limited to a fixed N level (nonlim). Parameter uncertainties are quantified using Bayesian calibration in which the model outputs are constrained to current forest growth and soil C / N ratio for four forest sites along a climate and N deposition gradient in Sweden and simulated over a 100-year period.

The nonlim approach could not describe the soil C / N ratio due to large overestimation of soil N sequestration but simulate the forest growth reasonably well. The ECM implicit and explicit approaches both describe the soil C / N ratio well but slightly underestimate the forest growth. The implicit approach simulated lower litter production and soil respiration than the explicit approach. The ECM explicit Coup-MYCOFON model provides a more detailed description of internal ecosystem fluxes and feedbacks of C and N between plants, soil, and ECM. Our modeling highlights the need to incorporate ECM and organic N uptake into ecosystem models, and the nonlim approach is not recommended for future long-term soil C and N predictions. We also provide a key set of posterior fungal parameters that can be further investigated and evaluated in future ECM studies.

Constraining 3-PG with a new δ13C submodel: a test using the δ13C of tree rings.

PubMed

Wei, Liang; Marshall, John D; Link, Timothy E; Kavanagh, Kathleen L; DU, Enhao; Pangle, Robert E; Gag, Peter J; Ubierna, Nerea

2014-01-01

A semi-mechanistic forest growth model, 3-PG (Physiological Principles Predicting Growth), was extended to calculate δ(13)C in tree rings. The δ(13)C estimates were based on the model's existing description of carbon assimilation and canopy conductance. The model was tested in two ~80-year-old natural stands of Abies grandis (grand fir) in northern Idaho. We used as many independent measurements as possible to parameterize the model. Measured parameters included quantum yield, specific leaf area, soil water content and litterfall rate. Predictions were compared with measurements of transpiration by sap flux, stem biomass, tree diameter growth, leaf area index and δ(13)C. Sensitivity analysis showed that the model's predictions of δ(13)C were sensitive to key parameters controlling carbon assimilation and canopy conductance, which would have allowed it to fail had the model been parameterized or programmed incorrectly. Instead, the simulated δ(13)C of tree rings was no different from measurements (P > 0.05). The δ(13)C submodel provides a convenient means of constraining parameter space and avoiding model artefacts. This δ(13)C test may be applied to any forest growth model that includes realistic simulations of carbon assimilation and transpiration. © 2013 John Wiley & Sons Ltd.

Bone fracture healing in mechanobiological modeling: A review of principles and methods.

PubMed

Ghiasi, Mohammad S; Chen, Jason; Vaziri, Ashkan; Rodriguez, Edward K; Nazarian, Ara

2017-06-01

Bone fracture is a very common body injury. The healing process is physiologically complex, involving both biological and mechanical aspects. Following a fracture, cell migration, cell/tissue differentiation, tissue synthesis, and cytokine and growth factor release occur, regulated by the mechanical environment. Over the past decade, bone healing simulation and modeling has been employed to understand its details and mechanisms, to investigate specific clinical questions, and to design healing strategies. The goal of this effort is to review the history and the most recent work in bone healing simulations with an emphasis on both biological and mechanical properties. Therefore, we provide a brief review of the biology of bone fracture repair, followed by an outline of the key growth factors and mechanical factors influencing it. We then compare different methodologies of bone healing simulation, including conceptual modeling (qualitative modeling of bone healing to understand the general mechanisms), biological modeling (considering only the biological factors and processes), and mechanobiological modeling (considering both biological aspects and mechanical environment). Finally we evaluate different components and clinical applications of bone healing simulation such as mechanical stimuli, phases of bone healing, and angiogenesis.

SU-E-T-751: Three-Component Kinetic Model of Tumor Growth and Radiation Response for Stereotactic Radiosurgery

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

Watanabe, Y; Dahlman, E; Leder, K

Purpose: To develop and study a kinetic model of tumor growth and its response to stereotactic radiosurgery (SRS) by assuming that the cells in irradiated tumor volume were made of three types. Methods: A set of ordinary differential equations (ODEs) were derived for three types of cells and a tumor growth rate. It is assumed that the cells were composed of actively proliferating cells, lethally damaged-dividing cells, and non-dividing cells. We modeled the tumor volume growth with a time-dependent growth rate to simulate the saturation of growth. After SRS, the proliferating cells were permanently damaged and converted to the lethallymore » damaged cells. The amount of damaged cells were estimated by the LQ-model. The damaged cells gradually stopped dividing/proliferating and died with a constant rate. The dead cells were cleared from their original location with a constant rate. The total tumor volume was the sum of the three components. The ODEs were numerically solved with appropriate initial conditions for a given dosage. The proposed model was used to model an animal experiment, for which the temporal change of a rhabdomyosarcoma tumor volume grown in a rat was measured with time resolution sufficient to test the model. Results: To fit the model to the experimental data, the following characteristics were needed with the model parameters. The α-value in the LQ-model was smaller than the commonly used value; furthermore, it decreased with increasing dose. At the same time, the tumor growth rate after SRS had to increase. Conclusions: The new 3-component model of tumor could simulate the experimental data very well. The current study suggested that the radiation sensitivity and the growth rate of the proliferating tumor cells may change after irradiation and it depended on the dosage used for SRS. These preliminary observations must be confirmed by future animal experiments.« less

Warm winter, thin ice?

NASA Astrophysics Data System (ADS)

Stroeve, Julienne C.; Schroder, David; Tsamados, Michel; Feltham, Daniel

2018-05-01

Winter 2016/2017 saw record warmth over the Arctic Ocean, leading to the least amount of freezing degree days north of 70° N since at least 1979. The impact of this warmth was evaluated using model simulations from the Los Alamos sea ice model (CICE) and CryoSat-2 thickness estimates from three different data providers. While CICE simulations show a broad region of anomalously thin ice in April 2017 relative to the 2011-2017 mean, analysis of three CryoSat-2 products show more limited regions with thin ice and do not always agree with each other, both in magnitude and direction of thickness anomalies. CICE is further used to diagnose feedback processes driving the observed anomalies, showing 11-13 cm reduced thermodynamic ice growth over the Arctic domain used in this study compared to the 2011-2017 mean, and dynamical contributions of +1 to +4 cm. Finally, CICE model simulations from 1985 to 2017 indicate the negative feedback relationship between ice growth and winter air temperatures may be starting to weaken, showing decreased winter ice growth since 2012, as winter air temperatures have increased and the freeze-up has been further delayed.

Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule.

PubMed

Mandal, Taraknath; Marson, Ryan L; Larson, Ronald G

2016-10-04

We describe a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules. In this method, a coarse-grained (CG) force field is obtained by inverse-Boltzmann iteration from the radial distribution function of atomistic simulations of the known crystal. With the force field obtained by this method, we show that CG simulations of the drug phenytoin predict growth of a crystalline slab from a melt of phenytoin, allowing determination of the fastest-growing surface, as well as giving the correct lattice parameters and crystal morphology. By applying meta-dynamics to the coarse-grained model, a new crystalline form of phenytoin (monoclinic, space group P2 1 ) was predicted which is different from the experimentally known crystal structure (orthorhombic, space group Pna2 1 ). Atomistic simulations and quantum calculations then showed the polymorph to be meta-stable at ambient temperature and pressure, and thermodynamically more stable than the conventional orthorhombic crystal at high pressure. The results suggest an efficient route to study crystal growth of small organic molecules that could also be useful for identification of possible polymorphs as well.

A Numerical and Experimental Study of Damage Growth in a Composite Laminate

NASA Technical Reports Server (NTRS)

McElroy, Mark; Ratcliffe, James; Czabaj, Michael; Wang, John; Yuan, Fuh-Gwo

2014-01-01

The present study has three goals: (1) perform an experiment where a simple laminate damage process can be characterized in high detail; (2) evaluate the performance of existing commercially available laminate damage simulation tools by modeling the experiment; (3) observe and understand the underlying physics of damage in a composite honeycomb sandwich structure subjected to low-velocity impact. A quasi-static indentation experiment has been devised to provide detailed information about a simple mixed-mode damage growth process. The test specimens consist of an aluminum honeycomb core with a cross-ply laminate facesheet supported on a stiff uniform surface. When the sample is subjected to an indentation load, the honeycomb core provides support to the facesheet resulting in a gradual and stable damage growth process in the skin. This enables real time observation as a matrix crack forms, propagates through a ply, and then causes a delamination. Finite element analyses were conducted in ABAQUS/Explicit(TradeMark) 6.13 that used continuum and cohesive modeling techniques to simulate facesheet damage and a geometric and material nonlinear model to simulate core crushing. The high fidelity of the experimental data allows a detailed investigation and discussion of the accuracy of each numerical modeling approach.

Simulated growth and production of endangered Snake River Sockeye Salmon: Assessing management strategies for the nursery lakes

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

Luecke, C.; Wurtsbaugh, W.A.; Budy, P.

1996-06-01

This document examines the potential of employing a series of lake management strategies to enhance production of endangered Snake River sockeye salmon (Oncorhynchus nerka) in its historical nursery lakes in central Idaho. A combination of limnological sampling, experimentation, and simulation modeling was used to assess effects of lake fertilization and kokanee reduction on growth and survival of juvenile sockeye salmon. Juvenile sockeye salmon from a broodstock of this endangered species are being introduced into the lakes from 1995 to 1998. Results of our analyses indicated that several lakes were suitable for receiving broodstock progeny. Field experimentation and simulation modeling indicatedmore » that lake fertilization, coupled with a program of kokanee reduction, provided the management option most likely to enhance the survival of stocked juvenile sockeye salmon. Simulation models that encompass physiological requirements, ecological interactions, and life-history consequences could be used as templates to help develop recovery plans for other endangered fishes. 4 figs., 2 tabs.« less

Ca-Pri a Cellular Automata Phenomenological Research Investigation: Simulation Results

NASA Astrophysics Data System (ADS)

Iannone, G.; Troisi, A.

2013-05-01

Following the introduction of a phenomenological cellular automata (CA) model capable to reproduce city growth and urban sprawl, we develop a toy model simulation considering a realistic framework. The main characteristic of our approach is an evolution algorithm based on inhabitants preferences. The control of grown cells is obtained by means of suitable functions which depend on the initial condition of the simulation. New born urban settlements are achieved by means of a logistic evolution of the urban pattern while urban sprawl is controlled by means of the population evolution function. In order to compare model results with a realistic urban framework we have considered, as the area of study, the island of Capri (Italy) in the Mediterranean Sea. Two different phases of the urban evolution on the island have been taken into account: a new born initial growth as induced by geographic suitability and the simulation of urban spread after 1943 induced by the population evolution after this date.

Modeling dislocation generation in high pressure Czochralski growth of indium phosphide single crystals

NASA Astrophysics Data System (ADS)

Pendurti, Srinivas

InP is an important material for opto-electronic and high speed electronics applications. Its main use today is as the substrate material for epitaxy to produce GaInAsP lasers. The present technology for growing bulk InP is the high pressure Czochralski process. Bulk InP grown through this technique suffers from presence of a high density of line defects or dislocations, which are produced by thermal stresses the material goes through during its growth in the high temperature furnace. Modeling of these thermal stresses and the resulting plastic deformation, giving rise to dislocation densities, entails simulation of the entire thermal history of the crystal during its growth in the furnace, and studying the deformation of the crystal through suitable visco-plastic constitutive equations. Accordingly, a suitable visco-plastic model for deformation of InP was constructed, integrated with the ABAQUS finite element code, and verified through experimental data for uniaxial constant strain rate deformation tests available in literature. This was then coupled with a computation fluid dynamics model, predicting the entire temperature history in the furnace during crystal growth, to study the plastic deformation and dislocation density evolution in the crystal during growth. Growth in a variety of conditions was simulated and those conditions that generate minimum dislocation density identified. Macroscopic controllable parameters that affect the dislocation densities the most, have also been delineated. It was found that the strength of gas convection in the Czochralski furnace has the strongest effect on the dislocation densities in the fully grown crystal. Comparison of the simulated dislocation densities on wafers, with experimentally recorded etch pit profiles on as-grown crystals was reasonable. Finally some limitations in the work are discussed and avenues for future work identified.

An evaluation of three growth and yield simulators for even-aged hardwood forests of the mid-Appalachian region

Treesearch

John R. Brooks; Gary W. Miller

2011-01-01

Data from even-aged hardwood stands in four ecoregions across the mid-Appalachian region were used to test projection accuracy for three available growth and yield software systems: SILVAH, the Forest Vegetation Simulator, and the Stand Damage Model. Average root mean squared error (RMSE) ranged from 20 to 140 percent of actual trees per acre while RMSE ranged from 2...

Simulation of the dc Plasma in Carbon Nanotube Growth

NASA Technical Reports Server (NTRS)

Hash, David; Bose, Deepak; Govindan, T. R.; Meyyappan, M.; Biegel, Bryan (Technical Monitor)

2003-01-01

A model for the dc plasma used in carbon nanotube growth is presented, and one-dimensional simulations of an acetylene/ammonia/argon system are performed. The effect of dc bias is illustrated by examining electron temperature, electron and ion densities, and neutral densities. Introducing a tungsten filament in the dc plasma, as in hot filament chemical vapor deposition with plasma assistance, shows negligible influence on the system characteristics.

Simulation of nucleation and growth of atomic layer deposition phosphorus for doping of advanced FinFETs

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

Seidel, Thomas E., E-mail: zoomtotom@gmail.com; Goldberg, Alexander; Halls, Mat D.

2016-01-15

Simulations for the nucleation and growth of phosphorus films were carried out using density functional theory. The surface was represented by a Si{sub 9}H{sub 12} truncated cluster surface model with 2 × 1-reconstructured (100) Si-OH terminations for the initial reaction sites. Chemistries included phosphorous halides (PF{sub 3}, PCl{sub 3}, and PBr{sub 3}) and disilane (Si{sub 2}H{sub 6}). Atomic layer deposition (ALD) reaction sequences were illustrated with three-dimensional molecular models using sequential PF{sub 3} and Si{sub 2}H{sub 6} reactions and featuring SiFH{sub 3} as a byproduct. Exothermic reaction pathways were developed for both nucleation and growth for a Si-OH surface. Energetically favorable reactionsmore » for the deposition of four phosphorus atoms including lateral P–P bonding were simulated. This paper suggests energetically favorable thermodynamic reactions for the growth of elemental phosphorus on (100) silicon. Phosphorus layers made by ALD are an option for doping advanced fin field-effect transistors (FinFETs). Phosphorus may be thermally diffused into the silicon or recoil knocked in; simulations of the recoil profile of phosphorus into a FinFET surface are illustrated.« less

Simulation of Population Processes with a Programmable Pocket Calculator.

ERIC Educational Resources Information Center

Kidd, N. A. C.

1979-01-01

Presents a set of simulation models for use in teaching population dynamics. These models are designed specifically for use with a programmable pocket calculator, and can be used to demonstrate growth of populations with discrete or overlapping generations and also to explore effects of density-dependent and -independent mortality. (Author/CS)

Hierarchical stochastic modeling of large river ecosystems and fish growth across spatio-temporal scales and climate models: the Missouri River endangered pallid sturgeon example

USGS Publications Warehouse

Wildhaber, Mark L.; Wikle, Christopher K.; Moran, Edward H.; Anderson, Christopher J.; Franz, Kristie J.; Dey, Rima

2017-01-01

We present a hierarchical series of spatially decreasing and temporally increasing models to evaluate the uncertainty in the atmosphere – ocean global climate model (AOGCM) and the regional climate model (RCM) relative to the uncertainty in the somatic growth of the endangered pallid sturgeon (Scaphirhynchus albus). For effects on fish populations of riverine ecosystems, cli- mate output simulated by coarse-resolution AOGCMs and RCMs must be downscaled to basins to river hydrology to population response. One needs to transfer the information from these climate simulations down to the individual scale in a way that minimizes extrapolation and can account for spatio-temporal variability in the intervening stages. The goal is a framework to determine whether, given uncertainties in the climate models and the biological response, meaningful inference can still be made. The non-linear downscaling of climate information to the river scale requires that one realistically account for spatial and temporal variability across scale. Our down- scaling procedure includes the use of fixed/calibrated hydrological flow and temperature models coupled with a stochastically parameterized sturgeon bioenergetics model. We show that, although there is a large amount of uncertainty associated with both the climate model output and the fish growth process, one can establish significant differences in fish growth distributions between models, and between future and current climates for a given model.

Development of a coupled model of a distributed hydrological model and a rice growth model for optimizing irrigation schedule

NASA Astrophysics Data System (ADS)

Tsujimoto, Kumiko; Homma, Koki; Koike, Toshio; Ohta, Tetsu

2013-04-01

A coupled model of a distributed hydrological model and a rice growth model was developed in this study. The distributed hydrological model used in this study is the Water and Energy Budget-based Distributed Hydrological Model (WEB-DHM) developed by Wang et al. (2009). This model includes a modified SiB2 (Simple Biosphere Model, Sellers et al., 1996) and the Geomorphology-Based Hydrological Model (GBHM) and thus it can physically calculate both water and energy fluxes. The rice growth model used in this study is the Simulation Model for Rice-Weather relations (SIMRIW) - rainfed developed by Homma et al. (2009). This is an updated version of the original SIMRIW (Horie et al., 1987) and can calculate rice growth by considering the yield reduction due to water stress. The purpose of the coupling is the integration of hydrology and crop science to develop a tool to support decision making 1) for determining the necessary agricultural water resources and 2) for allocating limited water resources to various sectors. The efficient water use and optimal water allocation in the agricultural sector are necessary to balance supply and demand of limited water resources. In addition, variations in available soil moisture are the main reasons of variations in rice yield. In our model, soil moisture and the Leaf Area Index (LAI) are calculated inside SIMRIW-rainfed so that these variables can be simulated dynamically and more precisely based on the rice than the more general calculations is the original WEB-DHM. At the same time by coupling SIMRIW-rainfed with WEB-DHM, lateral flow of soil water, increases in soil moisture and reduction of river discharge due to the irrigation, and its effects on the rice growth can be calculated. Agricultural information such as planting date, rice cultivar, fertilization amount are given in a fully distributed manner. The coupled model was validated using LAI and soil moisture in a small basin in western Cambodia (Sangker River Basin). This basin is mostly rainfed paddy so that irrigation scheme was firstly switched off. Several simulations with varying irrigation scheme were performed to determine the optimal irrigation schedule in this basin.

Population, internal migration, and economic growth: an empirical analysis.

PubMed

Moreland, R S

1982-01-01

The role of population growth in the development process has received increasing attention during the last 15 years, as manifested in the literature in 3 broad categories. In the 1st category, the effects of rapid population growth on the growth of income have been studied with the use of simulation models, which sometimes include endogenous population growth. The 2nd category of the literature is concerned with theoretical and empirical studies of the economic determinants of various demographic rates--most usually fertility. Internal migration and dualism is the 3rd population development category to recieve attention. An attempt is made to synthesize developments in these 3 categories by estimating from a consistent set of data a 2 sector economic demographic model in which the major demographic rates are endogenous. Due to the fact that the interactions between economic and demographic variables are nonlinear and complex, the indirect effects of changes in a particular variable may depend upon the balance of numerical coefficients. For this reason it was felt that the model should be empirically grounded. A brief overview of the model is provided, and the model is compared to some similar existing models. Estimation of the model's 9 behavior equations is discussed, followed by a "base run" simulation of a developing country "stereotype" and a report of a number of policy experiments. The relatively new field of economic determinants of demographic variables was drawn upon in estimating equations to endogenize demographic phenomena that are frequently left exogenous in simulation models. The fertility and labor force participation rate functions are fairly standard, but a step beyong existing literature was taken in the life expectancy and intersectorial migration equations. On the economic side, sectoral savings functions were estimated, and it was found that the marginal propensity to save is lower in agriculture than in nonagriculture. Testing to see the effect of a population's age structure on savings rather than assuming a particular direction as Coale-Hoover and Simon do in their models, it was found that a higher proportion of children compete with savings in agriculture but complement savings in industrial areas. This was consistent with the economic value of children in agricultural and nonagricultural regions of less developed countries. The estimated production functions showed that marginal products of labor were considerably higher in agriculture than in nonagriculture. As with other simulation models, the effect of reducing fertility was to accelerate income growth. Reductions in rural fertility were more equitable and raised the overall level of per capita income more than similar efforts directed to urban areas only.

A semi-empirical model for the complete orientation dependence of the growth rate for vapor phase epitaxy - Chloride VPE of GaAs

NASA Technical Reports Server (NTRS)

Seidel-Salinas, L. K.; Jones, S. H.; Duva, J. M.

1992-01-01

A semi-empirical model has been developed to determine the complete crystallographic orientation dependence of the growth rate for vapor phase epitaxy (VPE). Previous researchers have been able to determine this dependence for a limited range of orientations; however, our model yields relative growth rate information for any orientation. This model for diamond and zincblende structure materials is based on experimental growth rate data, gas phase diffusion, and surface reactions. Data for GaAs chloride VPE is used to illustrate the model. The resulting growth rate polar diagrams are used in conjunction with Wulff constructions to simulate epitaxial layer shapes as grown on patterned substrates. In general, this model can be applied to a variety of materials and vapor phase epitaxy systems.

Growth and Metabolism of the Green Alga, Chlorella Pyrenoidosa, in Simulated Microgravity

NASA Technical Reports Server (NTRS)

Mills, W. Ronald

2003-01-01

The effect of microgravity on living organisms during space flight has been a topic of interest for some time, and a substantial body of knowledge on the subject has accumulated. Despite this, comparatively little information is available regarding the influence of microgravity on algae, even though it has been suggested for long duration flight or occupancy in space that plant growth systems, including both higher plants and algae, are likely to be necessary for bioregenerative life support systems. High-Aspect-Ratio Rotating-Wall Vessel or HARV bioreactors developed at Johnson Space Center provide a laboratory-based approach to investigating the effects of microgravity on cellular reactions. In this study, the HARV bioreactor was used to examine the influence of simulated microgravity on the growth and metabolism of the green alga, Chlorella pyrenoidosa. After the first 2 days of culture, cell numbers increased more slowly in simulated microgravity than in the HARV gravity control; after 7 days, growth in simulated microgravity was just over half (58%) that of the gravity control and at 14 days it was less than half (42%). Chlorophyll and protein were also followed as indices of cell competence and function; as with growth, after 2-3 days, protein and chlorophyll levels were reduced in modeled microgravity compared to gravity controls. Photosynthesis is a sensitive biochemical index of the fitness of photosynthetic organisms; thus, CO2-dependent O2 evolution was tested as a measure of photosynthetic capacity of cells grown in simulated microgravity. When data were expressed with respect to cell number, modeled microgravity appeared to have little effect on CO2 fixation. Thus, even though the overall growth rate was lower for cells cultured in microgravity, the photosynthetic capacity of the cells appears to be unaffected. Cells grown in simulated microgravity formed loose clumps or aggregates within about 2 days of culture, with aggregation increasing over time. Presently, the basis for, or significance of, the cell aggregation is unknown. The results from this study suggest that cell growth and morphological characteristics of green algae may be altered by culture in simulated microgravity. The data obtained to date should provide a solid basis for additional experimentation regarding the influence of modeled microgravity on cell morphology, physiological activity, protein production and possibly gene expression in algal and plant cell systems. The final aim of the study is to provide useful information to elucidate the underlying mechanism for the biological effects of microgravity on cells.

Benchmark Data Set for Wheat Growth Models: Field Experiments and AgMIP Multi-Model Simulations.

NASA Technical Reports Server (NTRS)

Asseng, S.; Ewert, F.; Martre, P.; Rosenzweig, C.; Jones, J. W.; Hatfield, J. L.; Ruane, A. C.; Boote, K. J.; Thorburn, P.J.; Rotter, R. P.

2015-01-01

The data set includes a current representative management treatment from detailed, quality-tested sentinel field experiments with wheat from four contrasting environments including Australia, The Netherlands, India and Argentina. Measurements include local daily climate data (solar radiation, maximum and minimum temperature, precipitation, surface wind, dew point temperature, relative humidity, and vapor pressure), soil characteristics, frequent growth, nitrogen in crop and soil, crop and soil water and yield components. Simulations include results from 27 wheat models and a sensitivity analysis with 26 models and 30 years (1981-2010) for each location, for elevated atmospheric CO2 and temperature changes, a heat stress sensitivity analysis at anthesis, and a sensitivity analysis with soil and crop management variations and a Global Climate Model end-century scenario.

The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence

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

Staebler, G. M.; Candy, J.; Howard, N. T.

2016-06-15

The 2D spectrum of the saturated electric potential from gyrokinetic turbulence simulations that include both ion and electron scales (multi-scale) in axisymmetric tokamak geometry is analyzed. The paradigm that the turbulence is saturated when the zonal (axisymmetic) ExB flow shearing rate competes with linear growth is shown to not apply to the electron scale turbulence. Instead, it is the mixing rate by the zonal ExB velocity spectrum with the turbulent distribution function that competes with linear growth. A model of this mechanism is shown to be able to capture the suppression of electron-scale turbulence by ion-scale turbulence and the thresholdmore » for the increase in electron scale turbulence when the ion-scale turbulence is reduced. The model computes the strength of the zonal flow velocity and the saturated potential spectrum from the linear growth rate spectrum. The model for the saturated electric potential spectrum is applied to a quasilinear transport model and shown to accurately reproduce the electron and ion energy fluxes of the non-linear gyrokinetic multi-scale simulations. The zonal flow mixing saturation model is also shown to reproduce the non-linear upshift in the critical temperature gradient caused by zonal flows in ion-scale gyrokinetic simulations.« less

The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence

DOE PAGES

Staebler, Gary M.; Candy, John; Howard, Nathan T.; ...

2016-06-29

The 2D spectrum of the saturated electric potential from gyrokinetic turbulence simulations that include both ion and electron scales (multi-scale) in axisymmetric tokamak geometry is analyzed. The paradigm that the turbulence is saturated when the zonal (axisymmetic) ExB flow shearing rate competes with linear growth is shown to not apply to the electron scale turbulence. Instead, it is the mixing rate by the zonal ExB velocity spectrum with the turbulent distribution function that competes with linear growth. A model of this mechanism is shown to be able to capture the suppression of electron-scale turbulence by ion-scale turbulence and the thresholdmore » for the increase in electron scale turbulence when the ion-scale turbulence is reduced. The model computes the strength of the zonal flow velocity and the saturated potential spectrum from the linear growth rate spectrum. The model for the saturated electric potential spectrum is applied to a quasilinear transport model and shown to accurately reproduce the electron and ion energy fluxes of the non-linear gyrokinetic multi-scale simulations. Finally, the zonal flow mixing saturation model is also shown to reproduce the non-linear upshift in the critical temperature gradient caused by zonal flows in ionscale gyrokinetic simulations.« less

Potential effects of climate change on the growth of fishes from different thermal guilds in Lakes Michigan and Huron

USGS Publications Warehouse

Kao, Yu-Chun; Madenjian, Charles P.; Bunnell, David B.; Lofgren, Brent M.; Perroud, Marjorie

2015-01-01

We used a bioenergetics modeling approach to investigate potential effects of climate change on the growth of two economically important native fishes: yellow perch (Perca flavescens), a cool-water fish, and lake whitefish (Coregonus clupeaformis), a cold-water fish, in deep and oligotrophic Lakes Michigan and Huron. For assessing potential changes in fish growth, we contrasted simulated fish growth in the projected future climate regime during the period 2043-2070 under different prey availability scenarios with the simulated growth during the baseline (historical reference) period 1964-1993. Results showed that effects of climate change on the growth of these two fishes are jointly controlled by behavioral thermoregulation and prey availability. With the ability of behavioral thermoregulation, temperatures experienced by yellow perch in the projected future climate regime increased more than those experienced by lake whitefish. Thus simulated future growth decreased more for yellow perch than for lake whitefish under scenarios where prey availability remains constant into the future. Under high prey availability scenarios, simulated future growth of these two fishes both increased but yellow perch could not maintain the baseline efficiency of converting prey consumption into body weight. We contended that thermal guild should not be the only factor used to predict effects of climate change on the growth of a fish, and that ecosystem responses to climate change should be also taken into account.

Thermal system design and modeling of meniscus controlled silicon growth process for solar applications

NASA Astrophysics Data System (ADS)

Wang, Chenlei

The direct conversion of solar radiation to electricity by photovoltaics has a number of significant advantages as an electricity generator. That is, solar photovoltaic conversion systems tap an inexhaustible resource which is free of charge and available anywhere in the world. Roofing tile photovoltaic generation, for example, saves excess thermal heat and preserves the local heat balance. This means that a considerable reduction of thermal pollution in densely populated city areas can be attained. A semiconductor can only convert photons with the energy of the band gap with good efficiency. It is known that silicon is not at the maximum efficiency but relatively close to it. There are several main parts for the photovoltaic materials, which include, single- and poly-crystalline silicon, ribbon silicon, crystalline thin-film silicon, amorphous silicon, copper indium diselenide and related compounds, cadmium telluride, et al. In this dissertation, we focus on melt growth of the single- and poly-crystalline silicon manufactured by Czochralski (Cz) crystal growth process, and ribbon silicon produced by the edge-defined film-fed growth (EFG) process. These two methods are the most commonly used techniques for growing photovoltaic semiconductors. For each crystal growth process, we introduce the growth mechanism, growth system design, general application, and progress in the numerical simulation. Simulation results are shown for both Czochralski and EFG systems including temperature distribution of the growth system, velocity field inside the silicon melt and electromagnetic field for the EFG growth system. Magnetic field is applied on Cz system to reduce the melt convection inside crucible and this has been simulated in our numerical model. Parametric studies are performed through numerical and analytical models to investigate the relationship between heater power levels and solidification interface movement and shape. An inverse problem control scheme is developed to control the solidification interface of Cz system by adjusting heater powers. For the EFG system, parametric studies are performed to discuss the effect of several growth parameters including window opening size, argon gas flow rate and growth thermal environment on the temperature distribution, silicon tube thickness and pulling rate. Two local models are developed and integrated with the global model to investigate the detailed transport phenomena in a small region around the solidification interface including silicon crystal, silicon melt, free surface, liquid-solid interface and graphite die design. Different convection forms are taken into consideration.

Putting mechanisms into crop production models.

PubMed

Boote, Kenneth J; Jones, James W; White, Jeffrey W; Asseng, Senthold; Lizaso, Jon I

2013-09-01

Crop growth models dynamically simulate processes of C, N and water balance on daily or hourly time-steps to predict crop growth and development and at season-end, final yield. Their ability to integrate effects of genetics, environment and crop management have led to applications ranging from understanding gene function to predicting potential impacts of climate change. The history of crop models is reviewed briefly, and their level of mechanistic detail for assimilation and respiration, ranging from hourly leaf-to-canopy assimilation to daily radiation-use efficiency is discussed. Crop models have improved steadily over the past 30-40 years, but much work remains. Improvements are needed for the prediction of transpiration response to elevated CO₂ and high temperature effects on phenology and reproductive fertility, and simulation of root growth and nutrient uptake under stressful edaphic conditions. Mechanistic improvements are needed to better connect crop growth to genetics and to soil fertility, soil waterlogging and pest damage. Because crop models integrate multiple processes and consider impacts of environment and management, they have excellent potential for linking research from genomics and allied disciplines to crop responses at the field scale, thus providing a valuable tool for deciphering genotype by environment by management effects. © 2013 John Wiley & Sons Ltd.

Anisotropic diffusion and capture on surfaces: Time dependent modeling and visualization in 2 dimensions

NASA Astrophysics Data System (ADS)

Yang, Pu

Since the application of nanowires may lead to a new generation of electronic, optoelectronic and magnetic devices, there is much research on understanding the growth mechanism of various "self assembled" nanowires on semiconductor surfaces. The motivation of the present work is to use theoretical modeling to study the conditions required to form and grow elongated islands and nanowires. In this work, a modeling method is developed to study the time-dependent anisotropic diffusion and growth in two dimensions for an array of rectangular islands. This method uses discrete Fast Fourier Transformation (FFT) to solve the time-dependent diffusion equation on the surface. The ad-particles are captured and incorporated to the island edge to simulate island growth. Implemented in MATLABRTM programs, this model produces expected faceted shapes; the calculation runs very fast on a common personal computer. Time-dependent island growth and the evolving diffusion field have been visualized using simple MATLABRTM functions and can be made into MATLABRTM movies. This modeling method is applied to simulate elongated island and nanowire growth by incorporating anisotropic bonding at the island edge. When there is a full sink in one direction and partial sink in the other direction at the island edge, the model results in the growth of an elongated island with an aspect ratio that stabilizes after it reaches a certain value. This result agrees with experimental data on "endotaxial" nanowire growth. For the island edge with a full sink in one direction and no sink in the other direction, the island grows in length with constant width, which is comparable to experimental data on Bi nanoline and rare-earth metal nanowire growth.

Direct molecular dynamics simulation of Ge deposition on amorphous SiO 2 at experimentally relevant conditions

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

Chuang, Claire Y.; Zepeda-Ruiz, Luis A.; Han, Sang M.

2015-06-01

Molecular dynamics simulations were used to study Ge island nucleation and growth on amorphous SiO 2 substrates. This process is relevant in selective epitaxial growth of Ge on Si, for which SiO 2 is often used as a template mask. The islanding process was studied over a wide range of temperatures and fluxes, using a recently proposed empirical potential model for the Si–SiO 2–Ge system. The simulations provide an excellent quantitative picture of the Ge islanding and compare well with detailed experimental measurements. These quantitative comparisons were enabled by an analytical rate model as a bridge between simulations and experimentsmore » despite the fact that deposition fluxes accessible in simulations and experiments are necessarily different by many orders of magnitude. In particular, the simulations led to accurate predictions of the critical island size and the scaling of island density as a function of temperature. Lastly, the overall approach used here should be useful not just for future studies in this particular system, but also for molecular simulations of deposition in other materials.« less

Growth of nitrogen-doped graphene on copper: Multiscale simulations

NASA Astrophysics Data System (ADS)

Gaillard, P.; Schoenhalz, A. L.; Moskovkin, P.; Lucas, S.; Henrard, L.

2016-02-01

We used multiscale simulations to model the growth of nitrogen-doped graphene on a copper substrate by chemical vapour deposition (CVD). Our simulations are based on ab-initio calculations of energy barriers for surface diffusion, which are complemented by larger scale Kinetic Monte Carlo (KMC) simulations. Our results indicate that the shape of grown doped graphene flakes depends on the temperature and deposition flux they are submitted during the process, but we found no significant effect of nitrogen doping on this shape. However, we show that nitrogen atoms have a preference for pyridine-like sites compared to graphite-like sites, as observed experimentally.

Heat transfer simulation in a vertical Bridgman CdTe growth configuration

NASA Astrophysics Data System (ADS)

Martinez-Tomas, C.; Muñoz, V.; Triboulet, R.

1999-02-01

Modelling and numerical simulation of crystal growth processes have been shown to be powerful tools in order to understand the physical effects of different parameters on the growth conditions. In this study a finite difference/control volume technique for the study of heat transfer has been employed. This model takes into account the whole system: furnace temperature profile, air gap between furnace walls and ampoule, ampoule geometry, crucible coating if any, solid and liquid CdTe thermal properties, conduction, convection and radiation of heat and phase change. We have used the commercial code FLUENT for the numerical resolution that can be running on a personal computer. Results show that the temperature field is very sensitive to the charge and ampoule peculiarities. As a consequence, significant differences between the velocity of the ampoule and that of the isotherm determining the solid/liquid interface have been found at the onset of the growth.

The Impact of Detailed Snow Physics on the Simulation of Snow Cover and Subsurface Thermodynamics at Continental Scales

NASA Technical Reports Server (NTRS)

Stieglitz, Marc; Ducharne, Agnes; Koster, Randy; Suarez, Max; Busalacchi, Antonio J. (Technical Monitor)

2000-01-01

The three-layer snow model is coupled to the global catchment-based Land Surface Model (LSM) of the NASA Seasonal to Interannual Prediction Project (NSIPP) project, and the combined models are used to simulate the growth and ablation of snow cover over the North American continent for the period 1987-1988. The various snow processes included in the three-layer model, such as snow melting and re-freezing, dynamic changes in snow density, and snow insulating properties, are shown (through a comparison with the corresponding simulation using a much simpler snow model) to lead to an improved simulation of ground thermodynamics on the continental scale.

Substrate and metabolite diffusion within model medium for soft cheese in relation to growth of Penicillium camembertii.

PubMed

Aldarf, Mazen; Fourcade, Florence; Amrane, Abdeltif; Prigent, Yves

2006-08-01

Penicillium camembertii was cultivated on a jellified peptone-lactate based medium to simulate the composition of Camembert cheese. Diffusional limitations due to substrate consumption were not involved in the linear growth recorded during culture, while nitrogen (peptone) limitation accounted for growth cessation. Examination of gradients confirmed that medium neutralization was the consequence of lactate consumption and ammonium production. The diffusion of the lactate assimilated from the core to the rind and that of the ammonium produced from the rind to the core was described by means of a diffusion/reaction model involving a partial linking of consumption or production to growth. The model matched experimental data throughout growth.

Explosive response model evaluation using the explosive H6

NASA Astrophysics Data System (ADS)

Sutherland, Gerrit T.; Burns, Joseph

2000-04-01

Reactive rate model parameters for a two term Lee Tarver [simplified ignition and growth (SIG)] model were obtained for the explosive H6 from modified gap test data. These model was used to perform simulations of the underwater sensitivity test (UST) using the CTH hydrocode. Reaction was predicted in the simulations for the same water gaps that reaction was observed in the UST. The expansions observed for the UST samples were not simulated correctly, and this is attributed to the density equilibrium conditions imposed between unreacted and reacted components in CTH for the Lee-Tarver model.

COLA with scale-dependent growth: applications to screened modified gravity models

NASA Astrophysics Data System (ADS)

Winther, Hans A.; Koyama, Kazuya; Manera, Marc; Wright, Bill S.; Zhao, Gong-Bo

2017-08-01

We present a general parallelized and easy-to-use code to perform numerical simulations of structure formation using the COLA (COmoving Lagrangian Acceleration) method for cosmological models that exhibit scale-dependent growth at the level of first and second order Lagrangian perturbation theory. For modified gravity theories we also include screening using a fast approximate method that covers all the main examples of screening mechanisms in the literature. We test the code by comparing it to full simulations of two popular modified gravity models, namely f(R) gravity and nDGP, and find good agreement in the modified gravity boost-factors relative to ΛCDM even when using a fairly small number of COLA time steps.

Multiphysical simulation analysis of the dislocation structure in germanium single crystals

NASA Astrophysics Data System (ADS)

Podkopaev, O. I.; Artemyev, V. V.; Smirnov, A. D.; Mamedov, V. M.; Sid'ko, A. P.; Kalaev, V. V.; Kravtsova, E. D.; Shimanskii, A. F.

2016-09-01

To grow high-quality germanium crystals is one of the most important problems of growth industry. The dislocation density is an important parameter of the quality of single crystals. The dislocation densities in germanium crystals 100 mm in diameter, which have various shapes of the side surface and are grown by the Czochralski technique, are experimentally measured. The crystal growth is numerically simulated using heat-transfer and hydrodynamics models and the Alexander-Haasen dislocation model in terms of the CGSim software package. A comparison of the experimental and calculated dislocation densities shows that the dislocation model can be applied to study lattice defects in germanium crystals and to improve their quality.

Characterizing the growth to detonation in HNS with small-scale PDV "cutback" experiments

NASA Astrophysics Data System (ADS)

Wixom, Ryan R.; Yarrington, Cole D.; Knepper, Robert; Tappan, Alexander S.; Olles, Joseph D.; Damm, David L.

2017-01-01

For many decades, cutback experiments have been used to characterize the equation of state and growth to steady detonation in explosive formulations. More recently, embedded gauges have been used to capture the growth to steady detonation in gas-gun impacted samples. Data resulting from these experiments are extremely valuable for parameterizing equation of state and reaction models used in hydrocode simulations. Due to the extremely fast growth to detonation in typical detonator explosives, cutback and embedded gauge experiments are particularly difficult, if not impossible. Using frequency shifted photonic Doppler velocimetry (PDV) we have measured particle velocity histories from vapor-deposited explosive films impacted with electrically driven flyers. By varying the sample thickness and impact conditions we were able to capture the growth from inert shock to full detonation pressure within distances as short as 100 µm. These data are being used to assess and improve burn-model parameterization and equations of state for simulating shock initiation.

Application of remote sensing in crop growth simulation and an ensembles approach to reduce model uncertainties

NASA Astrophysics Data System (ADS)

Setiyono, T. D.; Nelson, A.; Ravis, J.; Maunahan, A.; Villano, L.; Li, T.; Bouman, B.

2012-12-01

A semi-empirical model derived from the water-cloud model was used to convert synthetic- aperture radar (SAR) backscattering data into LAI. The SAR-based LAI at early rice growth stages were in a close agreement (90%) with LAI derived from MODIS data for the same study location in Nueva Ecija, Philippines. ORYZA2000 simulated rice yield of 4.5 Mg ha-1 for the 2008 wet season in Nueva Ejica, Philippines when using LAI inputs derived from SAR data, which is closer to the observed yield of 3.9 Mg ha-1, whereas simulated yield without SAR-derived LAI inputs was 5.4 Mg ha-1. The dynamic water and nitrogen balances were accounted in these simulations based on site-specific soil properties and actual fertilizer N and water management. The use of remote sensing data was promising for model application to approximate actual growth conditions and to compensate for limitations in the model due to relevant underlining processes absent in model formulations such as detailed tillering, leaf shading effect, etc., and also limiting factors not accounted in the model such as biotic factors and abiotic factors other than water and N shortages. This study also demonstrated the use an ensembles approach for provincial level rice yield estimation in the Philippines. Such ensembles approach involved statistical classifications of agronomic management settings into 25% percentile, median, and 75% levels followed by generation of factorial combinations. For irrigated lowland system, 4 factors were considered that include transplanting date, plant density, fertilizer N rate, and amount of irrigation water. For rainfed lowland system, there were 3 agronomic management factors (transplanting date, plant density, fertilizer N) and 1 soil parameter (depth of ground water table). These 4 management/soil factors and 3 statistical levels resulted in 81 total factorial combinations representing simulation scenarios for each area of interest (province in the Philippines) and water environments (irrigated vs. rainfed). Finally a normal distribution was assumed and applied to the simulations outputs. This ensembles approach provided an efficient and yet effective method of aggregating point-based crop model results into a larger spatial level of interest. Lack of access to accurate model parameters (e.g. depth of ground water table) could be solved with this approach. The use of process-based crop growth model was critical because the ultimate aim of this study was not just to establish a reliable rice yield estimation system but also to allow yield estimation outputs explainable by the underlining agronomic practices such as transplanting date, fertilizer N application, and water management.

Coupled modelling of tumour angiogenesis, tumour growth and blood perfusion.

PubMed

Cai, Yan; Xu, Shixiong; Wu, Jie; Long, Quan

2011-06-21

We propose a mathematical modelling system to investigate the dynamic process of tumour cell proliferation, death and tumour angiogenesis by fully coupling the vessel growth, tumour growth and blood perfusion. Tumour growth and angiogenesis are coupled by the chemical microenvironment and the cell-matrix interaction. The haemodynamic calculation is carried out on the updated vasculature. The domains of intravascular, transcapillary and interstitial fluid flow were coupled in the model to provide a comprehensive solution of blood perfusion variables. An estimation of vessel collapse is made according to the wall shear stress criterion to provide feedback on vasculature remodelling. The simulation can show the process of tumour angiogenesis and the spatial distribution of tumour cells for periods of up to 24 days. It can show the major features of tumour and tumour microvasculature during the period such as the formation of a large necrotic core in the tumour centre with few functional vessels passing through, and a well circulated tumour periphery regions in which the microvascular density is high and associated with more aggressive proliferating cells of the growing tumour which are all consistent with physiological observations. The study also demonstrated that the simulation results are not dependent on the initial tumour and networks, which further confirms the application of the coupled model feedback mechanisms. The model enables us to examine the interactions between angiogenesis and tumour growth, and to study the dynamic response of a solid tumour to the changes in the microenvironment. This simulation framework can be a foundation for further applications such as drug delivery and anti-angiogenic therapies. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

In silico modeling for tumor growth visualization.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Cemernek, David; Holzinger, Andreas

2016-08-08

Cancer is a complex disease. Fundamental cellular based studies as well as modeling provides insight into cancer biology and strategies to treatment of the disease. In silico models complement in vivo models. Research on tumor growth involves a plethora of models each emphasizing isolated aspects of benign and malignant neoplasms. Biologists and clinical scientists are often overwhelmed by the mathematical background knowledge necessary to grasp and to apply a model to their own research. We aim to provide a comprehensive and expandable simulation tool to visualizing tumor growth. This novel Web-based application offers the advantage of a user-friendly graphical interface with several manipulable input variables to correlate different aspects of tumor growth. By refining model parameters we highlight the significance of heterogeneous intercellular interactions on tumor progression. Within this paper we present the implementation of the Cellular Potts Model graphically presented through Cytoscape.js within a Web application. The tool is available under the MIT license at https://github.com/davcem/cpm-cytoscape and http://styx.cgv.tugraz.at:8080/cpm-cytoscape/ . In-silico methods overcome the lack of wet experimental possibilities and as dry method succeed in terms of reduction, refinement and replacement of animal experimentation, also known as the 3R principles. Our visualization approach to simulation allows for more flexible usage and easy extension to facilitate understanding and gain novel insight. We believe that biomedical research in general and research on tumor growth in particular will benefit from the systems biology perspective.

A numerical model for predicting crack path and modes of damage in unidirectional metal matrix composites

NASA Technical Reports Server (NTRS)

Bakuckas, J. G.; Tan, T. M.; Lau, A. C. W.; Awerbuch, J.

1993-01-01

A finite element-based numerical technique has been developed to simulate damage growth in unidirectional composites. This technique incorporates elastic-plastic analysis, micromechanics analysis, failure criteria, and a node splitting and node force relaxation algorithm to create crack surfaces. Any combination of fiber and matrix properties can be used. One of the salient features of this technique is that damage growth can be simulated without pre-specifying a crack path. In addition, multiple damage mechanisms in the forms of matrix cracking, fiber breakage, fiber-matrix debonding and plastic deformation are capable of occurring simultaneously. The prevailing failure mechanism and the damage (crack) growth direction are dictated by the instantaneous near-tip stress and strain fields. Once the failure mechanism and crack direction are determined, the crack is advanced via the node splitting and node force relaxation algorithm. Simulations of the damage growth process in center-slit boron/aluminum and silicon carbide/titanium unidirectional specimens were performed. The simulation results agreed quite well with the experimental observations.

Growth factor involvement in tension-induced skeletal muscle growth

NASA Technical Reports Server (NTRS)

Vandenburgh, Herman W.

1987-01-01

New muscle tissue culture techniques were developed to grow embryonic skeletal myofibers which are able to differentiate into more adultlike myofibers. Studies on mechanical simulation of cultured muscle cell growth will now be more directly applicable to mechanically-induced growth in adult muscle, and lead to better models for understanding muscle tissue atrophy caused by disuse in the microgravity of space.

Chemical models for simulating single-walled nanotube production in arc vaporization and laser ablation processes

NASA Technical Reports Server (NTRS)

Scott, Carl D.

2004-01-01

Chemical kinetic models for the nucleation and growth of clusters and single-walled carbon nanotube (SWNT) growth are developed for numerical simulations of the production of SWNTs. Two models that involve evaporation and condensation of carbon and metal catalysts, a full model involving all carbon clusters up to C80, and a reduced model are discussed. The full model is based on a fullerene model, but nickel and carbon/nickel cluster reactions are added to form SWNTs from soot and fullerenes. The full model has a large number of species--so large that to incorporate them into a flow field computation for simulating laser ablation and arc processes requires that they be simplified. The model is reduced by defining large clusters that represent many various sized clusters. Comparisons are given between these models for cases that may be applicable to arc and laser ablation production. Solutions to the system of chemical rate equations of these models for a ramped temperature profile show that production of various species, including SWNTs, agree to within about 50% for a fast ramp, and within 10% for a slower temperature decay time.

Multiparticle Simulation of Intrabeam Scattering for SuperB

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

Biagini, M.; Boscolo, M.; Demma, T.

In this communication we present the structure of a multiparticle tracking code to investigate intrabeam scattering effects in low emittance colliders. Simulation results obtained with particular reference to the SuperB parameters are compared with those of conventional IBS theories.and with those of a novel semi-analythical model able to predict IBS effect in terms of emittance growths. Intrabeam scattering (IBS) is associated with multiple small angle scattering events leading to emittance growth. In most electron storage rings, the growth rates arising from IBS are usually much longer than damping times due to synchrotron radiation, and its effect is not observed. However,more » IBS growth rates increase with bunch charge density, and for machines such as SuperB, that operate with high bunch charges and very low emittances, the IBS growth rates can be large enough to observe significant emittance increase. Several formalisms have been developed for calculating IBS growth rates in storage rings, notably those by Piwinski, Bjorken and Mtingwa, and their high energy approximations. Calculations show that IBS should be manageable in both SuperB rings. However these analytical models, based on Gaussian bunch distributions, cannot investigate some interesting aspects of IBS such as its impact during the damping process and its effect on the beam distribution. We developed a multiparticle tracking code, based on the Zenkevich-Bolshakov algorithm, to investigate these effects. In this communication we present the structure of the code and some simulation results obtained with particular reference to the SuperB parameters. Simulation results are compared with those of conventional IBS theories.« less

Inferring the Impact of Regulatory Mechanisms that Underpin CD8+ T Cell Control of B16 Tumor Growth In vivo Using Mechanistic Models and Simulation.

PubMed

Klinke, David J; Wang, Qing

2016-01-01

A major barrier for broadening the efficacy of immunotherapies for cancer is identifying key mechanisms that limit the efficacy of tumor infiltrating lymphocytes. Yet, identifying these mechanisms using human samples and mouse models for cancer remains a challenge. While interactions between cancer and the immune system are dynamic and non-linear, identifying the relative roles that biological components play in regulating anti-tumor immunity commonly relies on human intuition alone, which can be limited by cognitive biases. To assist natural intuition, modeling and simulation play an emerging role in identifying therapeutic mechanisms. To illustrate the approach, we developed a multi-scale mechanistic model to describe the control of tumor growth by a primary response of CD8+ T cells against defined tumor antigens using the B16 C57Bl/6 mouse model for malignant melanoma. The mechanistic model was calibrated to data obtained following adenovirus-based immunization and validated to data obtained following adoptive transfer of transgenic CD8+ T cells. More importantly, we use simulation to test whether the postulated network topology, that is the modeled biological components and their associated interactions, is sufficient to capture the observed anti-tumor immune response. Given the available data, the simulation results also provided a statistical basis for quantifying the relative importance of different mechanisms that underpin CD8+ T cell control of B16F10 growth. By identifying conditions where the postulated network topology is incomplete, we illustrate how this approach can be used as part of an iterative design-build-test cycle to expand the predictive power of the model.

Theoretical accuracy in cosmological growth estimation

NASA Astrophysics Data System (ADS)

Bose, Benjamin; Koyama, Kazuya; Hellwing, Wojciech A.; Zhao, Gong-Bo; Winther, Hans A.

2017-07-01

We elucidate the importance of the consistent treatment of gravity-model specific nonlinearities when estimating the growth of cosmological structures from redshift space distortions (RSD). Within the context of standard perturbation theory (SPT), we compare the predictions of two theoretical templates with redshift space data from COLA (comoving Lagrangian acceleration) simulations in the normal branch of DGP gravity (nDGP) and general relativity (GR). Using COLA for these comparisons is validated using a suite of full N-body simulations for the same theories. The two theoretical templates correspond to the standard general relativistic perturbation equations and those same equations modeled within nDGP. Gravitational clustering nonlinear effects are accounted for by modeling the power spectrum up to one-loop order and redshift space clustering anisotropy is modeled using the Taruya, Nishimichi and Saito (TNS) RSD model. Using this approach, we attempt to recover the simulation's fiducial logarithmic growth parameter f . By assigning the simulation data with errors representing an idealized survey with a volume of 10 Gpc3/h3 , we find the GR template is unable to recover fiducial f to within 1 σ at z =1 when we match the data up to kmax=0.195 h /Mpc . On the other hand, the DGP template recovers the fiducial value within 1 σ . Further, we conduct the same analysis for sets of mock data generated for generalized models of modified gravity using SPT, where again we analyze the GR template's ability to recover the fiducial value. We find that for models with enhanced gravitational nonlinearity, the theoretical bias of the GR template becomes significant for stage IV surveys. Thus, we show that for the future large data volume galaxy surveys, the self-consistent modeling of non-GR gravity scenarios will be crucial in constraining theory parameters.

Modeling growth kinetics of thin films made by atomic layer deposition in lateral high-aspect-ratio structures

NASA Astrophysics Data System (ADS)

Ylilammi, Markku; Ylivaara, Oili M. E.; Puurunen, Riikka L.

2018-05-01

The conformality of thin films grown by atomic layer deposition (ALD) is studied using all-silicon test structures with long narrow lateral channels. A diffusion model, developed in this work, is used for studying the propagation of ALD growth in narrow channels. The diffusion model takes into account the gas transportation at low pressures, the dynamic Langmuir adsorption model for the film growth and the effect of channel narrowing due to film growth. The film growth is calculated by solving the diffusion equation with surface reactions. An efficient analytic approximate solution of the diffusion equation is developed for fitting the model to the measured thickness profile. The fitting gives the equilibrium constant of adsorption and the sticking coefficient. This model and Gordon's plug flow model are compared. The simulations predict the experimental measurement results quite well for Al2O3 and TiO2 ALD processes.

Nucleation and growth in alkaline zinc electrodeposition An Experimental and Theoretical study

NASA Astrophysics Data System (ADS)

Desai, Divyaraj

The current work seeks to investigate the nucleation and growth of zinc electrodeposition in alkaline electrolyte, which is of commercial interest to alkaline zinc batteries for energy storage. The morphology of zinc growth places a severe limitation on the typical cycle life of such batteries. The formation of mossy zinc leads to a progressive deterioration of battery performance while zinc dendrites are responsible for sudden catastrophic battery failure. The problems are identified as the nucleation-controlled formation of mossy zinc and the transport-limited formation of dendritic zinc. Consequently, this thesis work seeks to investigate and accurately simulate the conditions under which such morphologies are formed. The nucleation and early-stage growth of Zn electrodeposits is studied on carbon-coated TEM grids. At low overpotentials, the morphology develops by aggregation at two distinct length scales: ~5 nm diameter monocrystalline nanoclusters form ~50nm diameter polycrystalline aggregates, and second, the aggregates form a branched network. Epitaxial (0002) growth above a critical overpotential leads to the formation of hexagonal single-crystals. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment. The formation of dendritic zinc is investigated using in-operando transmission X-ray microscopy which is a unique technique for imaging metal electrodeposits. The nucleation density of zinc nuclei is lowered using polyaniline films to cover the active nucleation sites. The effect of overpotential is investigated and the morphology shows beautiful in-operando formation of symmetric zinc crystals. A linear perturbation model was developed to predict the growth and formation of these crystals to first-order accuracy. Existing phase-field models of solidification and electrodeposition are used to simulate the growth and formation of individual zinc crystals. The driving force for solidification models (i.e. supersaturation) is reinterpreted in terms of overpotential under the assumption of a conductive electrolyte. The final morphologies are astonishingly similar to those observed in dynamical experiments. Further, the phase-field models obey the predictions of the linear perturbation analysis, which gives good credibility to the phase-field approach to simulate electrodeposition processes.

Evaluation of two evapotranspiration approaches simulated with the CSM-CERES-Maize model under different irrigation strategies and the impact on maize growth, development and soil moisture content for semi-arid conditions

USDA-ARS?s Scientific Manuscript database

Water deficit is the most common adverse environmental condition that can seriously reduce crop productivity. Crop simulation models could assist in determining alternate crop management scenarios to deal with water-limited conditions. However, prior to the application of crop models, the appropriat...

Estimating the Uncertainty In Diameter Growth Model Predictions and Its Effects On The Uncertainty of Annual Inventory Estimates

Treesearch

Ronald E. McRoberts; Veronica C. Lessard

2001-01-01

Uncertainty in diameter growth predictions is attributed to three general sources: measurement error or sampling variability in predictor variables, parameter covariances, and residual or unexplained variation around model expectations. Using measurement error and sampling variability distributions obtained from the literature and Monte Carlo simulation methods, the...

Back to the future: assessing accuracy and sensitivity of a forest growth model

Treesearch

Susan Hummel; Paul Meznarich

2014-01-01

The Forest Vegetation Simulator (FVS) is a widely used computer model that projects forest growth and predicts the effects of disturbances such as fire, insects, harvests, or disease. Land managers often use these projections to decide among silvicultural options and estimate the potential effects of these options on forest conditions. Despite FVS's popularity,...

Growth models for ponderosa pine: I. Yield of unthinned plantations in northern California.

Treesearch

William W. Oliver; Robert F. Powers

1978-01-01

Yields for high-survival, unthinned ponderosa pine (Pinus ponderosa Laws.) plantations in northern California are estimated. Stems of 367 trees in 12 plantations were analyzed to produce a growth model simulating stand yields. Diameter, basal area, and net cubic volume yields by Site Indices50 40 through 120 are tabulated for...

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

PubMed

Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

2011-03-25

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment. Published by Elsevier B.V.

Simulation of EAST vertical displacement events by tokamak simulation code

NASA Astrophysics Data System (ADS)

Qiu, Qinglai; Xiao, Bingjia; Guo, Yong; Liu, Lei; Xing, Zhe; Humphreys, D. A.

2016-10-01

Vertical instability is a potentially serious hazard for elongated plasma. In this paper, the tokamak simulation code (TSC) is used to simulate vertical displacement events (VDE) on the experimental advanced superconducting tokamak (EAST). Key parameters from simulations, including plasma current, plasma shape and position, flux contours and magnetic measurements match experimental data well. The growth rates simulated by TSC are in good agreement with TokSys results. In addition to modeling the free drift, an EAST fast vertical control model enables TSC to simulate the course of VDE recovery. The trajectories of the plasma current center and control currents on internal coils (IC) fit experimental data well.

Approaches to simulating the “March of Bricks and Mortar”

USGS Publications Warehouse

Goldstein, Noah Charles; Candau, J.T.; Clarke, K.C.

2004-01-01

Re-creation of the extent of urban land use at different periods in time is valuable for examining how cities grow and how policy changes influence urban dynamics. To date, there has been little focus on the modeling of historical urban extent (other than for ancient cities). Instead, current modeling research has emphasized simulating the cities of the future. Predictive models can provide insights into urban growth processes and are valuable for land-use and urban planners, yet historical trends are largely ignored. This is unfortunate since historical data exist for urban areas and can be used to quantitatively test dynamic models and theory. We maintain that understanding the growth dynamics of a region's past allows more intelligent forecasts of its future. We compare using a spatio-temporal interpolation method with an agent-based simulation approach to recreate the urban extent of Santa Barbara, California, annually from 1929 to 2001. The first method uses current yet incomplete data on the construction of homes in the region. The latter uses a Cellular Automata based model, SLEUTH, to back- or hind-cast the urban extent. The success at historical urban growth reproduction of the two approaches used in this work was quantified for comparison. The performance of each method is described, as well as the utility of each model in re-creating the history of Santa Barbara. Additionally, the models’ assumptions about space are contrasted. As a consequence, we propose that both approaches are useful in historical urban simulations, yet the cellular approach is more flexible as it can be extended for spatio-temporal extrapolation.

Kinetic Monte Carlo Simulations of Rod Eutectics and the Surface Roughening Transition in Binary Alloys

NASA Technical Reports Server (NTRS)

Bentz, Daniel N.; Betush, William; Jackson, Kenneth A.

2003-01-01

In this paper we report on two related topics: Kinetic Monte Carlo simulations of the steady state growth of rod eutectics from the melt, and a study of the surface roughness of binary alloys. We have implemented a three dimensional kinetic Monte Carlo (kMC) simulation with diffusion by pair exchange only in the liquid phase. Entropies of fusion are first chosen to fit the surface roughness of the pure materials, and the bond energies are derived from the equilibrium phase diagram, by treating the solid and liquid as regular and ideal solutions respectively. A simple cubic lattice oriented in the {100} direction is used. Growth of the rods is initiated from columns of pure B material embedded in an A matrix, arranged in a close packed array with semi-periodic boundary conditions. The simulation cells typically have dimensions of 50 by 87 by 200 unit cells. Steady state growth is compliant with the Jackson-Hunt model. In the kMC simulations, using the spin-one Ising model, growth of each phase is faceted or nonfaceted phases depending on the entropy of fusion. There have been many studies of the surface roughening transition in single component systems, but none for binary alloy systems. The location of the surface roughening transition for the phases of a eutectic alloy determines whether the eutectic morphology will be regular or irregular. We have conducted a study of surface roughness on the spin-one Ising Model with diffusion using kMC. The surface roughness was found to scale with the melting temperature of the alloy as given by the liquidus line on the equilibrium phase diagram. The density of missing lateral bonds at the surface was used as a measure of surface roughness.

Phase-Field Modeling of Sigma-Phase Precipitation in 25Cr7Ni4Mo Duplex Stainless Steel

NASA Astrophysics Data System (ADS)

Malik, Amer; Odqvist, Joakim; Höglund, Lars; Hertzman, Staffan; Ågren, John

2017-10-01

Phase-field modeling is used to simulate the formation of sigma phase in a model alloy mimicking a commercial super duplex stainless steel (SDSS) alloy, in order to study precipitation and growth of sigma phase under linear continuous cooling. The so-called Warren-Boettinger-McFadden (WBM) model is used to build the basis of the multiphase and multicomponent phase-field model. The thermodynamic inconsistency at the multiple junctions associated with the multiphase formulation of the WBM model is resolved by means of a numerical Cut-off algorithm. To make realistic simulations, all the kinetic and the thermodynamic quantities are derived from the CALPHAD databases at each numerical time step, using Thermo-Calc and TQ-Interface. The credibility of the phase-field model is verified by comparing the results from the phase-field simulations with the corresponding DICTRA simulations and also with the empirical data. 2D phase-field simulations are performed for three different cooling rates in two different initial microstructures. A simple model for the nucleation of sigma phase is also implemented in the first case. Simulation results show that the precipitation of sigma phase is characterized by the accumulation of Cr and Mo at the austenite-ferrite and the ferrite-ferrite boundaries. Moreover, it is observed that a slow cooling rate promotes the growth of sigma phase, while a higher cooling rate restricts it, eventually preserving the duplex structure in the SDSS alloy. Results from the phase-field simulations are also compared quantitatively with the experiments, performed on a commercial 2507 SDSS alloy. It is found that overall, the predicted morphological features of the transformation and the composition profiles show good conformity with the empirical data.

An econometric simulation model of income and electricity demand in Alaska's Railbelt, 1982-2022

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

Maddigan, R.J.; Hill, L.J.; Hamblin, D.M.

1987-01-01

This report describes the specification of-and forecasts derived from-the Alaska Railbelt Electricity Load, Macroeconomic (ARELM) model. ARELM was developed as an independent, modeling tool for the evaluation of the need for power from the Susitna Hydroelectric Project which has been proposed by the Alaska Power Authority. ARELM is an econometric simulation model consisting of 61 equations - 46 behavioral equations and 15 identities. The system includes two components: (1) ARELM-MACRO which is a system of equations that simulates the performance of both the total Alaskan and Railbelt macroeconomies and (2) ARELM-LOAD which projects electricity-related activity in the Alaskan Railbelt region.more » The modeling system is block recursive in the sense that forecasts of population, personal income, and employment in the Railbelt derived from ARELM-MACRO are used as explanatory variables in ARELM-LOAD to simulate electricity demand, the real average price of electricity, and the number of customers in the Railbelt. Three scenarios based on assumptions about the future price of crude oil are simulated and documented in the report. The simulations, which do not include the cost-of-power impacts of Susitna-based generation, show that the growth rate in Railbelt electricity load is between 2.5 and 2.7% over the 1982 to 2022 forecast period. The forecasting results are consistent with other projections of load growth in the region using different modeling approaches.« less

TiOx deposited by magnetron sputtering: a joint modelling and experimental study

NASA Astrophysics Data System (ADS)

Tonneau, R.; Moskovkin, P.; Pflug, A.; Lucas, S.

2018-05-01

This paper presents a 3D multiscale simulation approach to model magnetron reactive sputter deposition of TiOx⩽2 at various O2 inlets and its validation against experimental results. The simulation first involves the transport of sputtered material in a vacuum chamber by means of a three-dimensional direct simulation Monte Carlo (DSMC) technique. Second, the film growth at different positions on a 3D substrate is simulated using a kinetic Monte Carlo (kMC) method. When simulating the transport of species in the chamber, wall chemistry reactions are taken into account in order to get the proper content of the reactive species in the volume. Angular and energy distributions of particles are extracted from DSMC and used for film growth modelling by kMC. Along with the simulation, experimental deposition of TiOx coatings on silicon samples placed at different positions on a curved sample holder was performed. The experimental results are in agreement with the simulated ones. For a given coater, the plasma phase hysteresis behaviour, film composition and film morphology are predicted. The used methodology can be applied to any coater and any films. This paves the way to the elaboration of a virtual coater allowing a user to predict composition and morphology of films deposited in silico.

Gyrokinetic particle simulations of the effects of compressional magnetic perturbations on drift-Alfvenic instabilities in tokamaks

DOE PAGES

Dong, Ge; Bao, Jian; Bhattacharjee, Amitava; ...

2017-08-10

The compressional component of magnetic perturbation δB- || to can play an important role in drift-Alfvenic instabilities in tokamaks, especially as the plasma β increases (β is the ratio of kinetic pressure to magnetic pressure). In this work, we have formulated a gyrokinetic particle simulation model incorporating δB- ||, and verified the model in kinetic Alfven wave simulations using the Gyrokinetic Toroidal Code in slab geometry. Simulations of drift-Alfvenic instabilities in tokamak geometry shows that the kinetic ballooning mode (KBM) growth rate decreases more than 20% when δB- || is neglected for β e = 0.02, and that δB- ||more » to has stabilizing effects on the ion temperature gradient instability, but negligible effects on the collisionless trapped electron mode. Lastly, the KBM growth rate decreases about 15% when equilibrium current is neglected.« less

Development of a model for on-line control of crystal growth by the AHP method

NASA Astrophysics Data System (ADS)

Gonik, M. A.; Lomokhova, A. V.; Gonik, M. M.; Kuliev, A. T.; Smirnov, A. D.

2007-05-01

The possibility to apply a simplified 2D model for heat transfer calculations in crystal growth by the axial heat close to phase interface (AHP) method is discussed in this paper. A comparison with global heat transfer calculations with the CGSim software was performed to confirm the accuracy of this model. The simplified model was shown to provide adequate results for the shape of the melt-crystal interface and temperature field in an opaque (Ge) and a transparent crystal (CsI:Tl). The model proposed is used for identification of the growth setup as a control object, for synthesis of a digital controller (PID controller at the present stage) and, finally, in on-line simulations of crystal growth control.

Monolayers of hard rods on planar substrates. II. Growth

NASA Astrophysics Data System (ADS)

Klopotek, M.; Hansen-Goos, H.; Dixit, M.; Schilling, T.; Schreiber, F.; Oettel, M.

2017-02-01

Growth of hard-rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with kinetic Monte Carlo simulations and dynamic density functional theory while the continuum model is studied by dynamic Monte Carlo simulations equivalent to diffusive dynamics. The evolution of nematic order (excess of upright particles, "standing-up" transition) is an entropic effect and is mainly governed by the equilibrium solution, rendering a continuous transition [Paper I, M. Oettel et al., J. Chem. Phys. 145, 074902 (2016)]. Strong non-equilibrium effects (e.g., a noticeable dependence on the ratio of rates for translational and rotational moves) are found for attractive substrate potentials favoring lying rods. Results from the lattice and the continuum models agree qualitatively if the relevant characteristic times for diffusion, relaxation of nematic order, and deposition are matched properly. Applicability of these monolayer results to multilayer growth is discussed for a continuum-model realization in three dimensions where spherocylinders are deposited continuously onto a substrate via diffusion.

Time delay and noise explaining the behaviour of the cell growth in fermentation process

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

Ayuobi, Tawfiqullah; Rosli, Norhayati; Bahar, Arifah

2015-02-03

This paper proposes to investigate the interplay between time delay and external noise in explaining the behaviour of the microbial growth in batch fermentation process. Time delay and noise are modelled jointly via stochastic delay differential equations (SDDEs). The typical behaviour of cell concentration in batch fermentation process under this model is investigated. Milstein scheme is applied for solving this model numerically. Simulation results illustrate the effects of time delay and external noise in explaining the lag and stationary phases, respectively for the cell growth of fermentation process.

Time delay and noise explaining the behaviour of the cell growth in fermentation process

NASA Astrophysics Data System (ADS)

Ayuobi, Tawfiqullah; Rosli, Norhayati; Bahar, Arifah; Salleh, Madihah Md

2015-02-01

This paper proposes to investigate the interplay between time delay and external noise in explaining the behaviour of the microbial growth in batch fermentation process. Time delay and noise are modelled jointly via stochastic delay differential equations (SDDEs). The typical behaviour of cell concentration in batch fermentation process under this model is investigated. Milstein scheme is applied for solving this model numerically. Simulation results illustrate the effects of time delay and external noise in explaining the lag and stationary phases, respectively for the cell growth of fermentation process.

An Individual-Tree Growth and Yield Prediction System for Uneven-Aged Shortleaf Pine Stands

Treesearch

Michael M. Huebschmann; Lawrence R. Gering; Thomas B. Lynch; Onesphore Bitoki; Paul A. Murphy

2000-01-01

A system of equations modeling the growth and development of uneven-aged shortleaf pine (Pinus echinata Mill.) stands is described. The prediction system consists of two main components: (1) a distance-independent, individual-tree simulator containing equations that forecast ingrowth, basal-area growth, probability of survival, total and...

Empirically Derived Optimal Growth Equations For Hardwoods and Softwoods in Arkansas

Treesearch

Don C. Bragg

2002-01-01

Accurate growth projections are critical to reliable forest models, and ecologically based simulators can improve siivicultural predictions because of their sensitivity to change and their capacity to produce long-term forecasts. Potential relative increment (PRI) optimal diameter growth equations for loblolly pine, shortleaf pine, sweetgum, and white oak were fit to...

Modeling of Dendritic Structure and Microsegregation in Solidification of Al-Rich Quaternary Alloys

NASA Astrophysics Data System (ADS)

Dai, Ting; Zhu, Mingfang; Chen, Shuanglin; Cao, Weisheng

A two-dimensional cellular automaton (CA) model is coupled with a CALPHAD tool for the simulation of dendritic growth and microsegregation in solidification of quaternary alloys. The dynamics of dendritic growth is calculated according to the difference between the local equilibrium liquidus temperature and the actual temperature, incorporating with the Gibbs—Thomson effect and preferential dendritic growth orientations. Based on the local liquid compositions determined by solving the solutal transport equation in the domain, the local equilibrium liquidus temperature and the solid concentrations at the solid/liquid (SL) interface are calculated by the CALPHAD tool. The model was validated through the comparisons of the simulated results with the Scheil predictions for the solid composition profiles as a function of solid fraction in an Al-6wt%Cu-0.6wt%Mg-1wt%Si alloy. It is demonstrated that the model is capable of not only reproducing realistic dendrite morphologies, but also reasonably predicting microsegregation patterns in solidification of Al-rich quaternary alloys.

Phase-field crystal modeling of heteroepitaxy and exotic modes of crystal nucleation

NASA Astrophysics Data System (ADS)

Podmaniczky, Frigyes; Tóth, Gyula I.; Tegze, György; Pusztai, Tamás; Gránásy, László

2017-01-01

We review recent advances made in modeling heteroepitaxy, two-step nucleation, and nucleation at the growth front within the framework of a simple dynamical density functional theory, the Phase-Field Crystal (PFC) model. The crystalline substrate is represented by spatially confined periodic potentials. We investigate the misfit dependence of the critical thickness in the StranskiKrastanov growth mode in isothermal studies. Apparently, the simulation results for stress release via the misfit dislocations fit better to the PeopleBean model than to the one by Matthews and Blakeslee. Next, we investigate structural aspects of two-step crystal nucleation at high undercoolings, where an amorphous precursor forms in the first stage. Finally, we present results for the formation of new grains at the solid-liquid interface at high supersaturations/supercoolings, a phenomenon termed Growth Front Nucleation (GFN). Results obtained with diffusive dynamics (applicable to colloids) and with a hydrodynamic extension of the PFC theory (HPFC, developed for simple liquids) will be compared. The HPFC simulations indicate two possible mechanisms for GFN.

Generation of a modeling and simulation system for a semi-closed plant growth chamber

NASA Technical Reports Server (NTRS)

Blackwell, A. L.; Maa, S.; Kliss, M.; Blackwell, C. C.

1993-01-01

The fluid and thermal dynamics of the environment of plants in a small controlled-environment system have been modeled. The results of the simulation under two scenarios have been compared to measurements taken during tests on the actual system. The motivation for the modeling effort and the status of the modeling exercise and system scenario studies are described. An evaluation of the model and a discussion of future studies are included.

Growth Dynamics of Information Search Services

ERIC Educational Resources Information Center

Lindquist, Mats G.

1978-01-01

An analysis of computer-based search services (ISSs) from a system's viewpoint, using a continuous simulation model to reveal growth and stagnation of a typical system is presented, as well as an analysis of decision making for an ISS. (Author/MBR)

Modeling Calculation and Synthesis of Alumina Whiskers Based on the Vapor Deposition Process.

PubMed

Gong, Wei; Li, Xiangcheng; Zhu, Boquan

2017-10-17

This study simulated the bulk structure and surface energy of Al₂O₃ based on the density of states (DOS) and studied the synthesis and microstructure of one-dimensional Al₂O₃ whiskers. The simulation results indicate that the (001) surface has a higher surface energy than the others. The growth mechanism of Al₂O₃ whiskers follows vapor-solid (VS) growth. For the (001) surface with the higher surface energy, the driving force of crystal growth would be more intense in the (001) plane, and the alumina crystal would tend to grow preferentially along the direction of the (001) plane from the tip of the crystal. The Al₂O₃ grows to the shape of whisker with [001] orientation, which is proved both through modeling and experimentation.

Design of a triple-bend isochronous achromat with minimum coherent-synchrotron-radiation-induced emittance growth

NASA Astrophysics Data System (ADS)

Venturini, M.

2016-06-01

Using a 1D steady-state free-space coherent synchrotron radiation (CSR) model, we identify a special design setting for a triple-bend isochronous achromat that yields vanishing emittance growth from CSR. When a more refined CSR model with transient effects is included in the analysis, numerical simulations show that the main effect of the transients is to shift the emittance growth minimum slightly, with the minimum changing only modestly.

Design of a triple-bend isochronous achromat with minimum coherent-synchrotron-radiation-induced emittance growth

DOE PAGES

Venturini, M.

2016-06-09

Using a 1D steady-state free-space coherent synchrotron radiation (CSR) model, we identify a special design setting for a triple-bend isochronous achromat that yields vanishing emittance growth from CSR. When a more refined CSR model with transient effects is included in the analysis, numerical simulations show that the main effect of the transients is to shift the emittance growth minimum slightly, with the minimum changing only modestly.

Numerical Modeling of Solidification in Space With MEPHISTO-4. Part 2

NASA Technical Reports Server (NTRS)

Simpson, James E.; Yoa, Minwu; deGroh, Henry C., III; Garimella, V. Suresh

1998-01-01

A pre-flight analysis of the directional solidification of BiSn with MEPHISTO-4 is presented. Simplified Bridgman growth under microgravity conditions is simulated using a two dimensional finite element model. This numerical model is a single domain, pseudo-steady state model, and includes the effects of both thermal and solutal convection. The results show that for all orientations of the applied steady state gravity vector, of magnitude 1 micro-g, the directional solidification process remains diffusion controlled. The maximum convective velocity was found to be 4.424 x 10(exp -5) cm/s for the horizontal Bridgman growth configuration. This value is an order of magnitude lower than the growth velocity. The maximum and minimum values or solute concentration in the liquid at the crystal-melt interface were 13.867 at.% and 13.722 at.%, respectively. This gives a radial segregation value of xi = 1.046% at the interface. A secondary objective of this work was to compare the results obtained to those that consider thermal convection only (no solutal convection). It was found that the convective flow patterns in simulations which included solutal convection were significantly different from those which ignored solutal convection. The level of radial segregation predicted by the current simulations is an order of magnitude lower than that found in simulations which ignore solutal convection. The final aim was to investigate the effect of g-jitter on the crystal growth process. A simulation was performed to calculate the system response to a 1 second, 100 micro-g gravity impulse acting normal to the direction of growth. This pulse is consistent with that induced by Orbiter thruster firings. The results obtained indicate that such a gravity pulse causes an increase in the level of radial solute segregation at the interface from the steady state values. The maximum value of solute concentration in the liquid was found to be 13.888 at.%, the minimum value calculated was 13.706 at.%, yielding a radial segregation value of xi = 1.31% at the interface. These values occurred 126 seconds after the pulse terminated. Thus it is anticipated that the process will remain diffusion controlled even when subjected to such g-jitter.

Genome-scale biological models for industrial microbial systems.

PubMed

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Simulating adaptive wood harvest in a changing climate

NASA Astrophysics Data System (ADS)

Yousefpour, Rasoul; Nabel, Julia; Pongratz, Julia

2016-04-01

The world's forest experience substantial carbon exchange fluxes between land and atmosphere. Large carbon sinks occur in response to changes in environmental conditions (such as climate change and increased atmospheric CO2 concentrations), removing about one quarter of current anthropogenic CO2-emissions. Large sinks also occur due to regrowth of forest on areas of agricultural abandonment or forest management. Forest management, on the other hand, also leads to substantial amounts of carbon being eventually released to the atmosphere. Both sinks and sources attributable to forests are therefore dependent on the intensity of management. Forest management in turn depends on the availability of resources, which is influenced by environmental conditions and sustainability of management systems applied. Estimating future carbon fluxes therefore requires accounting for the interaction of environmental conditions, forest growth, and management. However, this interaction is not fully captured by current modeling approaches: Earth system models depict in detail interactions between climate, the carbon cycle, and vegetation growth, but use prescribed information on management. Resource needs and land management, however, are simulated by Integrated Assessment Models that typically only have coarse representations of the influence of environmental changes on vegetation growth and are typically based on the demand for wood driven by regional population growth and energy needs. Here we present a study that provides the link between environmental conditions, forest growth and management. We extend the land component JSBACH of the Max Planck Institute's Earth system model (MPI-ESM) to simulate potential wood harvest in response to altered growth conditions and thus as adaptive to changing climate and CO2 conditions. We apply the altered model to estimate potential wood harvest for future climates (representative concentration pathways, RCPs) for the management scenario of "sustained yields" (SY), i.e. that wood harvest is not allowed to reduce wood carbon stocks below their present-day average state. We find that the potentials for SY range from about 420 to 610 PgC cumulatively until 2100 depending on assumed future climate (RCPs 2.6, 4.5 or 8.5). They are thus substantially higher than the harvest prescribed in the context of the same RCPs for the coupled model intercomparison project (CMIP5), which ranged from about 130 to 210 PgC. The underlying drivers of the higher potentials of SY as compared to the RCP harvest are in all scenarios foremost avoided natural mortality, followed by avoided losses due to fire and windbreak. Further, usage of the increase in forest carbon stocks simulated with time under RCP harvest plays a large role in the first decades of the 21st century. The potential wood harvest that we simulate accounting for environmental changes does not include considerations on biodiversity and other ecosystem services or technical feasibility. However, the substantially higher simulated harvest from SY as compared to that prescribed from the RCPs and the difference found between climate scenarios highlights the need to account for effects of environmental changes on vegetation growth also in socio-economic models and thus the need for a consistent representation of climate-landuse interactions.

A computational model for telomere-dependent cell-replicative aging.

PubMed

Portugal, R D; Land, M G P; Svaiter, B F

2008-01-01

Telomere shortening provides a molecular basis for the Hayflick limit. Recent data suggest that telomere shortening also influence mitotic rate. We propose a stochastic growth model of this phenomena, assuming that cell division in each time interval is a random process which probability decreases linearly with telomere shortening. Computer simulations of the proposed stochastic telomere-regulated model provides good approximation of the qualitative growth of cultured human mesenchymal stem cells.

Evaluation of aqua crop simulation of early season evaporation and water flux in a semiarid environment

USDA-ARS?s Scientific Manuscript database

The AquaCrop model of crop growth, water use, yield and water use efficiency (WUE) is intended for use by extension personnel, farm and irrigation managers, planners and other less advanced users of simulation models in irrigation planning and scheduling. It could be useful in estimating changes in ...

Forest growth and timber quality: crown models and simulation methods for sustainable forest management

Treesearch

Dennis P. Dykstra; Robert A. Monserud

2009-01-01

The purpose of the international conference from which these proceedings are drawn was to explore relationships between forest management activities and timber quality. Sessions were organized to explore models and simulation methodologies that contribute to an understanding of tree development over time and the ways that management and harvesting activities can...

A foundation for initial attack simulation: the Fried and Fried fire containment model

Treesearch

Jeremy S. Fried; Burton D. Fried

2010-01-01

The Fried and Fried containment algorithm, which models the effect of suppression efforts on fire growth, allows simulation of any mathematically representable fire shape, provides for "head" and "tail" attack tactics as well as parallel attack (building fireline parallel to but at some offset distance from the free-burning fire perimeter, alone and...

The GP problem: quantifying gene-to-phenotype relationships.

PubMed

Cooper, Mark; Chapman, Scott C; Podlich, Dean W; Hammer, Graeme L

2002-01-01

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.

Crop monitoring & yield forecasting system based on Synthetic Aperture Radar (SAR) and process-based crop growth model: Development and validation in South and South East Asian Countries

NASA Astrophysics Data System (ADS)

Setiyono, T. D.

2014-12-01

Accurate and timely information on rice crop growth and yield helps governments and other stakeholders adapting their economic policies and enables relief organizations to better anticipate and coordinate relief efforts in the wake of a natural catastrophe. Such delivery of rice growth and yield information is made possible by regular earth observation using space-born Synthetic Aperture Radar (SAR) technology combined with crop modeling approach to estimate yield. Radar-based remote sensing is capable of observing rice vegetation growth irrespective of cloud coverage, an important feature given that in incidences of flooding the sky is often cloud-covered. The system allows rapid damage assessment over the area of interest. Rice yield monitoring is based on a crop growth simulation and SAR-derived key information, particularly start of season and leaf growth rate. Results from pilot study sites in South and South East Asian countries suggest that incorporation of SAR data into crop model improves yield estimation for actual yields. Remote-sensing data assimilation into crop model effectively capture responses of rice crops to environmental conditions over large spatial coverage, which otherwise is practically impossible to achieve. Such improvement of actual yield estimates offers practical application such as in a crop insurance program. Process-based crop simulation model is used in the system to ensure climate information is adequately captured and to enable mid-season yield forecast.

Simulation of Channel Segregation During Directional Solidification of In—75 wt pct Ga. Qualitative Comparison with In Situ Observations

NASA Astrophysics Data System (ADS)

Saad, Ali; Gandin, Charles-André; Bellet, Michel; Shevchenko, Natalia; Eckert, Sven

2015-11-01

Freckles are common defects in industrial casting. They result from thermosolutal convection due to buoyancy forces generated from density variations in the liquid. The present paper proposes a numerical analysis for the formation of channel segregation using the three-dimensional (3D) cellular automaton (CA)—finite element (FE) model. The model integrates kinetics laws for the nucleation and growth of a microstructure with the solution of the conservation equations for the casting, while introducing an intermediate modeling scale for a direct representation of the envelope of the dendritic grains. Directional solidification of a cuboid cell is studied. Its geometry, the alloy chosen as well as the process parameters are inspired from experimental observations recently reported in the literature. Snapshots of the convective pattern, the solute distribution, and the morphology of the growth front are qualitatively compared. Similitudes are found when considering the coupled 3D CAFE simulations. Limitations of the model to reach direct simulation of the experiments are discussed.

Computational Combustion

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

Westbrook, C K; Mizobuchi, Y; Poinsot, T J

2004-08-26

Progress in the field of computational combustion over the past 50 years is reviewed. Particular attention is given to those classes of models that are common to most system modeling efforts, including fluid dynamics, chemical kinetics, liquid sprays, and turbulent flame models. The developments in combustion modeling are placed into the time-dependent context of the accompanying exponential growth in computer capabilities and Moore's Law. Superimposed on this steady growth, the occasional sudden advances in modeling capabilities are identified and their impacts are discussed. Integration of submodels into system models for spark ignition, diesel and homogeneous charge, compression ignition engines, surfacemore » and catalytic combustion, pulse combustion, and detonations are described. Finally, the current state of combustion modeling is illustrated by descriptions of a very large jet lifted 3D turbulent hydrogen flame with direct numerical simulation and 3D large eddy simulations of practical gas burner combustion devices.« less

Direct simulation Monte Carlo investigation of the Richtmyer-Meshkov instability

DOE PAGES

Gallis, Michail A.; Koehler, Timothy P.; Torczynski, John R.; ...

2015-08-14

The Rayleigh-Taylor instability (RTI) is investigated using the Direct Simulation Monte Carlo (DSMC) method of molecular gas dynamics. Here, fully resolved two-dimensional DSMC RTI simulations are performed to quantify the growth of flat and single-mode perturbed interfaces between two atmospheric-pressure monatomic gases as a function of the Atwood number and the gravitational acceleration. The DSMC simulations reproduce all qualitative features of the RTI and are in reasonable quantitative agreement with existing theoretical and empirical models in the linear, nonlinear, and self-similar regimes. At late times, the instability is seen to exhibit a self-similar behavior, in agreement with experimental observations. Formore » the conditions simulated, diffusion can influence the initial instability growth significantly.« less

On System Engineering a Barter-Based Re-allocation of Space System Key Development Resources

NASA Astrophysics Data System (ADS)

Kosmann, William J.

NASA has had a decades-long problem with cost growth during the development of space science missions. Numerous agency-sponsored studies have produced average mission level development cost growths ranging from 23 to 77%. A new study of 26 historical NASA science instrument set developments using expert judgment to re-allocate key development resources has an average cost growth of 73.77%. Twice in history, during the Cassini and EOS-Terra science instrument developments, a barter-based mechanism has been used to re-allocate key development resources. The mean instrument set development cost growth was -1.55%. Performing a bivariate inference on the means of these two distributions, there is statistical evidence to support the claim that using a barter-based mechanism to re-allocate key instrument development resources will result in a lower expected cost growth than using the expert judgment approach. Agent-based discrete event simulation is the natural way to model a trade environment. A NetLogo agent-based barter-based simulation of science instrument development was created. The agent-based model was validated against the Cassini historical example, as the starting and ending instrument development conditions are available. The resulting validated agent-based barter-based science instrument resource re-allocation simulation was used to perform 300 instrument development simulations, using barter to re-allocate development resources. The mean cost growth was -3.365%. A bivariate inference on the means was performed to determine that additional significant statistical evidence exists to support a claim that using barter-based resource re-allocation will result in lower expected cost growth, with respect to the historical expert judgment approach. Barter-based key development resource re-allocation should work on science spacecraft development as well as it has worked on science instrument development. A new study of 28 historical NASA science spacecraft developments has an average cost growth of 46.04%. As barter-based key development resource re-allocation has never been tried in a spacecraft development, no historical results exist, and an inference on the means test is not possible. A simulation of using barter-based resource re-allocation should be developed. The NetLogo instrument development simulation should be modified to account for spacecraft development market participant differences. The resulting agent-based barter-based spacecraft resource re-allocation simulation would then be used to determine if significant statistical evidence exists to prove a claim that using barter-based resource re-allocation will result in lower expected cost growth.

For how long can we predict the weather? - Insights into atmospheric predictability from global convection-allowing simulations

NASA Astrophysics Data System (ADS)

Judt, Falko

2017-04-01

A tremendous increase in computing power has facilitated the advent of global convection-resolving numerical weather prediction (NWP) models. Although this technological breakthrough allows for the seamless prediction of weather from local to global scales, the predictability of multiscale weather phenomena in these models is not very well known. To address this issue, we conducted a global high-resolution (4-km) predictability experiment using the Model for Prediction Across Scales (MPAS), a state-of-the-art global NWP model developed at the National Center for Atmospheric Research. The goals of this experiment are to investigate error growth from convective to planetary scales and to quantify the intrinsic, scale-dependent predictability limits of atmospheric motions. The globally uniform resolution of 4 km allows for the explicit treatment of organized deep moist convection, alleviating grave limitations of previous predictability studies that either used high-resolution limited-area models or global simulations with coarser grids and cumulus parameterization. Error growth is analyzed within the context of an "identical twin" experiment setup: the error is defined as the difference between a 20-day long "nature run" and a simulation that was perturbed with small-amplitude noise, but is otherwise identical. It is found that in convectively active regions, errors grow by several orders of magnitude within the first 24 h ("super-exponential growth"). The errors then spread to larger scales and begin a phase of exponential growth after 2-3 days when contaminating the baroclinic zones. After 16 days, the globally averaged error saturates—suggesting that the intrinsic limit of atmospheric predictability (in a general sense) is about two weeks, which is in line with earlier estimates. However, error growth rates differ between the tropics and mid-latitudes as well as between the troposphere and stratosphere, highlighting that atmospheric predictability is a complex problem. The comparatively slower error growth in the tropics and in the stratosphere indicates that certain weather phenomena could potentially have longer predictability than currently thought.

Continental-scale simulation of burn probabilities, flame lengths, and fire size distribution for the United States

Treesearch

Mark A. Finney; Charles W. McHugh; Isaac Grenfell; Karin L. Riley

2010-01-01

Components of a quantitative risk assessment were produced by simulation of burn probabilities and fire behavior variation for 134 fire planning units (FPUs) across the continental U.S. The system uses fire growth simulation of ignitions modeled from relationships between large fire occurrence and the fire danger index Energy Release Component (ERC). Simulations of 10,...

Simulated Long-term Effects of the MOFEP Cutting Treatments

Treesearch

David R. Larsen

1997-01-01

Changes in average basal area and volume per acre were simulated for a 35-year pertod using the treatments designated for sites 4, 5, and 6 of the Missouri Ozark Forest Ecosystem Project. A traditional growth and yield model (Central States TWIGS variant of the Forest Vegetation Simulator) was used with Landscape Management System Software to simulate and display...

Simulation of chemical-vapor-deposited silicon carbide for a cold wall vertical reactor

NASA Astrophysics Data System (ADS)

Lee, Y. L.; Sanchez, J. M.

1997-07-01

The growth rate of silicon carbide obtained by low-pressure chemical vapor deposition from tetramethylsilane is numerically simulated for a cold wall vertical reactor. The transport equations for momentum, heat, and mass transfer are simultaneously solved by employing the finite volume method. A model for reaction rate is also proposed in order to predict the measured growth rates [A. Figueras, S. Garelik, J. Santiso, R. Rodroguez-Clemente, B. Armas, C. Combescure, R. Berjoan, J.M. Saurel and R. Caplain, Mater. Sci. Eng. B 11 (1992) 83]. Finally, the effects of thermal diffusion on the growth rate are investigated.

Numerical Simulation of Nanostructure Growth

NASA Technical Reports Server (NTRS)

Hwang, Helen H.; Bose, Deepak; Govindan, T. R.; Meyyappan, M.

2004-01-01

Nanoscale structures, such as nanowires and carbon nanotubes (CNTs), are often grown in gaseous or plasma environments. Successful growth of these structures is defined by achieving a specified crystallinity or chirality, size or diameter, alignment, etc., which in turn depend on gas mixture ratios. pressure, flow rate, substrate temperature, and other operating conditions. To date, there has not been a rigorous growth model that addresses the specific concerns of crystalline nanowire growth, while demonstrating the correct trends of the processing conditions on growth rates. Most crystal growth models are based on the Burton, Cabrera, and Frank (BCF) method, where adatoms are incorporated into a growing crystal at surface steps or spirals. When the supersaturation of the vapor is high, islands nucleate to form steps, and these steps subsequently spread (grow). The overall bulk growth rate is determined by solving for the evolving motion of the steps. Our approach is to use a phase field model to simulate the growth of finite sized nanowire crystals, linking the free energy equation with the diffusion equation of the adatoms. The phase field method solves for an order parameter that defines the evolving steps in a concentration field. This eliminates the need for explicit front tracking/location, or complicated shadowing routines, both of which can be computationally expensive, particularly in higher dimensions. We will present results demonstrating the effect of process conditions, such as substrate temperature, vapor supersaturation, etc. on the evolving morphologies and overall growth rates of the nanostructures.

Semantic World Modelling and Data Management in a 4d Forest Simulation and Information System

NASA Astrophysics Data System (ADS)

Roßmann, J.; Hoppen, M.; Bücken, A.

2013-08-01

Various types of 3D simulation applications benefit from realistic forest models. They range from flight simulators for entertainment to harvester simulators for training and tree growth simulations for research and planning. Our 4D forest simulation and information system integrates the necessary methods for data extraction, modelling and management. Using modern methods of semantic world modelling, tree data can efficiently be extracted from remote sensing data. The derived forest models contain position, height, crown volume, type and diameter of each tree. This data is modelled using GML-based data models to assure compatibility and exchangeability. A flexible approach for database synchronization is used to manage the data and provide caching, persistence, a central communication hub for change distribution, and a versioning mechanism. Combining various simulation techniques and data versioning, the 4D forest simulation and information system can provide applications with "both directions" of the fourth dimension. Our paper outlines the current state, new developments, and integration of tree extraction, data modelling, and data management. It also shows several applications realized with the system.

Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

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

McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.

2015-09-01

In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expandmore » the number of potential types of graphene electronic devices.« less

Comparing root architectural models

NASA Astrophysics Data System (ADS)

Schnepf, Andrea; Javaux, Mathieu; Vanderborght, Jan

2017-04-01

Plant roots play an important role in several soil processes (Gregory 2006). Root architecture development determines the sites in soil where roots provide input of carbon and energy and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural models have been widely used and been further developed into functional-structural models that are able to simulate the fate of water and solutes in the soil-root system (Dunbabin et al. 2013). Still, a systematic comparison of the different root architectural models is missing. In this work, we focus on discrete root architecture models where roots are described by connected line segments. These models differ (a) in their model concepts, such as the description of distance between branches based on a prescribed distance (inter-nodal distance) or based on a prescribed time interval. Furthermore, these models differ (b) in the implementation of the same concept, such as the time step size, the spatial discretization along the root axes or the way stochasticity of parameters such as root growth direction, growth rate, branch spacing, branching angles are treated. Based on the example of two such different root models, the root growth module of R-SWMS and RootBox, we show the impact of these differences on simulated root architecture and aggregated information computed from this detailed simulation results, taking into account the stochastic nature of those models. References Dunbabin, V.M., Postma, J.A., Schnepf, A., Pagès, L., Javaux, M., Wu, L., Leitner, D., Chen, Y.L., Rengel, Z., Diggle, A.J. Modelling root-soil interactions using three-dimensional models of root growth, architecture and function (2013) Plant and Soil, 372 (1-2), pp. 93 - 124. Gregory (2006) Roots, rhizosphere and soil: the route to a better understanding of soil science? European Journal of Soil Science 57: 2-12.

Radial Growth and Physiological Response of Coniferous Trees to Arctic Amplification

NASA Astrophysics Data System (ADS)

Tei, Shunsuke; Sugimoto, Atsuko; Liang, Maochang; Yonenobu, Hitoshi; Matsuura, Yojiro; Osawa, Akira; Sato, Hisashi; Fujinuma, Junichi; Maximov, Trofim

2017-11-01

We describe the physiological responses of boreal conifers to climate change for the past 112 years using ring-width and carbon isotope ratio (δ13C) chronologies at six forest sites in northern Eurasia and Canada. Responses differed among regions, depending on their climatic and/or geographic characteristics. Tree radial growth decreased over the past 52 years in central eastern Siberia with the higher rate of summer temperature increase than other regions, as indicated by the negative correlation between radial growth and summer temperature, but increased in northern Europe and Canada. Changes in tree-ring δ13C indicated that recent climatic conditions have induced stronger drought stress for trees from central eastern Siberia than for those from other regions. The observed tree growth trends were compared to those simulated using a dynamic global vegetation model. Although the modeled annual net primary production (NPP) for trees generally exhibited similar decadal variation to radial growth, simulations did not show a recent decrease in tree growth, even in central eastern Siberia. This was probably due to an overestimation of the sensitivity of modeled tree NPP to precipitation. Our results suggest that the tree NPP forecasted under the expected future increases in temperature and average precipitation might be overestimated, especially in severely dry regions such as central eastern Siberia.

Dispersal leads to spatial autocorrelation in species distributions: A simulation model

USGS Publications Warehouse

Bahn, V.; Krohn, W.B.; O'Connor, R.J.

2008-01-01

Compared to population growth regulated by local conditions, dispersal has been underappreciated as a central process shaping the spatial distribution of populations. This paper asks: (a) which conditions increase the importance of dispersers relative to local recruits in determining population sizes? and (b) how does dispersal influence the spatial distribution patterns of abundances among connected populations? We approached these questions with a simulation model of populations on a coupled lattice with cells of continuously varying habitat quality expressed as carrying capacities. Each cell contained a population with the basic dynamics of density-regulated growth, and was connected to other populations by immigration and emigration. The degree to which dispersal influenced the distribution of population sizes depended most strongly on the absolute amount of dispersal, and then on the potential population growth rate. Dispersal decaying in intensity with distance left close neighbours more alike in population size than distant populations, leading to an increase in spatial autocorrelation. The spatial distribution of species with low potential growth rates is more dependent on dispersal than that of species with high growth rates; therefore, distribution modelling for species with low growth rates requires particular attention to autocorrelation, and conservation management of these species requires attention to factors curtailing dispersal, such as fragmentation and dispersal barriers. ?? 2007 Elsevier B.V. All rights reserved.

Annualized diameter and height growth equations for Pacific Northwest plantation-grown Douglas-fir, western hemlock, and red alder.

Treesearch

A.R. Weiskittel; S.M. Garber; G.P. Johnson; D.A. Maguire; R.A. Monserud

2007-01-01

Simulating the influence of intensive management and annual weather fluctuations on tree growth requires a shorter time step than currently employed by most regional growth models. High-quality data sets are available for several plantation species in the Pacific Northwest region of the United States, but the growth periods ranged from 2 to 12 years. Measurement...

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

Upadhyaya, Mihir; Jindal, Vibhu; Basavalingappa, Adarsh

The availability of defect-free masks is considered to be a critical issue for enabling extreme ultraviolet lithography (EUVL) as the next generation technology. Since completely defect-free masks will be hard to achieve, it is essential to have a good understanding of the printability of the native EUV mask defects. In this work, we performed a systematic study of native mask defects to understand the defect printability caused by them. The multilayer growth over native substrate mask blank defects was correlated to the multilayer growth over regular-shaped defects having similar profiles in terms of their width and height. To model themore » multilayer growth over the defects, a novel level-set multilayer growth model was used that took into account the tool deposition conditions of the Veeco Nexus ion beam deposition tool. The same tool was used for performing the actual deposition of the multilayer stack over the characterized native defects, thus ensuring a fair comparison between the actual multilayer growth over native defects, and modeled multilayer growth over regular-shaped defects. Further, the printability of the characterized native defects was studied with the SEMATECH-Berkeley Actinic Inspection Tool (AIT), an EUV mask-imaging microscope at Lawrence Berkeley National Laboratory (LBNL). Printability of the modeled regular-shaped defects, which were propagated up the multilayer stack using level-set growth model was studied using defect printability simulations implementing the waveguide algorithm. Good comparison was observed between AIT and the simulation results, thus demonstrating that multilayer growth over a defect is primarily a function of a defect’s width and height, irrespective of its shape. This would allow us to predict printability of the arbitrarily-shaped native EUV mask defects in a systematic and robust manner.« less

A functional-structural kiwifruit vine model integrating architecture, carbon dynamics and effects of the environment.

PubMed

Cieslak, Mikolaj; Seleznyova, Alla N; Hanan, Jim

2011-04-01

Functional-structural modelling can be used to increase our understanding of how different aspects of plant structure and function interact, identify knowledge gaps and guide priorities for future experimentation. By integrating existing knowledge of the different aspects of the kiwifruit (Actinidia deliciosa) vine's architecture and physiology, our aim is to develop conceptual and mathematical hypotheses on several of the vine's features: (a) plasticity of the vine's architecture; (b) effects of organ position within the canopy on its size; (c) effects of environment and horticultural management on shoot growth, light distribution and organ size; and (d) role of carbon reserves in early shoot growth. Using the L-system modelling platform, a functional-structural plant model of a kiwifruit vine was created that integrates architectural development, mechanistic modelling of carbon transport and allocation, and environmental and management effects on vine and fruit growth. The branching pattern was captured at the individual shoot level by modelling axillary shoot development using a discrete-time Markov chain. An existing carbon transport resistance model was extended to account for several source/sink components of individual plant elements. A quasi-Monte Carlo path-tracing algorithm was used to estimate the absorbed irradiance of each leaf. Several simulations were performed to illustrate the model's potential to reproduce the major features of the vine's behaviour. The model simulated vine growth responses that were qualitatively similar to those observed in experiments, including the plastic response of shoot growth to local carbon supply, the branching patterns of two Actinidia species, the effect of carbon limitation and topological distance on fruit size and the complex behaviour of sink competition for carbon. The model is able to reproduce differences in vine and fruit growth arising from various experimental treatments. This implies it will be a valuable tool for refining our understanding of kiwifruit growth and for identifying strategies to improve production.

Cirrus cloud model parameterizations: Incorporating realistic ice particle generation

NASA Technical Reports Server (NTRS)

Sassen, Kenneth; Dodd, G. C.; Starr, David OC.

1990-01-01

Recent cirrus cloud modeling studies have involved the application of a time-dependent, two dimensional Eulerian model, with generalized cloud microphysical parameterizations drawn from experimental findings. For computing the ice versus vapor phase changes, the ice mass content is linked to the maintenance of a relative humidity with respect to ice (RHI) of 105 percent; ice growth occurs both with regard to the introduction of new particles and the growth of existing particles. In a simplified cloud model designed to investigate the basic role of various physical processes in the growth and maintenance of cirrus clouds, these parametric relations are justifiable. In comparison, the one dimensional cloud microphysical model recently applied to evaluating the nucleation and growth of ice crystals in cirrus clouds explicitly treated populations of haze and cloud droplets, and ice crystals. Although these two modeling approaches are clearly incompatible, the goal of the present numerical study is to develop a parametric treatment of new ice particle generation, on the basis of detailed microphysical model findings, for incorporation into improved cirrus growth models. For example, the relation between temperature and the relative humidity required to generate ice crystals from ammonium sulfate haze droplets, whose probability of freezing through the homogeneous nucleation mode are a combined function of time and droplet molality, volume, and temperature. As an example of this approach, the results of cloud microphysical simulations are presented showing the rather narrow domain in the temperature/humidity field where new ice crystals can be generated. The microphysical simulations point out the need for detailed CCN studies at cirrus altitudes and haze droplet measurements within cirrus clouds, but also suggest that a relatively simple treatment of ice particle generation, which includes cloud chemistry, can be incorporated into cirrus cloud growth.

Understanding Ice Supersaturation, Particle Growth, and Number Concentration in Cirrus Clouds

NASA Technical Reports Server (NTRS)

Comstock, Jennifer M.; Lin, Ruei-Fong; Starr, David O'C.; Yang, Ping

2008-01-01

Many factors control the ice supersaturation and microphysical properties in cirrus clouds. We explore the effects of dynamic forcing, ice nucleation mechanisms, and ice crystal growth rate on the evolution and distribution of water vapor and cloud properties in nighttime cirrus clouds using a one-dimensional cloud model with bin microphysics and remote sensing measurements obtained at the Department of Energy's Atmospheric Radiation Measurement (ARM) Climate Research Facility located near Lamont, OK. We forced the model using both large-scale vertical ascent and, for the first time, mean mesoscale velocity derived from radar Doppler velocity measurements. Both heterogeneous and homogeneous nucleation processes are explored, where a classical theory heterogeneous scheme is compared with empirical representations. We evaluated model simulations by examining both bulk cloud properties and distributions of measured radar reflectivity, lidar extinction, and water vapor profiles, as well as retrieved cloud microphysical properties. Our results suggest that mesoscale variability is the primary mechanism needed to reproduce observed quantities. Model sensitivity to the ice growth rate is also investigated. The most realistic simulations as compared with observations are forced using mesoscale waves, include fast ice crystal growth, and initiate ice by either homogeneous or heterogeneous nucleation. Simulated ice crystal number concentrations (tens to hundreds particles per liter) are typically two orders of magnitude smaller than previously published results based on aircraft measurements in cirrus clouds, although higher concentrations are possible in isolated pockets within the nucleation zone.

Modeling tradeoffs in avian life history traits and consequences for population growth

USGS Publications Warehouse

Clark, M.E.; Martin, T.E.

2007-01-01

Variation in population dynamics is inherently related to life history characteristics of species, which vary markedly even within phylogenetic groups such as passerine birds. We computed the finite rate of population change (??) from a matrix projection model and from mark-recapture observations for 23 bird species breeding in northern Arizona. We used sensitivity analyses and a simulation model to separate contributions of different life history traits to population growth rate. In particular we focused on contrasting effects of components of reproduction (nest success, clutch size, number of clutches, and juvenile survival) versus adult survival on ??. We explored how changes in nest success or adult survival coupled to costs in other life history parameters affected ?? over a life history gradient provided by our 23 Arizona species, as well as a broader sample of 121 North American passerine species. We further examined these effects for more than 200 passeriform and piciform populations breeding across North America. Model simulations indicate nest success and juvenile survival exert the largest effects on population growth in species with moderate to high reproductive output, whereas adult survival contributed more to population growth in long-lived species. Our simulations suggest that monitoring breeding success in populations across a broad geographic area provides an important index for identifying neotropical migratory populations at risk of serious population declines and a potential method for identifying large-scale mechanisms regulating population dynamics. ?? 2007 Elsevier B.V. All rights reserved.

Kinetic Monte Carlo simulations of GaN homoepitaxy on c- and m-plane surfaces

DOE PAGES

Xu, Dongwei; Zapol, Peter; Stephenson, G. Brian; ...

2017-04-12

The surface orientation can have profound effects on the atomic-scale processes of crystal growth and is essential to such technologies as GaN-based light-emitting diodes and high-power electronics. We investigate the dependence of homoepitaxial growth mechanisms on the surface orientation of a hexagonal crystal using kinetic Monte Carlo simulations. To model GaN metal-organic vapor phase epitaxy, in which N species are supplied in excess, only Ga atoms on a hexagonal close-packed (HCP) lattice are considered. The results are thus potentially applicable to any HCP material. Growth behaviors on c-plane (0001) and m-plane (011¯0) surfaces are compared. We present a reciprocal spacemore » analysis of the surface morphology, which allows extraction of growth mode boundaries and direct comparison with surface X-ray diffraction experiments. For each orientation, we map the boundaries between 3-dimensional, layer-by-layer, and step flow growth modes as a function of temperature and growth rate. Two models for surface diffusion are used, which produce different effective Ehrlich-Schwoebel step-edge barriers and different adatom diffusion anisotropies on m-plane surfaces. Simulation results in agreement with observed GaN island morphologies and growth mode boundaries are obtained. These indicate that anisotropy of step edge energy, rather than adatom diffusion, is responsible for the elongated islands observed on m-plane surfaces. As a result, island nucleation spacing obeys a power-law dependence on growth rate, with exponents of –0.24 and –0.29 for the m- and c-plane, respectively.« less

Kinetic Monte Carlo simulations of GaN homoepitaxy on c- and m-plane surfaces

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

Xu, Dongwei; Zapol, Peter; Stephenson, G. Brian

The surface orientation can have profound effects on the atomic-scale processes of crystal growth and is essential to such technologies as GaN-based light-emitting diodes and high-power electronics. We investigate the dependence of homoepitaxial growth mechanisms on the surface orientation of a hexagonal crystal using kinetic Monte Carlo simulations. To model GaN metal-organic vapor phase epitaxy, in which N species are supplied in excess, only Ga atoms on a hexagonal close-packed (HCP) lattice are considered. The results are thus potentially applicable to any HCP material. Growth behaviors on c-plane (0001) and m-plane (011¯0) surfaces are compared. We present a reciprocal spacemore » analysis of the surface morphology, which allows extraction of growth mode boundaries and direct comparison with surface X-ray diffraction experiments. For each orientation, we map the boundaries between 3-dimensional, layer-by-layer, and step flow growth modes as a function of temperature and growth rate. Two models for surface diffusion are used, which produce different effective Ehrlich-Schwoebel step-edge barriers and different adatom diffusion anisotropies on m-plane surfaces. Simulation results in agreement with observed GaN island morphologies and growth mode boundaries are obtained. These indicate that anisotropy of step edge energy, rather than adatom diffusion, is responsible for the elongated islands observed on m-plane surfaces. As a result, island nucleation spacing obeys a power-law dependence on growth rate, with exponents of –0.24 and –0.29 for the m- and c-plane, respectively.« less

Validation databases for simulation models: aboveground biomass and net primary productive, (NPP) estimation using eastwide FIA data

Treesearch

Jennifer C. Jenkins; Richard A. Birdsey

2000-01-01

As interest grows in the role of forest growth in the carbon cycle, and as simulation models are applied to predict future forest productivity at large spatial scales, the need for reliable and field-based data for evaluation of model estimates is clear. We created estimates of potential forest biomass and annual aboveground production for the Chesapeake Bay watershed...

PREDICTING THE REGIONAL IMPACT OF OZONE AND PRECIPITATION ON THE GROWTH OF LOBLOLLY PINE AND YELLOW-POPLAR USING LINKED TREGRO AND ZELIG MODELS

EPA Science Inventory

To simulate the long-term effects of ozone on forests in the US, we linked TREGRO, a mechanistic model of an individual tree, to ZELIG, a forest stand model, to examine the response of forests to 5 ozone exposure regimes (0 to 100 ppm-hr SUM06 per year) in 100 year simulations. ...

Materials processing in a centrifuge - Numerical modeling of macrogravity effects

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Downey, J. P.; Jones, J. C.; Curreri, P. A.

1992-01-01

The fluid mechanics associated with crystal growth processes on a centrifuge is investigated. A simple scaling analysis is used to examine the relative magnitudes of the forces acting on the system and good agreement is obtained with previous studies. A two-dimensional model of crystal growth on a centrifuge is proposed and calculations are undertaken to help in understanding the fundamental transport processes within the crystal growth cell. Results from three-dimensional calculations of actual centrifuge-based crystal growth systems are presented both for the thermodynamically stable and unstable configurations. The calculations show the existence of flow bifurcations in certain configurations but not in all instances. The numerical simulations also show that the centrifugal force is the dominant stabilizing force on fluid convection in the stable configuration. The stabilizing influence of the Coriolis force is found to be only secondary in nature. No significant impact of gravity gradient is found in the calculations. Simulations of unstable configurations show that the Coriolis force has a stabilizing influence on fluid motion by delaying the onset of unsteady convection. Detailed flow and thermal field characteristics are presented for all the different cases that are simulated.

Global simulation of the Czochralski silicon crystal growth in ANSYS FLUENT

NASA Astrophysics Data System (ADS)

Kirpo, Maksims

2013-05-01

Silicon crystals for high efficiency solar cells are produced mainly by the Czochralski (CZ) crystal growth method. Computer simulations of the CZ process established themselves as a basic tool for optimization of the growth process which allows to reduce production costs keeping high quality of the crystalline material. The author shows the application of the general Computational Fluid Dynamics (CFD) code ANSYS FLUENT to solution of the static two-dimensional (2D) axisymmetric global model of the small industrial furnace for growing of silicon crystals with a diameter of 100 mm. The presented numerical model is self-sufficient and incorporates the most important physical phenomena of the CZ growth process including latent heat generation during crystallization, crystal-melt interface deflection, turbulent heat and mass transport, oxygen transport, etc. The demonstrated approach allows to find the heater power for the specified pulling rate of the crystal but the obtained power values are smaller than those found in the literature for the studied furnace. However, the described approach is successfully verified with the respect to the heater power by its application for the numerical simulations of the real CZ pullers by "Bosch Solar Energy AG".

Magnetic flow control in growth and casting of photovoltaic silicon: Numerical and experimental results

NASA Astrophysics Data System (ADS)

Poklad, A.; Pal, J.; Galindo, V.; Grants, I.; Heinze, V.; Meier, D.; Pätzold, O.; Stelter, M.; Gerbeth, G.

2017-07-01

A novel, vertical Bridgman-type technique for growing multi-crystalline silicon ingots in an induction furnace is described. In contrast to conventional growth, a modified setup with a cone-shaped crucible and susceptor is used. A detailed numerical simulation of the setup is presented. It includes a global thermal simulation of the furnace and a local simulation of the melt, which aims at the influence of the melt flow on the temperature and concentration fields. Furthermore, seeded growth of cone-shaped Si ingots using either a monocrystalline seed or a seed layer formed by pieces of poly-Si is demonstrated and compared to growth without seeds. The influences of the seed material on the grain structure and the dislocation density of the ingots are discussed. The second part addresses model experiments for the Czochralski technique using the room temperature liquid metal GaInSn. The studies were focused on the influence of a rotating and a horizontally static magnetic field on the melt flow and the related heat transport in crucibles being heated from bottom and/or side, and cooled by a crystal model covering about 1/3 of the upper melt surface.

Emergent Behaviors from a Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments

PubMed Central

Jiao, Yang; Torquato, Salvatore

2011-01-01

Understanding tumor invasion and metastasis is of crucial importance for both fundamental cancer research and clinical practice. In vitro experiments have established that the invasive growth of malignant tumors is characterized by the dendritic invasive branches composed of chains of tumor cells emanating from the primary tumor mass. The preponderance of previous tumor simulations focused on non-invasive (or proliferative) growth. The formation of the invasive cell chains and their interactions with the primary tumor mass and host microenvironment are not well understood. Here, we present a novel cellular automaton (CA) model that enables one to efficiently simulate invasive tumor growth in a heterogeneous host microenvironment. By taking into account a variety of microscopic-scale tumor-host interactions, including the short-range mechanical interactions between tumor cells and tumor stroma, degradation of the extracellular matrix by the invasive cells and oxygen/nutrient gradient driven cell motions, our CA model predicts a rich spectrum of growth dynamics and emergent behaviors of invasive tumors. Besides robustly reproducing the salient features of dendritic invasive growth, such as least-resistance paths of cells and intrabranch homotype attraction, we also predict nontrivial coupling between the growth dynamics of the primary tumor mass and the invasive cells. In addition, we show that the properties of the host microenvironment can significantly affect tumor morphology and growth dynamics, emphasizing the importance of understanding the tumor-host interaction. The capability of our CA model suggests that sophisticated in silico tools could eventually be utilized in clinical situations to predict neoplastic progression and propose individualized optimal treatment strategies. PMID:22215996

Comparing TCV experimental VDE responses with DINA code simulations

NASA Astrophysics Data System (ADS)

Favez, J.-Y.; Khayrutdinov, R. R.; Lister, J. B.; Lukash, V. E.

2002-02-01

The DINA free-boundary equilibrium simulation code has been implemented for TCV, including the full TCV feedback and diagnostic systems. First results showed good agreement with control coil perturbations and correctly reproduced certain non-linear features in the experimental measurements. The latest DINA code simulations, presented in this paper, exploit discharges with different cross-sectional shapes and different vertical instability growth rates which were subjected to controlled vertical displacement events (VDEs), extending previous work with the DINA code on the DIII-D tokamak. The height of the TCV vessel allows observation of the non-linear evolution of the VDE growth rate as regions of different vertical field decay index are crossed. The vertical movement of the plasma is found to be well modelled. For most experiments, DINA reproduces the S-shape of the vertical displacement in TCV with excellent precision. This behaviour cannot be modelled using linear time-independent models because of the predominant exponential shape due to the unstable pole of any linear time-independent model. The other most common equilibrium parameters like the plasma current Ip, the elongation κ, the triangularity δ, the safety factor q, the ratio between the averaged plasma kinetic pressure and the pressure of the poloidal magnetic field at the edge of the plasma βp, and the internal self inductance li also show acceptable agreement. The evolution of the growth rate γ is estimated and compared with the evolution of the closed-loop growth rate calculated with the RZIP linear model, confirming the origin of the observed behaviour.

Revision and application of the LINKAGES model to simulate forest growth in central hardwood landscapes in response to climate change

Treesearch

William D. Dijak; Brice B. Hanberry; Jacob S. Fraser; Hong S. He; Wen J. Wang; Frank R. Thompson

2017-01-01

Context. Global climate change impacts forest growth and methods of modeling those impacts at the landscape scale are needed to forecast future forest species composition change and abundance. Changes in forest landscapes will affect ecosystem processes and services such as succession and disturbance, wildlife habitat, and production of forest...

Validating the southern variant forest vegetation simulator height predictions on southeastern hardwoods in Kentucky and Tennessee

Treesearch

Bernard R. Parresol; Steven C. Stedman

2004-01-01

The accuracy of forest growth and yield forecasts affects the quality of forest management decisions (Rauscher et al. 2000). Users of growth and yield models want assurance that model outputs are reasonable and mimic local/regional forest structure and composition and accurately reflect the influences of stand dynamics such as competition and disturbance. As such,...

Interfacial properties in a discrete model for tumor growth

NASA Astrophysics Data System (ADS)

Moglia, Belén; Guisoni, Nara; Albano, Ezequiel V.

2013-03-01

We propose and study, by means of Monte Carlo numerical simulations, a minimal discrete model for avascular tumor growth, which can also be applied for the description of cell cultures in vitro. The interface of the tumor is self-affine and its width can be characterized by the following exponents: (i) the growth exponent β=0.32(2) that governs the early time regime, (ii) the roughness exponent α=0.49(2) related to the fluctuations in the stationary regime, and (iii) the dynamic exponent z=α/β≃1.49(2), which measures the propagation of correlations in the direction parallel to the interface, e.g., ξ∝t1/z, where ξ is the parallel correlation length. Therefore, the interface belongs to the Kardar-Parisi-Zhang universality class, in agreement with recent experiments of cell cultures in vitro. Furthermore, density profiles of the growing cells are rationalized in terms of traveling waves that are solutions of the Fisher-Kolmogorov equation. In this way, we achieved excellent agreement between the simulation results of the discrete model and the continuous description of the growth front of the culture or tumor.

Impact of coastal forcing and groundwater recharge on the growth of a fresh groundwater lens in a mega-scale beach nourishment

NASA Astrophysics Data System (ADS)

Huizer, Sebastian; Radermacher, Max; de Vries, Sierd; Oude Essink, Gualbert H. P.; Bierkens, Marc F. P.

2018-02-01

For a large beach nourishment called the Sand Engine - constructed in 2011 at the Dutch coast - we have examined the impact of coastal forcing (i.e. natural processes that drive coastal hydro- and morphodynamics) and groundwater recharge on the growth of a fresh groundwater lens between 2011 and 2016. Measurements of the morphological change and the tidal dynamics at the study site were incorporated in a calibrated three-dimensional and variable-density groundwater model of the study area. Simulations with this model showed that the detailed incorporation of both the local hydro- and morphodynamics and the actual recharge rate can result in a reliable reconstruction of the growth in fresh groundwater resources. In contrast, the neglect of tidal dynamics, land-surface inundations, and morphological changes in model simulations can result in considerable overestimations of the volume of fresh groundwater. In particular, wave runup and coinciding coastal erosion during storm surges limit the growth in fresh groundwater resources in dynamic coastal environments, and should be considered at potential nourishment sites to delineate the area that is vulnerable to salinization.

A Reduced Model for the Magnetorotational Instability

NASA Astrophysics Data System (ADS)

Jamroz, Ben; Julien, Keith; Knobloch, Edgar

2008-11-01

The magnetorotational instability is investigated within the shearing box approximation in the large Elsasser number regime. In this regime, which is of fundamental importance to astrophysical accretion disk theory, shear is the dominant source of energy, but the instability itself requires the presence of a weaker vertical magnetic field. Dissipative effects are weaker still. However, they are sufficiently large to permit a nonlinear feedback mechanism whereby the turbulent stresses generated by the MRI act on and modify the local background shear in the angular velocity profile. To date this response has been omitted in shearing box simulations and is captured by a reduced pde model derived here from the global MHD fluid equations using multiscale asymptotic perturbation theory. Results from numerical simulations of the reduced pde model indicate a linear phase of exponential growth followed by a nonlinear adjustment to algebraic growth and decay in the fluctuating quantities. Remarkably, the velocity and magnetic field correlations associated with these algebraic growth and decay laws conspire to achieve saturation of the angular momentum transport. The inclusion of subdominant ohmic dissipation arrests the algebraic growth of the fluctuations on a longer, dissipative time scale.

Simulation of fatigue crack growth under large scale yielding conditions

NASA Astrophysics Data System (ADS)

Schweizer, Christoph; Seifert, Thomas; Riedel, Hermann

2010-07-01

A simple mechanism based model for fatigue crack growth assumes a linear correlation between the cyclic crack-tip opening displacement (ΔCTOD) and the crack growth increment (da/dN). The objective of this work is to compare analytical estimates of ΔCTOD with results of numerical calculations under large scale yielding conditions and to verify the physical basis of the model by comparing the predicted and the measured evolution of the crack length in a 10%-chromium-steel. The material is described by a rate independent cyclic plasticity model with power-law hardening and Masing behavior. During the tension-going part of the cycle, nodes at the crack-tip are released such that the crack growth increment corresponds approximately to the crack-tip opening. The finite element analysis performed in ABAQUS is continued for so many cycles until a stabilized value of ΔCTOD is reached. The analytical model contains an interpolation formula for the J-integral, which is generalized to account for cyclic loading and crack closure. Both simulated and estimated ΔCTOD are reasonably consistent. The predicted crack length evolution is found to be in good agreement with the behavior of microcracks observed in a 10%-chromium steel.

High-grade glioma diffusive modeling using statistical tissue information and diffusion tensors extracted from atlases.

PubMed

Roniotis, Alexandros; Manikis, Georgios C; Sakkalis, Vangelis; Zervakis, Michalis E; Karatzanis, Ioannis; Marias, Kostas

2012-03-01

Glioma, especially glioblastoma, is a leading cause of brain cancer fatality involving highly invasive and neoplastic growth. Diffusive models of glioma growth use variations of the diffusion-reaction equation in order to simulate the invasive patterns of glioma cells by approximating the spatiotemporal change of glioma cell concentration. The most advanced diffusive models take into consideration the heterogeneous velocity of glioma in gray and white matter, by using two different discrete diffusion coefficients in these areas. Moreover, by using diffusion tensor imaging (DTI), they simulate the anisotropic migration of glioma cells, which is facilitated along white fibers, assuming diffusion tensors with different diffusion coefficients along each candidate direction of growth. Our study extends this concept by fully exploiting the proportions of white and gray matter extracted by normal brain atlases, rather than discretizing diffusion coefficients. Moreover, the proportions of white and gray matter, as well as the diffusion tensors, are extracted by the respective atlases; thus, no DTI processing is needed. Finally, we applied this novel glioma growth model on real data and the results indicate that prognostication rates can be improved. © 2012 IEEE

Growth Mechanism of Microbial Colonies

NASA Astrophysics Data System (ADS)

Zhu, Minhui; Martini, K. Michael; Kim, Neil H.; Sherer, Nicholas; Lee, Jia Gloria; Kuhlman, Thomas; Goldenfeld, Nigel

Experiments on nutrient-limited E. coli colonies, growing on agar gel from single cells reveal a power-law distribution of sizes, both during the growth process and in the final stage when growth has ceased. We developed a Python simulation to study the growth mechanism of the bacterial population and thus understand the broad details of the experimental findings. The simulation takes into account nutrient uptake, metabolic function, growth and cell division. Bacteria are modeled in two dimensions as hard circle-capped cylinders with steric interactions and elastic stress dependent growth characteristics. Nutrient is able to diffuse within and between the colonies. The mechanism of microbial colony growth involves reproduction of cells within the colonies and the merging of different colonies. We report results on the dynamic scaling laws and final state size distribution, that capture in semi-quantitative detail the trends observed in experiment. Supported by NSF Grant 0822613.

Effect of Solute Diffusion on Dendrite Growth in the Molten Pool of Al-Cu Alloy

NASA Astrophysics Data System (ADS)

Zhan, Xiaohong; Gu, Cheng; Liu, Yun; Wei, Yanhong

2017-10-01

A cellular automaton (CA)-finite difference model is developed to simulate dendrite growth and solute diffusion during solidification process in the molten pool of Al-Cu alloy. In order to explain the interaction between the dendritic growth and solute distribution, a series of CA simulations with different solute diffusion velocity coefficients are carried out. It is concluded that the solute concentration increases with dendrite growing and solute accumulation in the dendrite tip. Converged value of the dendrite tip growth velocity is about 480 μm/s if the mesh size is refined to 2 μm or less. Growth of the primary dendrite and the secondary dendrite is mainly influenced by solute diffusion at the dendrite tips. And growth of secondary and tertiary dendrites is mainly influenced by solute diffusion at interdendrite.

Mechanisms Determining the Structure of Gold-Catalyzed GaAs Nanowires Studied by in Situ X-ray Diffraction

DOE PAGES

Takahasi, Masamitu; Kozu, Miwa; Sasaki, Takuo; ...

2015-09-02

The evolution of polytypism during GaAs nanowire growth was investigated with in situ X-ray diffraction. The growth of nanowires was found to start with the formation of zincblende structure, followed by the growth of wurtzite structure. The growth process was well reproduced by a simulation based on a layer-by-layer nucleation model. The good agreement between the measured and simulated results confirms that nucleation costs higher energy for the stackings changing the crystal structure than for those conserving the preceding structure. The transition in prevalent structure can be accounted for by the change of local growth conditions related to the shapemore » of triple phase line rather than by the change in supersaturation level, which quickly reaches steady state after starting growth.« less

Simulations of stress evolution and the current density scaling of electromigration-induced failure times in pure and alloyed interconnects

NASA Astrophysics Data System (ADS)

Park, Young-Joon; Andleigh, Vaibhav K.; Thompson, Carl V.

1999-04-01

An electromigration model is developed to simulate the reliability of Al and Al-Cu interconnects. A polynomial expression for the free energy of solution by Murray [Int. Met. Rev. 30, 211 (1985)] was used to calculate the chemical potential for Al and Cu while the diffusivities were defined based on a Cu-trapping model by Rosenberg [J. Vac. Sci. Technol. 9, 263 (1972)]. The effects of Cu on stress evolution and lifetime were investigated in all-bamboo and near-bamboo stud-to-stud structures. In addition, the significance of the effect of mechanical stress on the diffusivity of both Al and Cu was determined in all-bamboo and near-bamboo lines. The void nucleation and growth process was simulated in 200 μm, stud-to-stud lines. Current density scaling behavior for void-nucleation-limited failure and void-growth-limited failure modes was simulated in long, stud-to-stud lines. Current density exponents of both n=2 for void nucleation and n=1 for void growth failure modes were found in both pure Al and Al-Cu lines. Limitations of the most widely used current density scaling law (Black's equation) in the analysis of the reliability of stud-to-stud lines are discussed. By modifying the input materials properties used in this model (when they are known), this model can be adapted to predict the reliability of other interconnect materials such as pure Cu and Cu alloys.

Non-steady state simulation of BOM removal in drinking water biofilters: model development.

PubMed

Hozalski, R M; Bouwer, E J

2001-01-01

A numerical model was developed to simulate the non-steady-state behavior of biologically-active filters used for drinking water treatment. The biofilter simulation model called "BIOFILT" simulates the substrate (biodegradable organic matter or BOM) and biomass (both attached and suspended) profiles in a biofilter as a function of time. One of the innovative features of BIOFILT compared to previous biofilm models is the ability to simulate the effects of a sudden loss in attached biomass or biofilm due to filter backwash on substrate removal performance. A sensitivity analysis of the model input parameters indicated that the model simulations were most sensitive to the values of parameters that controlled substrate degradation and biofilm growth and accumulation including the substrate diffusion coefficient, the maximum rate of substrate degradation, the microbial yield coefficient, and a dimensionless shear loss coefficient. Variation of the hydraulic loading rate or other parameters that controlled the deposition of biomass via filtration did not significantly impact the simulation results.